Annotation Track Descriptions
| This page contains an alphabetical listing of the annotation tracks available on various Genome Browser assemblies. This page was last updated on 3 March 2005 and is no longer maintained. For more current information on a specific annotation track, see the description page associated with the track in the Genome Browser. To learn more about configuring and using the tracks displayed in the Genome Browser track window, see the section Interpreting and fine-tuning the Genome Browser display in the Genome Browser User's Guide. [A] [B] [C] [D] [E] [F] [G] [H] [J] [K] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [X] [Y] [Z] 2X Reg Potential This track displays the 2-way regulatory potential (RP) score computed from alignments of the human and mouse assemblies. RP scores compare frequencies of short alignment patterns between regulatory elements and neutral DNA.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Table details: To view a text version of the data set, select the regPotential2X positional table in the Table Browser. To view the table definition, click here.
3X Reg Potential This track displays the 3-way regulatory potential (RP) score computed from alignments of the human, mouse, and rat assemblies. RP scores compare frequencies of short alignment patterns between regulatory elements and neutral DNA.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Table details: To view a text version of the data set, select the regPotential3X positional table in the Table Browser. To view the table definition, click here.
Acembly Genes This track shows gene models reconstructed solely from mRNA and EST evidence by Danielle and Jean Thierry-Mieg and Vahan Simonyan using the Acembly program. Acembly attempts to find the best alignment of each mRNA against the genome, and considers alternative splice models. If more than one gene model is produced that has statistical significance, all of these models are displayed.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show position information, links to translated protein, predicted mRNA, and genomic sequence, and a link to an extensive text and graphical annotation of supporting data at NCBI's AceView.
-- | Table details: To view a text version of the data set, select the acembly positional table in the Table Browser. To view the table definition, click here.
Affy GNF1H This track shows the location of the sequences used for the selection of probes on Affymetrix GNF1H chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnf1h positional table in the Table Browser. To view the table definition, click here.
Affy GNF1M This track shows the location of the sequences used for the selection of probes on Affymetrix GNF1M chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnf1m positional table in the Table Browser. To view the table definition, click here.
Affy GNF1H This track shows the location of the sequences used for the selection of probes on Affymetrix GNF1M chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnf1m positional table in the Table Browser. To view the table definition, click here.
Affy MOE430 This track shows the location of the sequences used for the selection of probes on the Affymetrix Mouse MOE430 set of chips (A and B).
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: Clicking on an item in one of the fuller modes displays positional and % identity information.
-- | Table details: To view a text version of the data set, select the affyMOE430 positional table in the Table Browser. To view the table definition, click here.
Affy RAE230 This track shows the location of the sequences used for the selection of probes on Affymetrix RAE230 chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyRAE230 positional table in the Table Browser. To view the table definition, click here.
Affy RG-U34A This track shows the location of the sequences used for the selection of probes on Affymetrix RG-U34A chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyU34A positional table in the Table Browser. To view the table definition, click here.
Affy U74 This track shows the location of sequences used for the selection of probes on the Affymetrix MG-U74v2 set of chips (A, B, and C).
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: Clicking on an item in one of the fuller modes displays positional and % identity information.
-- | Table details: To view a text version of the data set, select the affyU74 positional table in the Table Browser. To view the table definition, click here.
Affy U95 This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U95Av2 chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: Clicking on an item in one of the fuller modes displays positional and % identity information.
-- | Table details: To view a text version of the data set, select the affyU95 positional table in the Table Browser. To view the table definition, click here.
Affy U133 This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133A and HG-U133B chips.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: Clicking on an item in one of the fuller modes displays positional and % identity information.
-- | Table details: To view a text version of the data set, select the affyU133 positional table in the Table Browser. To view the table definition, click here.
Affy U133Plus2 This track shows the location of the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133 Plus 2.0 chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: Clicking on an item in one of the fuller modes displays positional and % identity information.
-- | Table details: To view a text version of the data set, select the affyU133Plus2 positional table in the Table Browser. To view the table definition, click here.
Affy Zebrafish (Zebrafish) This track shows the location of the sequences used for the selection of probes on the Affymetrix Zebrafish chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyZebrafish positional table in the Table Browser. To view the table definition, click here.
All Ciona ESTs See the description for Human ESTs. Alt-Splicing This track summarizes the alternative splicing shown in the mRNA and EST tracks.
-- | Display conventions: Exons are represented by blocks; possible splice junctions by lines. In full mode with the resolution set to approximately gene-level, alternative exons are laid out with minimal overlap and are therefore easier to view. The level of shading of exons and splice junctions reflects the quantity of ESTs and mRNAs that contain that exon or splice junction.
-- | Track details: Clicking on an item in one of the fuller modes displays positional information and alt-splicing plots, as well as a link to a zoomed-in browser view of that feature.
-- | Table details: To view a text version of the data set, select the altGraphX positional table in the Table Browser. To view the table definition, click here.
A. gambiae Chain This track shows A. gambiae genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. A. gambiae ESTs See the description for Human ESTs. A. gambiae mRNAs See the description for Human mRNAs. A. gambiae Net This track shows the best A. gambiae chain for every part of the selected genome. See the Human Net track description for more information. A. mellifera Chain This track shows A. mellifera genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. A. mel. ESTs A. mellifera ESTs. See the description for Human ESTs. A. mel. mRNAs A. mellifera mRNAs. See the description for Human mRNAs. A. mellifera Net This track shows the best A. mellifera chain for every part of the selected genome. See the Human Net track description for more information. Anopheles Ecores This track shows Anopheles evolutionary conserved regions (ecores) computed against the selected assembly genome by the Exofish program at Genoscope. For information on this track, see the Human Ecores track description. Assembly This track shows the draft assembly of the human genome. This assembly merges contigs from overlapping draft and finished clones into longer sequence contigs. The sequence contigs are ordered and oriented when possible by mRNA, EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs.
-- | Display conventions: In dense display mode, this track depicts in alternating gold and brown the path through the draft and finished clones (aka the golden path) used to create the assembled sequence. Individual boxes show the assembly extractable from a single clone fragment. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If the relative order and orientation of the contigs between the two blocks is known, a line is drawn to bridge the blocks. The display must be sufficiently zoomed in to view the gap and bridge features.
-- | Track details: Clicking on an item in full display mode will show information about the clone fragment and bases, position information, and the DNA sequence corresponding to the fragment.
-- | Table details: To view a text version of the data set, select the gold positional table in the Table Browser. To view the table definition, click here.
BAC End Pairs This track shows the genome sequence of bacterial artificial chromosomes (BACs) in which a small amount of the both ends have been sequenced to place the full insert on the assembly. A valid pair of BAC end sequences must be separated by at least 50Kb but no more than 600Kb, and must have opposite orientations. Strand assignment follows Clone Registry storage conventions. The BAC end sequences are placed on the assembled sequence using BLAT.
-- | Display conventions: The sequenced BAC ends are represented by black boxes connected by a line with hatch marks indicating the direction of transcription.
-- | Track details: Clicking on an entry in full display mode will show hyperlinks to the NCBI clone registry and GenBank, position information, and genomic alignments.
-- | Table details: To view a text version of the data set, select the bacEndPairs positional table in the Table Browser. To view the table definition, click here.
Bactigs The rat genome assembly is pieced together from bactig assemblies rather than clone-by-clone assemblies. Bactigs are reassemblies of the reads from sets of overlapping skimmed BAC clones, including mapped whole shotgun reads. The assembly process reworks the contigs (splitting some) and selects them under more stringent criteria than is used for the BAC submissions.
-- | Display conventions: Bactig positions are indicated by rectangular blocks. Bactig names are of the form gaab_gnmm, the internal names of the two bracketing projects.
-- | Track details: Clicking on an entry in full display mode will show position information and the first and last contig in the bactig.
-- | Table details: To view a text version of the data set, select the bactigPos positional table in the Table Browser. To view the table definition, click here.
Base Position Shows the chromosomal coordinates as numbered starting from the telomere of the short p arm. The coordinates differ between assemblies.
-- | Display conventions: Clicking on a position in this track will zoom in the display by 3x, centered around the click. This track has only on and off modes, and no dense mode.
-- | Track details: None.
-- | Table details: None.
BDGP Genes (D. melanogaster) This track shows protein-coding genes annotated by the Berkeley Drosophila Genome Project (BDGP). For a description of the methods used to generate the data, see the BDGP Methods web page.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, and related links to outside databases.
-- | Track configuration: The track description page contains a filter that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the bdgpGene positional table in the Table Browser. To view the table definition, click here.
BDGP Insertions (D. melanogaster) This track shows the locations of P transposable element insertions from P-Screen, the online database of the BDGP Gene Disruption Project. When a stock order number is available for the strain, a link is provided to the Bloomington stock center. The project's strain library contains more than 7140 strains disrupting at least 5362 different genes, corresponding to 39% of the 13,666 currently annotated Drosophila genes.
-- | Display conventions: Triangular arrows on the reference sequence indicate the approximate locations where P elements have inserted themselves in the mutant strain. Left-pointing arrows indicate insertions that are oriented in a backwards direction; right-pointing arrows indicated forwards-oriented insertions. The item name indicates the strain having a P element disruption at that location.
-- | Track details: Clicking on an entry in full display mode provides position and strand information, strain name, a link to the Bloomington stock center (when applicable), and a link to the underlying DNA for the feature.
-- | Track configuration: The track description page allows the user to set the minimum unnormalized score of the data displayed in the track.
-- | Table details: To view a text version of the data set, select the pscreen positional table in the Table Browser. To view the table definition, click here.
BDGP Non-Coding Genes (D. melanogaster) This track shows non-coding genes annotated by the Berkeley Drosophila Genome Project (BDGP). For a description of the methods used to generate the data, see the BDGP Methods web page.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, and related links to outside databases.
-- | Track configuration: The track description page contains a filter that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the bdgpNonCoding positional table in the Table Browser. To view the table definition, click here.
Best Human This track displays Blastz alignments of the Nov. 2002 human draft assembly to the mouse genome filtered to display only the best alignment for any given region of the mouse genome. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show mouse and human position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzBestHuman positional table in the Table Browser. To view the table definition, click here.
Best Mouse This track displays Blastz alignments of the specified mouse draft assembly to the human genome filtered to display only the best alignment for any given region of the human genome. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show human and mouse position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzBestMouse positional table in the Table Browser. To view the table definition, click here.
Best Rat This track displays Blastz alignments of the Nov. 2002 rat draft assembly to the mouse genome filtered to display only the best alignment for any given region of the mouse genome. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show rat and mouse position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzBestRat positional table in the Table Browser. To view the table definition, click here.
BGI Coverage This track shows areas of coverage for genomic regions of 3 alternate strains of chicken sequenced by the Beijing Genomics Institute (BGI): Broiler, Layer, and Silkie. Single reads from those three strains were mapped to the reference assembly for the Red Jungle Fowl (RJF).
-- | Display conventions: Coverage regions are represented by solid blocks.
-- | Track details: Clicking on an entry in full display mode shows position information and a link to the DNA underlying this feature.
-- | Table details: To view a text version of the data set, select the bgiCov positional table in the Table Browser. To view the table definition, click here.
BGI Genes This track shows protein-coding genes annotated by the Beijing Genomics Institute (BGI). If Single Nucleotide Polymorphisms (SNPs) and/or insertions/deletions from BGI have been associated with a gene, those SNPs are listed with links to their details pages.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode shows position information, GO and InterPro terms from BGI, BGI SNPs associated with the gene, and links to the predicted protein, mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the bgiGene positional table in the Table Browser. To view the table definition, click here.
BGI SNPs This track shows the single nucleotide polymorphisms (SNPs) and/or insertions/deletions (indels) determined by the Beijing Genomics Institute (BGI). Genomic sequence reads from 3 alternate strains of chicken (Broiler, Layer and Silkie) were used to determine the SNPs relative to the reference assembly for the Red Jungle Fowl (RJF). SNPs and indels are associated with genes (annotations by BGI until Ensembl annotations are ready). Information on the association can be displayed along with a link to the details page for the gene.
-- | Display conventions: SNP locations are indicated by thin vertical lines. SNP names are of the format [supercontig].[contig].[position].[type].[strain]. See the track description page for more information. |
-- | Track details: Clicking in full display mode shows information position and SNP information, primer sequences, and a link to the DNA underlying the feature.
-- | Table details: To view a text version of the data set, select the bgiSnp positional table in the Table Browser. To view the table definition, click here.
Binomial Cons This track displays the conservation scores resulting from an analysis of Zoo blastz alignments. Conservation scores were generated by weighing the relative contribution of each species sequence to the overall conservation score, based on how diverged each species was from the reference sequence. This weighting scheme was determined by calculating the neutral substitution rates at 4-fold degenerate positions.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show genome position information for the window and a link to the underlying DNA sequence. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the binomialCons2 positional table in the Table Browser. To view the table definition, click here.
Blastz Mouse This track displays blastz alignments of the specified mouse draft assembly to the selected genome.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will position information for the mouse and the selected genome, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzX positional table in the Table Browser, where X represents the assembly version in which you are interested, e.g. Mm4). To view the table definition, click here.
Briggsae Aligns This track shows best-in-genome C. elegans/C. briggsae alignments based on the C. elegans/C. briggsae alignment net, i.e. the best chain for every part of the C. elegans genome. See the D. pseud Aligns track description for more information. Briggsae Blastz This track displays Blastz alignments of the C. briggsae assembly to selected assembly. See the Blastz Mouse track description for more information. Briggsae Chain This track shows C. briggsae genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Briggsae Net This track shows the best C. briggsae chain for every part of the selected genome. See the Human Net track description for more information. Briggsae Waba This track shows alignments of C. briggsae to C. elegans using the Wobble Aware Bulk Aligner (WABA), an alignment tool developed by Jim Kent for doing large-scale alignments between genomic DNA of different species.
-- | Display conventions: Aligning regions are represented by blocks. The shading indicates the hidden Markov model (HMM) states of the bases.
-- | Track details: Clicking on an item in full display mode will show alignment details and the HMM state for each alignment pair`. Markov model .
-- | Table details: To view a text version of the data set, select the wabaCbr positional table in the Table Browser. To view the table definition, click here.
C. briggsae ESTs See the description for Human ESTs. C. briggsae mRNAs See the description for Human mRNAs. C. elegans ESTs See the description for Human ESTs. C. elegans mRNAs See the description for Human mRNAs. Chicken Chain This track shows chicken genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Chicken ESTs See the description for Human ESTs. Chicken mRNAs See the description for Human mRNAs. Chicken Net This track shows the best chicken chain for every part of the selected genome. See the Human Net track description for more information. Chimp BAC Ends This track displays BAC alignments of the chimp genome (Pan troglodytes) to human, based on BLAT alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
-- | Display conventions: This track follows the display conventions for BLAT tracks.
-- | Track details: Clicking on an item will show details on the chimp sequence fragment and alignment details, as well as a link to more information on the track data.
-- | Table details: To view a text version of the data set, select the chimpBac positional table in the Table Browser. To view the table definition, click here.
Chimp Blat This track displays alignments of the chimp genome (Pan troglodytes) to human, based on Blat alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
-- | Display conventions: This track follows the display conventions for BLAT tracks.
-- | Track details: Clicking on an item will show details on the chimp sequence fragment and alignment details, as well as a link to more information on the track data.
-- | Table details: To view a text version of the data set, select the chimpBlat positional table in the Table Browser. To view the table definition, click here.
Chimp Chain This track shows chimp genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Chimp Deletions This track displays regions of the human assembly that are deleted in the chimp assembly. Only regions of between 80 and 12000 bases are included. The name of each deletion is a unique pointer to that deletion followed by an underscore and then its length. A similar track, showing human deletions in the chimp assembly, appears in the chimp Genome Browser.
-- | Display conventions: Deletions are indicated by thin vertical lines.
-- | Track details: Clicking on a deletion in full display mode provides the item name, position, genomic size, and a link to the DNA underlying the feature.
-- | Table details: To view a text version of the data set, select the chimpDels positional table in the Table Browser. To view the table definition, click here.
Chimp Diff This track shows simple differences between chimp alignments and the human assembly within regions of high quality chimp sequence. For a difference to be included in this track, it had to meet the following criteria: the difference must occur at a base of quality 30 or better all bases within an 11-base window around this base must have a quality of 25 or better the 11-base window must contain no more than two base differences no insertions or deletions may be present within the window Only reciprocal best chimp alignments were considered for this track (see the Chimp Net track description page for more information about this alignment strategy).
-- | Display conventions: Differences are indicated by thin vertical lines.
-- | Track details: Clicking on a deletion in full display mode provides the item name, position, genomic size, and a link to the DNA underlying the feature.
-- | Table details: To view a text version of the data set, select the chimpSimpleDiff positional table in the Table Browser. To view the table definition, click here.
Chimp ESTs See the description for Human ESTs. Chimp mRNAs See the description for Human mRNAs. Chimp Recip Chain This track displays "reciprocal best" human/chimpanzee genomic alignment chains.
-- | Display conventions: This track uses the display conventions for chain tracks.
Track details: In full display mode, clicking on a box shows details information about the chain as a whole, while clicking on a line shows information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.
-- | Table details: To view a text version of the data set, select the rBestChainPanTro1 positional table in the Table Browser. To view the table definition, click here.
Chimp Recip Net This track shows the reciprocal best alignment net between the chimpanzee and the selected genome assembly. Due to the draft nature of the initial chimp assembly, this track uses a "reciprocal best" strategy that attempts to minimize paralog fill-in for missing orthologous chimp sequence by filtering out of the human net all sequences not in the chimp side of the net. See the track description page for more information about the methods used to generate this track.
-- | Display conventions: This track uses the display conventions for net tracks.
-- | Track details: In full display mode, clicking on a box shows details information about the chain as a whole, while clicking on a line shows information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.
-- | Table details: To view a text version of the data set, select the rBestNetPanTro1 positional table in the Table Browser, where X is the assembly version in which you're interested. To view the table definition, click here.
Chromosome Band The light and dark blocks indicate the approximate location of traditional cytological bands seen on Giemsa-stained chromosomes at an 850 band resolution. The bands were mapped by fluorescent in situ hybridization (FISH) of large-insert clones with sequence tags, STS markers, and BAC end sequence locations. resolution of 862 bands genome-wide. The uncertainty of mapping to band staining is still a megabase or more.
-- | Display conventions: The light and dark blocks indicate the approximate location of the bands on the assembly sequence.
-- | Track details: Clicking on a band in full display mode will show more details about the track, a discussion of mapping methods used, and lab credits.
-- | Table details: To view a text version of the data set, select the cytoBand positional table in the Table Browser. To view the table definition, click here.
C. intestinalis ESTs See the description for Human mRNAs. C. intestinalis mRNAs See the description for Human mRNAs. Ciona mRNAs See the description for Human mRNAs. Conservation This track shows a measure of evolutionary conservation among several species, based on a phylogenetic hidden Markov model (phylo-HMM). The multiz alignments of the various assemblies were used to construct the annotation. The raw conservation scores used to generate this track can be downloaded from the [assembly_name]/phastCons directory on the Genome Browser FTP server.
-- | Display conventions: In full display mode, the track displays pairwise alignments of several species aligned to the human genome. The pairwise alignments are displayed in standard UCSC browser "dense" mode using a grey-scale density gradient. When zoomed-in to the base-display level, the track shows the base composition of each alignment. The numbers and symbols on the "human gap" line indicate the lengths of gaps in the human sequence at those alignment positions. If the gap size is greater than 9, the "+" symbol is displayed. The track must be zoomed-in to 30,000 or fewer bases to access detailed information about the alignments at a specific position.
-- | Track details: Clicking on an entry in full display mode will show detailed alignment information for each of the organisms.
-- | Table details:
-- | To view an index of the multiz multiple alignment data used to generate this track, select one of the following positional tables from the Table Browser: multiNway (most recent assemblies), mz*_pHMM (hg16), mz*_phast (canFam1, dm1), c_briggsae_pwMaf (C. elegans).
-- | To view the wiggle track data used to generate the conservation display, select onf of the following positional tables: phastCons (most assemblies), mz*_wig (hg16), mz*phast_wig (canFam1, dm1).
-- | To download the raw conservation scores displayed in the Conservation track, download the data files from the [assembly_name]/phastCons directory on the Genome Browser FTP server.
-- | To view the table definition for the multiz multiple alignment tables, click here.
-- | To view the table definition for the phastCons tables, click here.
Contamination (Chicken) This track shows locations of likely contamination in the chicken (galGal2) assembly, i.e. high-scoring alignments of E.coli, vector and maize mitochondrion sequence. The name of each feature indicates the type of contamination found there.
-- | Display conventions: Area of contamination are represented by solid blocks.
-- | Track details: Clicking on an entry in full display mode will show the type of contamination, position and size information, and a link to display the DNA for the feature.
-- | Table details: To view a text version of the data set, select the contamination positional table in the Table Browser. To view the table definition, click here.
Contigs (Zebrafish) This track shows the whole genome shotgun (WGS) contigs of the zebrafish assembly from The Wellcome Trust Sanger Institute.
-- | Display conventions: Contigs are represented by blocks that indicate their location on the assembly sequence.
-- | Track details: Clicking on an item in full display mode will show contig and positional information.
-- | Table details: To view a text version of the data set, select the ctgPos2 positional table in the Table Browser. To view the table definition, click here.
Coverage Shows the coverage level and positions of all clones in the genome.
-- | Display conventions: In dense display mode, this track shows the coverage level of the genome. Finished regions are shown in black. Draft regions are shown in various shades of gray that correspond to the level of coverage: o White: no coverage (gap) o Light Gray: predraft (less than 4x shotgun) o Medium Gray: draft (at least 4x shotgun) o Dark Gray: covered by multiple draft clones o Black: covered by a finished clone
| In full display mode, this track shows the position of each clone that aligns to the genome sequence. Finished clones are shown in black and unfinished clones are shown in gray. In assemblies prior to the April 2003 human release, coverage for each unfinished clone is represented as a two-tiered gray box. The fragments inside the clone are shown as numbered black boxes. Their positions correspond to their relative assembly placement, including strand assignment. For some assemblies, clones in the sequencing center tiling path are shown with blue rather than gray backgrounds.
-- | Track details: Clicking on an item in full display mode will show the clone hyperlink to GenBank record and the fasta format sequence (one per fragment).
-- | Table details: To view a text version of the data set, select the clonePos positional table in the Table Browser. To view the table definition, click here.
Cow Chain This track shows cow genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Cow ESTs See the description for Human ESTs. Cow mRNAs the description for Human mRNAs. Cow Net This track shows the best cow chain for every part of the selected genome. See the Human Net track description for more information. CpG Islands This track shows CpG islands, areas rich in the dinucleotide CG. A CpG island is a region where C's followed by G's (CpGs) are present at significantly higher levels than is typical for the genome as a whole. The CpG islands displayed in this browser are all at least 200 bases long, and have a GC content of at least 50%. CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. They are particularly common near transcription start sites, and may be associated with promoter regions. Normally a CpG is rare in vertebrate DNA because the C's in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated C's tend to turn into T's due to spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some reason, perhaps having to do with the regulation of gene expression.
-- | Display conventions: CpG islands are represented by green boxes. Darker green items indicate CpG islands that contain 300 or more bases.
-- | Display conventions: Clicking on a CpG entry in full display mode will show basic track information, detailed information about the CpG island, and sequence information.
-- | Table details: To view a text version of the data set, select the cpgIsland positional table in the Table Browser. To view the table definition, click here.
C. savignyi Blat This track displays translated BLAT alignments of the C. savignyi genome against the C. intestinalis genome assembly. The alignments were done with Blat in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The C. intestinalis genome was masked with RepeatMasker and Tandem Repeats Finder before running Blat.
-- | Display conventions: This track uses the display conventions for BLAT tracks.
-- | Track details: Clicking on an entry in full display mode displays links to the DNA sequence and the alignment.
-- | Table details: To view a text version of the data set, select the blatCioSav1 positional table in the Table Browser. To view the table definition, click here.
Cytokine Genes (Tetraodon) This track shows cytokine genes annotated by human experts using sequence similarity information between Tetraodon and human, mouse and zebrafish cytokine protein and nucleotide sequences. These annotations are available only on the following chromosomes: 1, 2, 3, 4, 7, 8, 10, 12, 13, 15, 16, 1_random, 3_random, and Un_random.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track configuration: The track description page contains a control that can be used to turn on codon coloring.
-- | Track details: Clicking on a track feature in full display mode shows position information and provides links to the translated protein, predicted mRNA, and genome sequences.
-- | Table details: To view a text version of the data set, select the cytokines positional table in the Table Browser. To view the table definition, click here.
DBTSS mRNA This track shows RefSeq mRNA sequences extended to the 5' end, based on sequence information in the DataBase of Transcriptional Start Sites (DBTSS). For more information on the process used to construct this track, refer to the track's description page.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track details: Clicking on an entry in full display mode will show PSL output information about the item.
-- | Table details: To view a text version of the data set, select the dbtssAli positional table in the Table Browser. To view the table definition, click here.
D. mel. Chain This track shows D. melanogaster genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. mel. Net This track shows the best D. melanogaster chain for every part of the selected genome. See the Human Net track description for more information. D. mel. Proteins (A. gambiae, A. mellifera This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the specified version of FlyBase.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track details: Clicking on an entry in full display mode will provide positional information, a link to the related FlyBase record, protein length, and links to the alignment and peptide sequences.
-- | Table details: To view a text version of the data set, select the blastDm1FB positional table in the Table Browser. To view the table definition, click here.
D. melanogaster ESTs See the description for Human ESTs. D. melanogaster mRNAs See the description for Human mRNAs. DNAse HyperSens (Zoo) This track depicts DNAse I hypersensitive sites (DHS) mapped to the human genome sequence. Each track element represents the surrounding 500 bp from the position of the estimated DHS, as determined from Smith et al. (2000) "Multiple Potential Intragenic Regulatory Elements in the CFTR Gene", Genomics 64(1):90-6.
-- | Display conventions: Each DHS is depicted by a block representing the 500 bp surrounding the position of the estimated DHS.
-- | Track details: Clicking on an entry in full display mode will show position information and a link to the underlying DNA sequence.
-- | Table details: To view a text version of the data set, select the dhs positional table in the Table Browser. To view the table definition, click here.
Dog Chain This track shows dog genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Dog ESTs See the description for Human ESTs. Dog mRNAs See the description for Human mRNAs. Dog Net This track shows the best dog chain for every part of the selected genome. See the Human Net track description for more information. D. ananassae Chain This track shows D. ananassae genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. anan. mRNAs D. ananassae mRNAs. See the description for Human mRNAs. D. ananassae Net This track shows the best D. ananassae chain for every part of the selected genome. See the Human Net track description for more information. D. mojavensis Chain This track shows D. mojavensis genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. moj. mRNAs D. mojavensis mRNAs. See the description for Human mRNAs. D. mojavensis Net This track shows the best D. mojavensis chain for every part of the selected genome. See the Human Net track description for more information. D. pseudo. Aligns (D. melanogaster) This track shows blastz scores from the D. pseudoobscura/D. melanogaster alignment Net track, i.e. the best D. pseudoobscura/D. melanogaster chain for every part of the D. melanogaster genome.
-- | Display conventions: In dense display mode, darker shading indicates those best chained and netted alignments that have the higher scores. In full display mode, the height of the vertical line corresponds to the score.
-- | Track details: Clicking on an entry in full display mode will show position information and -- when zoomed in to the base level -- the base composition of the alignments.
-- | Table details: To view a text version of the data set, select the axtNetX positional table in the Table Browser, where X represents the assembly that is being aligned, e.g. Dp1. To view the table definition, click here.
D. pseudo. Chain (D. melanogaster) This track shows D. pseudoobscura genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. pseudo. ESTs D. pseudoobscura ESTs. See the description for Human ESTs. D. pseudo. mRNAs D. pseudoobscura mRNAs. See the description for Human mRNAs. D. pseudo. Net (D. melanogaster) This track shows the best D. pseudoobscura chain for every part of the selected genome. See the Human Net track description for more information. D. virilis Chain This track shows D. virilis genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. vir. mRNAs D. virilis mRNAs. See the description for Human mRNAs. D. virilis Net This track shows the best D. virilis chain for every part of the selected genome. See the Human Net track description for more information. D. yakuba Chain This track shows D. yakuba genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. D. yakuba ESTs D. yakuba ESTs. See the description for Human ESTs. D. yakuba mRNAs D. yakuba mRNAs. See the description for Human mRNAs. D. yakuba Net This track shows the best D. yakuba chain for every part of the selected genome. See the Human Net track description for more information. Duplications This track shows genomic duplications greater than 1,000 bp if not overly repeat-masked. Duplications are more common in unordered and unassigned contigs (i.e., difficult to assign to their proper position).
-- | Display conventions: Duplications are show as red if 99%+ identity (likely unmerged assembly overlap artifact), as yellow for 98-99% identity (origin uncertain), and as gray for 90-98% identity (below draft sequencing error, often genuine pericentromeric or subtelomeric duplication).
-- | Track details: In the left panel of the browser, duplications are named by the chromosome and start of the other member of the duplication pair. Clicking on an individual duplication gives details of both locations and match quality parameters.
D. yakuba ESTs See the description for Human ESTs. D. yakuba mRNAs See the description for Human mRNAs. ECgene Genes This track shows gene predictions generated by combining genome-based EST clustering and transcript assembly methods. The EST clustering is based on genomic alignment of mRNA and ESTs similar to that of NCBI's UniGene for the human genome. The transcript assembly procedure yields gene models for each cluster that include alternative splicing variants. This algorithm was developed by Prof. Sanghyuk Lee's Lab of Bioinformatics at Ewha Womans University in Seoul, Korea. For more information, see the ECgene web site.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, links to the predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the ECgene positional table in the Table Browser. To view the table definition, click here.
Elegans Blastz This track displays Blastz alignments of the C. elegans assembly to the C. briggsae assembly
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show human and mouse position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzX positional table in the Table Browser, where X represents the C. elegans assembly, e.g. Ce2. To view the table definition, click here.
Elegans Chain This track shows C. elegans genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. ENCODE Regions This track depicts target regions for the NHGRI ENCODE project, which is described in The ENCODE Project: ENCyclopedia of DNA Elements. The long-term goal of this project is to identify all functional elements in the human genome sequence to facilitate a better understanding of human biology and disease. During the pilot phase, 44 regions comprising 30 Mb -- approximately 1% of the human genome -- have been selected for intensive study to identify, locate and analyze functional elements within the regions. These targets are being studied by a diverse public research consortium to test and evaluate the efficacy of various methods, technologies, and strategies for locating genomic features. The outcome of this initial phase will form the basis for a larger-scale effort to analyze the entire human genome. See the track description page for more information.
-- | Display conventions: ENCODE regions are represented by blocks.
-- | Track details: Clicking on an item in full display mode shows position information and provides a link to the DNA sequence associated with this feature.
-- | Table details: To view a text version of the data set, select the encodeRegions positional table in the Table Browser, where X is the assembly version in which you're interested. To view the table definition, click here.
Ensembl ESTs This track shows gene predictions from Project Ensembl based on ESTs. For a description of the methods used in Ensembl gene prediction, refer to The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, links to the translated protein, predicted mRNA, and genomic sequences, plus a link to detailed supporting evidence.
-- | Table details: To view a text version of the data set, select the ensEst positional table in the Table Browser. To view the table definition, click here.
Ensembl Genes This track shows gene predictions from Project Ensembl. For a description of the methods used in Ensembl gene prediction, refer to The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, links to the translated protein, predicted mRNA, and genomic sequences, plus a link to detailed supporting evidence.
-- | Table details: To view a text version of the data set, select the ensGene positional table in the Table Browser. To view the table definition, click here.
Exofish ecores The track displays conserved regions, generally protein-coding homologs, from a genomics project of long random reads in the pufferfish, Tetraodon nigroviridis. Ecore is an acronym for evolutionary conserved region. The data was used to estimate the number of human genes.
-- | Display conventions: Regions of greater homology are displayed in a darker blue.
-- | Track details: Clicking on an entry in full mode brings up information on a particular ecore, access the relevant Genoscope page, and the relevant DNA.
-- | Table details: To view a text version of the data set, select the exoFish positional table in the Table Browser. To view the table definition, click here.
Exoniphy The exoniphy program identifies evolutionarily conserved protein-coding exons in multiple sequences aligned with multiz using a phylogenetic hidden Markov model (phylo-HMM), a statistical model that simultaneously describes exon structure and exon evolution.
-- | Display conventions: Evoluntionarily-conserved protein-coding exons are represented by blocks. Arrows indicated the direction of transcription.
-- | Track details: Clicking on an entry in full mode displays positional information and related sequence links.
-- | Table details: To view a text version of the data set, select the exoniphy positional table in the Table Browser. To view the table definition, click here.
Fgenesh++ Genes This tracks shows Fgenesh++ gene predictions based on Softberry Inc.'s gene-finding software. Fgenesh++ uses both hidden Markov models (HMMs) and protein similarity to find genes in a completely automated manner, with less emphasis on cDNA/EST data. See the paper "Ab initio gene finding in Drosophila genomic DNA", Genome Research 10(4) 516-522 for more information. NOTE: The data in the softberryGene.txt and softberryPep.txt tables is free for academic and nonprofit use. Commercial users should contact Softberry Inc..
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, links to the translated protein, predicted mRNA, and genomic sequences, plus a link to the best matching protein at GenBank.
-- | Table details: To view a text version data set, select the softberryGene positional table in the Table Browser. To view the table definition, click here.
First EF This track displays predictions from First Exon Finder (FirstEF), a 5' terminal exon and promoter prediction program. Three types of predictions are shown: exon, promoter and CpG window. If two consecutive predictions are separated by less than 1000 bp, FirstEF treats them as one cluster of alternative first exons that may belong to same gene. Each predicted exon is either CpG-related or non-CpG-related, based on a score of the frequency of CpG dinucleotides. An exon is classified as CpG-related if the CpG score is greater than a threshhold value and non-CpG-related if less than the threshold. If an exon is CpG-related, its associated CpG-window is displayed.
-- | Display conventions: This track uses the display conventions for BLAT tracks. Higher CpG scores are shown in darker shades of gray/black. The cluster number is displayed in parentheses in the item label. For example, "exon(405-)" represents the exon prediction in cluster number 405 on the minus strand. The exon, promoter and CpG-window are interconnected by this cluster number. Alternative predictions within the same cluster are denoted by "#N" where "N" is the serial number of an alternative prediction in the cluster.
-- | Track details: Clicking on an entry in full display mode displays probability, size, and position information, and a link to the DNA sequence.
-- | Table details: To view a text version of the data set, select the firstEF positional table in the Table Browser. To view the table definition, click here.
Fish Blat This track displays translated alignments of 728 million bases of Tetraodon nigroviridis whole genome shotgun reads vs. the draft human genome. Areas painted by this track are quite likely to be coding regions. The alignments were done with BLAT in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human genome was masked with RepeatMasker and Tandem Repeats Finder before running BLAT. The Tetraodon sequence was provided by Genoscope.
-- | Display conventions: This track uses the display conventions for BLAT tracks.
-- | Track details: Clicking on an entry in full display mode brings up links to the DNA sequence and the alignment.
-- | Table details: To view a text version of the data set, select the blatFish positional table in the Table Browser. To view the table definition, click here.
FISH Clones Shows the location of fluorescent in situ hybridization (FISH) mapped clones along the draft assembly sequence.
-- | Display conventions: The green blocks depict the clone placements on the assembly sequence.
-- | Track details: Clicking on a specific marker in full display mode will show information on clone placement, clone registry, its STS markers, and BAC end sequences.
-- | Table details: To view a text version of the data set, select the fishClones positional table in the Table Browser. To view the table definition, click here.
FlyBase Genes (D. melanogaster) This track shows protein-coding genes annotated by FlyBase (version 3.2).
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, microarray expression data, protein structure information, homology information and related links to several tools and databases, including FlyBase.
-- | Table details: To view a text version of the data set, select the bdgpGene positional table in the Table Browser. To view the table definition, click here.
FlyBase Non-coding (D. melanogaster) This track shows non-coding genes annotated by FlyBase (version 3.2).
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to FlyBase and BDGP, basic track information, and links to the corresponding predicted genomic and predicted mRNA sequences.
-- | Table details: To view a text version of the data set, select the bdgpGene positional table in the Table Browser. To view the table definition, click here.
FlyReg (D. melanogaster) This track shows DNase I Footprint data from the FlyReg version 2.0 database. FlyReg provides access to results of the systematic curation and genome annotation of 1,350 DNase I footprints for the fruitfly D. melanogaster reported in Bergman, C.M. et al., Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, D. melanogaster, Bioinformatics 2004 Nov. 30 [Epub ahead of print].
-- | Display conventions: Footprint regions are represented by blocks.
-- | Track details: Clicking on an entry in full display provides footprint information, links to external databases, and a link to view the related genomic DNA. When available, a footprint motif is also displayed, based on a MEME matrix computed by Dan Pollard on the set of footprints for the factor.
-- | Table details: To view a text version of the data set, select the flyreg2 positional table in the Table Browser. To view the table definition, click here.
Fosmid End Pairs A valid pair of fosmid end sequences must be at least 32Kb but no more than 47Kb away from each other. The orientation of the first fosmid end sequence must be "+" and the orientation of the second fosmid end sequence must be "-". End sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikan. The trimmed end sequences were placed on the assembled sequence using Jim Kent's BLAT program.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track details: Clicking on an entry in full display mode will show position information and provide links to genomic alignments of the Fosmid ends.
-- | Table details: To view a text version of the data set, select the fosEndPairs positional table in the Table Browser. To view the table definition, click here.
Fugu Blat This track displays translated BLAT alignments of Takifugu rubripes whole genome shotgun reads against the currently selected genome assembly. The alignments were done with BLAT in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human genome was masked with RepeatMasker and Tandem Repeats Finder before running BLAT. The fugu sequence used in this track is version 3.0, provided by the DOE Joint Genome Institute (JGI).
-- | Display conventions: This track uses the display conventions for BLAT tracks.
-- | Track details: Clicking on an entry in full display mode brings up links to the DNA sequence and the alignment.
-- | Table details: To view a text version of the data set, select the blatFugu positional table in the Table Browser. To view the table definition, click here.
Fugu Chain This track shows Fugu genomic alignment to the selected genome using blastz and axtChain.
-- | Display conventions: This track uses the display conventions for chain tracks.
-- | Track details: Clicking on an item in full display mode shows position information in the Fugu and the selected genome, the chain ID and score, and provides links to view details of parts of the chain or to open the Fugu browser to the corresponding position.
-- | Table details: To view a text version of the data set, select the chainFrX positional table in the Table Browser, where X is the assembly version in which you're interested. To view the table definition, click here.
Fugu Ecores This track shows Fugu evolutionary conserved regions (ecores) computed against the selected assembly genome by the Exofish program at Genoscope. For information on this track, see the Human Ecores track description. Fugu ESTs See the description for Human ESTs. Fugu mRNAs See the description for Human mRNAs. Fugu Net This track shows the best Fugu chain for every part of the selected genome. See the Human Net track description for more information. Gap This track depicts gaps in the assembly. These gaps - with the exception of intractable heterochromatic gaps - are closed during the finishing process.
-- | Display conventions: Gaps are represented as black boxes. If the relative order and orientation of the contigs on either side of the gap is known from mRNA, ESTs, or paired BAC end reads, it is a "bridged" gap and a white line is drawn through the black box representing the gap. The display must be sufficiently zoomed in to view these features: at a coarser scale, the gaps can appear to coalesce in the the graphic. In full display mode, the gap label indicates the type of gap (see below) and whether the gap is bridged.
| Strand misorientation errors can occur adjacent to unbridged gaps. Unbridged gaps are assigned somewhat arbitrary sequence sizes (runs of N's in genomic DNA); uncertainty is less with bridged gaps. A gap within contig fragments of a clone is typically smaller than a gap between draft clones.
-- | Track details: Clicking on an item in full display mode will show the gap type, bridging information and position information about the gap. Unfinished clones may have gaps of uncertain size between fragments.
-- | Table details: To view a text version of the data set, select the gap positional table in the Table Browser. To view the table definition, click here.
GC Percent This shows the percentage of bases that are G or C in a 5-base window. High GC content is associated with gene rich areas.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show position information and provide a link to the underlying DNA sequence. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the gc5Base positional table in the Table Browser. To view the table definition, click here.
GC Samples (Zoo) This track shows the percentage of bases that are G or C in small regions across the genome. Windows with high GC content are plotted at higher vertical positions than windows with low GC content. High GC content is associated with gene-rich areas.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show position information and provide a link to the underlying DNA sequence. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the pGC positional table in the Table Browser. To view the table definition, click here.
Gene Annotations (Zoo) This track displays NISC-generated, curated gene annotations for each of the zoo species and human. Exon locations of known genes were determined by aligning human and/or mouse reference cDNA sequences with each species' assembled genomic sequence. Any splice-site consensus, exon structure, or protein translation errors encountered were manually inspected and corrected.
-- | Display conventions: This track uses the display conventions for gene prediction tracks. As with other tracks in this category, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an item in full mode provides position, size, and score information, and a link to dsplay the DNA sequence associated with this feature.
-- | Table details: To view a text version of the data set, select the pjt_gene positional table in the Table Browser. To view the table definition, click here.
Gene Bounds This track shows the boundaries of genes and the direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. When there are many spliced variants of the same gene, this track shows the variant that spans the greatest distance in the genome.
-- | Display conventions: This track uses the display conventions for EST tracks. As with other tracks in this category, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an item in full mode provides position, size, and score information, and a link to dsplay the DNA sequence associated with this feature.
-- | Table details: To view a text version of the data set, select the rnaCluster positional table in the Table Browser. To view the table definition, click here.
Geneid Gene Predictions This track shows gene predictions from the geneid program, which is being developed at the Grup de Recerca en Informatica Biomedica at IMIM in Barcelona. Geneid uses information from sequence signals involved in genes specification, as well as coding coding statistics, to define exons and genes.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, plus links to the translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the geneid positional table in the Table Browser. To view the table definition, click here.
GenMapDB Clones This track shows BAC clones from the GenMapDB database placed on the draft sequence using BAC end sequence information and confirmed using STS markers by Vivian Cheung's lab at the Department of Pediatrics, University of Pennsylvania.
-- | Display conventions: The clone positions are shown in black.
-- | Track details: Clicking on an entry in full display mode brings up basic position information and additional information about the clones and STS markers.
-- | Table details: To view a text version of the data set, select the genMapDb positional table in the Table Browser. To view the table definition, click here.
Genoscope GAZE (Tetraodon) This track shows Genoscope gene model annotations from the GAZE program written by Kevin Howe. These annotaions were computed using GAZE with a i custom-designed gene model. GAZE integrates information from Geneid, Genscan, Exofish (Human, Mouse and Fugu), Genewise (Human and Mouse) and Tetraodon cDNAs.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track configuration: The track description page contains a control that can be used to turn on codon coloring.
-- | Track details: Clicking on a track feature in full display mode shows position information and provides links to the translated protein, predicted mRNA, and genome sequences.
-- | Table details: To view a text version of the data set, select the gaze positional table in the Table Browser. To view the table definition, click here.
Genscan Genes This track shows gene predictions from GenScan. These predictions are based on transcriptional, translational, and donor and acceptor splicing signals, plus length and compositional distributions of exons, introns and intergenic regions. The program does not use similarity to known proteins like GenomeScan. For a description of the Genscan program and the model that underlies it, refer to Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268(1):78-94.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, plus links to the translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the genscan positional table in the Table Browser. To view the table definition, click here.
Genscan Genes (Zoo) This track shows gene predictions from the GenScan program written by Chris Burge.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode shows basic track information and provides a link to view the underlying genomic sequence.
-- | Table details: To view a text version of the data set, select the pjt_genscan positional table in the Table Browser. To view the table definition, click here.
GNF Atlas 2 This track shows expression data from the GNF (The Genomics Institute of the Novartis Research Foundation) Gene Expression Atlas 2. The data contains 2 replicates each of 61 mouse tissues and 79 human tissues run over Affymetrix microarrays. For more information about the experiments, refer to the description page for this track.
-- | Display conventions: This track uses display conventions similar to those for PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the gnfAtlas2 positional table in the Table Browser. To view the table definition, click here.
GNF Ratio This track shows expression data from GNF (The Genomics Institute of the Novartis Research Foundation) using Affymetrix GeneChips. For more information about the experiments, refer to the description page for this track.
-- | Display conventions: In dense display mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full display mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe.
-- | Track configuration: The track description page contains options to change the display mode, group the displayed results, and change the display colors.
-- | Table details: To view a text version of the data set, select the affyRatio positional table in the Table Browser. To view the table definition, click here.
GNF U74A This track shows expression data from GNF using the Affymetrix U74A chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnfU74A positional table in the Table Browser. To view the table definition, click here.
GNF U74B This track shows expression data from GNF using the Affymetrix U74B chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnfU74B positional table in the Table Browser. To view the table definition, click here.
GNF U74C This track shows expression data from GNF using the Affymetrix U74C chip.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the affyGnfU74C positional table in the Table Browser. To view the table definition, click here.
Haplotype Blocks (chr21) See the description for Perlegen. Haplotype Blocks (chr22) This track shows haplotype blocks on Chromosome 22 from The University of Oxford and The Wellcome Trust Sanger Institute, as described in Dawson E. et. al. (2002), "A first-generation linkage disequilibrium map of human chromosome 22", Nature 418:544-8.
-- | Display conventions: The location of each haplotype block is represented by a blue horizontal line with tall vertical blue bars at the first and last SNPs of the block. Blocks are displayed as starting at the first SNP and ending at the last SNP of the block. Individual SNPs are denoted by smaller black vertical bars. At multi-megabase resolution in dense display mode, clusters of tall blue bars may indicate hotspots for recombination.
-- | Track details: Clicking on an entry in full display mode will show basic position information, SNP information for the block, and a link to sequence information for the feature.
-- | Table details: To view a text version of the data set, select the haplotype positional table in the Table Browser. To view the table definition, click here.
H-Inv This track shows alignments of full-length cDNAs used as the basis of the H-Invitational Gene Database (HInv-DB). Entries in this track include gene structures, functions, functional domains, metabolic pathways, and many other entities.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track details: Clicking on an entry in full display mode provides gene ID, cluster ID, and cDNA accession information and a link to sequence information for the feature.
-- | Table details: To view a text version of the data set, select the HInvGeneMrna positional table in the Table Browser. To view the table definition, click here.
HOX Genes (Tetraodon chr2, 8, 9, 17, 21, and un_random only) This track shows HOX genes annotated using information on sequence similarity between Tetraodon vs. human, mouse and zebrafish HOX protein and nucleotide sequences.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode provides position, size, and CDS information, and links to the related translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the hoxGenes positional table in the Table Browser. To view the table definition, click here.
Human Best This track displays best-in-genome alignments of the specified human draft assembly to the selected genome baed on the associated alignment net, i.e. the best chain for every part of the human genome. See the track description page for the Human Net track for more information about the methods used to generate this track.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show position information for the human alignment and the selected genome, alignment details, and a link to a detailed view of parts of the alignment.
-- | Table details: To view a text version of the data set, select the axtNetHgX positional table in the Table Browser, where X is the assembly version in which you're interested. To view the table definition, click here.
Human Blat This track displays translated BLAT alignments of the human genome vs. the mouse genome. The alignments were done with BLAT in translated protein mode using the parameters -q=dnax -t=dnax and otherwise the default settings. Both genomes were masked with RepeatMasker and Tandem Repeats Finder before running BLAT. Places where more than 250 alignments occurred over the same place were filtered out. Beware of alignments of greater than 97% identity: these may reflect mouse contamination in the human genome or human contamination in the mouse genome.
-- | Display conventions: This track uses the display conventions for a BLAT alignment track.
-- | Track details: Clicking on an entry in full display mode will show basic track information and a link to sequence information for the alignment.
-- | Table details: To view a text version of the data set, select the blatHuman positional table in the Table Browser. To view the table definition, click here.
Human Chain This track shows human genomic alignment to the selected genome using blastz and axtChain.
-- | Display conventions: This track uses the display conventions for chain tracks.
-- | Track details: Clicking on an item in full display mode shows position information in the mouse and the selected genome, the chain ID and score, and provides links to view details of parts of the chain or to open the mouse browser to the corresponding position.
-- | Table details: To view a text version of the data set, select the chainX positional table in the Table Browser, where X is the assembly version in which you're interested, e.g. Hg16. To view the table definition, click here.
Human Cons This track displays the conservation between the mouse and human genomes for 50bp windows in the mouse genome that have at least 15bp aligned to human. The score for a window reflects the probability that the level of observed conservation in that 50bp region would occur by chance under neutral evolution. It is given on a logarithmic scale, and thus it is called the "L-score". An L-score of 1 means there is a 1/10 probability that the observed conservation level would occur by chance, an L-score of 2 means a 1/100 probability, an L-score of 3 means a 1/1000 probability, etc. The L-scores display as "mountain ranges".
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show human genome position information for the window, as well as position information for the corresponding region in the human genome. The details page provides links to the underlying sequence for the alignment and to the sequence underlying the individual alignment windows. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the musHumL positional table in the Table Browser. To view the table definition, click here.
Human Deletions This track displays regions of the chimp assembly that are deleted in the human assembly. Only regions of between 80 and 12000 bases are included. The name of each deletion is a unique pointer to that deletion followed by an underscore and then its length. A similar track, showing chimp deletions in the human assembly, appears in the human Genome Browser.
-- | Display conventions: Deletions are indicated by thin vertical lines.
-- | Track details: Clicking on a deletion in full display mode provides the item name, position, genomic size, and a link to the DNA underlying the feature.
-- | Table details: To view a text version of the data set, select the humanDels positional table in the Table Browser. To view the table definition, click here.
Human Ecores This track shows human evolutionary conserved regions (ecores) computed against the selected assembly by the Exofish program at Genoscope.
-- | Display conventions: This track uses display conventions similar to PSL alignment tracks. Each singleton block corresponds to an ecore. Blocks connected by a line correspond to an "ecotig", a set of colinear ecores in a syntenic region.
-- | Track details: Clicking on an entry in full display mode will show positional information, a link to the Exofish browser, and a link to display the DNA sequence.
-- | Table details: To view a text version of the data set, select the ecores positional table in the Table Browser, where X is the assembly version in which you're interested (e.g. hg16). To view the table definition, click here.
Human ESTs This track shows alignments between Expressed Sequence Tags (ESTs) - spliced and unspliced - in GenBank and the genome. ESTs are single read (typically approximately 500 base) sequences that usually represent fragments of transcribed genes. To view only spliced ESTs, see the Spliced EST track. This track was generated by aligning human ESTs from GenBank against the genome using the BLAT program. Note that the maximum intron length allowed by BLAT is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within 1% of the best are kept. Alignments must also have at least 93% base identity to be kept.
-- | Display conventions: This track uses the display conventions for EST tracks. Hatch marks on the introns indicate the direction of transcription. In the December 2001 assembly and later, this direction is taken by looking at the splice sites. In previous assemblies, the direction of transcription was taken from the GenBank annotations, which frequently were inaccurate; these should be verified in the details page alignment on the basis of the GT-AG splice donor/acceptor rule. As with otherEST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track configuration: The track description page contains a filter to restrict the display to only those entries that match certain keywords and to change the color of the selected entries.
-- | Track details: Clicking on an individual EST entry will show basic track information, the accession number, GenBank highlights, and links to EST/Genomic Alignments.
-- | Table details: To view a text version of the data set, select the all_est positional table in the Table Browser. To view the table definition, click here.
Human mRNAs This track shows alignments between mRNAs from the current assembly in GenBank and the genome. The mRNAs are aligned against the genome using the BLAT program. When a single mRNA aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within 1% of the best are kept. Alignments must also have at least 95% base identity to be kept.
-- | Display conventions: This track follows the display conventions for PSL alignment tracks.
-- | Track configuration: The track description page contains a filter to restrict the display to only those entries that match certain keywords and to change the color of the selected entries.
-- | Track details: Clicking on an entry in full display mode will show a summary of the GenBank entry on that mRNA, convenient hyperlinks to major databases, and base-by-base mRNA/genomic alignments.
-- | Table details: To view a text version of the data set, select the all_mrna positional table in the Table Browser. To view the table definition, click here.
Human Net This track shows the best human chain for every part of the selected genome.
-- | Display conventions: This track uses the display conventions for net tracks.
-- | Track details: In full display mode, clicking on a box shows details information about the chain as a whole, while clicking on a line shows information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.
-- | Table details: To view a text version of the data set, select the netX positional table in the Table Browser, where X is the assembly version in which you're interested, e.g. Hg16. To view the table definition, click here.
Human Proteins This track shows tBLASTn alignments of the peptides from the predicted and known genes indentified in the specified Known Genes track.
-- | Display conventions: This track follows the display conventions for PSL alignment tracks.
-- | Track configuration: The track description page contains options to configure the information shown in the track element labels.
-- | Track details: Clicking on an entry in full display mode will show position information, external links to human mRNA and UniProtKB information, and links to the alignment and peptide sequences.
-- | Table details: To view a text version of the data set, select the blastHg16KG positional table in the Table Browser. To view the table definition, click here.
Human Synteny This track shows syntenous (corresponding) regions between mouse and human chromosomes. The track was created by passing a 100k non-overlapping window over the genome and using the blastz best in human genome alignments to look for high-scoring regions where at least 40% of the bases aligned with the same region in mouse. 100k segments were joined together if they agreed in direction and were within 500kb of each other in the mouse genome and within 4mb of each other in the human. Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with synteny (direction and human location). The syntenic block was extended to include these areas.
-- | Display conventions: This track uses the display conventions for synteny tracks.
-- | Track details: Clicking on an item in full display mode shows details of the mouse-human correspondence and provides a link to the genomic sequence for this feature.
-- | Table details: To view a text version of the data set, select the syntenyHuman positional table in the Table Browser. To view the table definition, click here.
Human Tight This track displays Blastz alignments of the human assembly to the current genome, filtered by axtBest and subsetAxt with very stringent constraints. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show position information for the human and the current genome, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzTightHg positional table in the Table Browser, where X is the number of the assembly. To view the table definition, click here.
JGI Genes (C. intestinalis) This track contains alignments of predicted transcripts from the DOE Joint Genome Institute (JGI) to the C. intestinalis genome.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, plus links to the translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the jgiGene positional table in the Table Browser. To view the table definition, click here.
Known Genes The Known Genes track shows known protein coding genes based on proteins from UniProtKB the corresponding mRNAs from GenBank. Features are colored according to origin and review status: Black: Feature has a corresponding entry in the Protein Data Bank (PDB). Dark blue: Feature has a corresponding protein in UniProtKB or a corresponding NCBI Reference Sequence mRNA with a "Reviewed" status. Lighter blue: Feature has a corresponding NCBI Reference Sequence mRNA with "Provisional" status. Lightest blue: All other features. All mRNAs of a species are aligned against the genome using the BLAT program. When a single mRNA aligns in multiple places, only the best alignments with at least 98% sequence identity are kept. The set of alignments is further reduced by keeping only those mRNAs that are referenced by a protein in UniProtKB. When a single protein references multiple mRNAs, the best mRNA is chosen based on a quality score that depends on its length, how good its translation matches the protein sequence, and its release date. The resulting list of mRNA and protein pairs is trimmed by removing short invalid entries and consolidating entries with identical CDS regions. Finally, RefSeq entries derived from DNA sequences instead of mRNA sequences are added.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks. See above description of color coding conventions.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, microarray expression data, protein structure information, homology information and related links to several tools and databases.
-- | Table details: To view a text version of the data set, select the knownGene positional table in the Table Browser. To view the table definition, click here.
Map Contigs This track shows the locations of contigs of clones on the physical map. In assembly versions prior to the August 6 2001 assembly, this track was based on the Washington University accession map, which in turn was based on a fingerprint contig (FPC) map described in 'A physical map of the human genome' in Nature volume 409 pages 934-941. Starting with the August 6 2001 assembly, this track is based on tiling path fingerprint (TPF) maps curated by the sequencing centers responsible for each chromosome. The TPF maps are merged with the FPC map, favoring the TPF map where conflicts occur. This step increases the clone coverage substantially over that in the TPF maps. The clone contigs in this merged map are shown in this track.
-- | Display conventions: The clone contigs are represented by blocks that indicate their location on the assembly sequence.
-- | Track details: Clicking on an item in full display mode will show a brief description of the extent and number of clones in contig, and the DNA sequence.
-- | Table details: To view a text version of the data set, select the ctgPos positional table in the Table Browser. To view the table definition, click here.
Mapped Human (X. tropicalis) This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the specified version of the Known Genes track.
-- | Display conventions: This track follows the display conventions for BLAT tracks.
-- | Track details: Clicking on an item in full display mode shows positional information, related mRNA and UniProtKB links, the protein length, and links to the alignment an peptide sequences.
-- | Table details: To view a text version of the data set, select the blastHg17KG positional table in the Table Browser. To view the table definition, click here.
MCS Binomial (Zoo) This track shows Multi-Species Conserved Sequences (MCSs) defined using a conservation score threshold from the binomial-based method that selects the top 5% most conserved sequence.
-- | Display conventions: Sequence positions are depicted by blocks.
-- | Track details: Clicking on an item in full display mode shows position and size information, and provides a link to the underlying DNA sequence.
-- | Table details: To view a text version of the data set, select the mcs_b positional table in the Table Browser. To view the table definition, click here.
MCS Inter (Zoo) This track shows Multi-Species Conserved Sequences (MCSs) found by intersecting the sequences generated using the binomial-based and parsimony p-value-based methods (see the MCS Binomial and MCS ParsPVal track descriptions).
-- | Display conventions: Sequence positions are depicted by blocks.
-- | Track details: Clicking on an item in full display mode shows position and size information, and provides a link to the underlying DNA sequence.
-- | Table details: To view a text version of the data set, select the intersectingMCS positional table in the Table Browser. To view the table definition, click here.
MCS InterMerged (Zoo) Same as MCS Inter, but regions less than 10 bp apart have been merged into one region.
-- | Display conventions: Sequence positions are depicted by blocks.
-- | Track details: Clicking on an item in full display mode shows position and size information, and provides a link to the underlying DNA sequence.
-- | Table details: To view a text version of the data set, select the intersectingMergedMCS positional table in the Table Browser. To view the table definition, click here.
MCS ParsPVal (Zoo) This track shows Multi-Species Conserved Sequences (MCSs) defined using a conservation score threshold from the parsimony p-value method that selects the top 5% most conserved sequence.
-- | Display conventions: Sequence positions are depicted by blocks.
-- | Track details: Clicking on an item in full display mode shows position and size information, and provides a link to the underlying DNA sequence.
-- | Table details: To view a text version of the data set, select the mcs_p positional table in the Table Browser. To view the table definition, click here.
MGC Genes This track displays alignments between Mammalian Gene Collection (MGC) human mRNAs with full-length ORFs and the human genome.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information and links to the mRNA, genomic, and comparative sequences.
-- | Track configuration: The track description page offers configuration options that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the mgcGenes positional table in the Table Browser. To view the table definition, click here.
Microsatellites This track contains all perfect microsatellite repeats with between 2 and 10 bp repeat units and 10 or more perfect copies. Over 90% of the items will be multi-allelic polymorphisms. This track was created by using three programs: Tandyman, display_VNTR and Primeleftright. See the track description page for more information.
-- | Display conventions: Microsatellite locations are indicated by thin grey vertical lines.
-- | Track details: Clicking on an item in full display mode shows position information, details about the repeat, and a link to the DNA sequence associated with the feature.
-- | Table details: To view a text version of the data set, select the vntr positional table in the Table Browser. To view the table definition, click here.
miRNA This track shows microRNAs from the miRNA Registry at the Wellcome Trust Sanger Institute.
-- | Display conventions: Mature miRNAs (miRs) are represented by thick lines; the predicted stem-loop portions of the primary transcripts are indicated by thinner lines. miRNAs in the sense orientation are shown in black; those in the reverse orientation are colored grey. When a single precursor produces two mature miRs from its 5' and 3' parts, it is displayed twice with the two different positions of the mature miR.
-- | Track details: Clicking in full mode displays positional information and a link to item's entry in the miRNA registry.
-- | Table details: To view a text version of the data set, select the miRNA positional table in the Table Browser. To view the table definition, click here.
Most Conserved This track shows predictions of conserved elements produced by the phastCons program. Predictions are based on a phylogenetic hidden Markov model (phylo-HMM), a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next. For more information on the methods used to produce this track, see the track's description page.
-- | Display conventions: Rectangular blocks indicate the positions of conserved elements.
-- | Track details: Clicking on an entry in full display mode will show position information and a list of the top-scoring elements in the window.
-- | Table details: To view a text version of the data set, select the phastConsElements positional table from the Table Browser. To view the table definition, click here.
Mouse Blat This track displays alignments of mouse genome to human. The mouse genomic DNA is from the Arachne assembly of mouse whole genome shotgun reads available at the Trace Repository. The alignments were done with BLAT in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human genome was masked with RepeatMasker and Tandem Repeats Finder prior to running BLAT. Regions with more than 300 aligned reads were assumed novel repeat elements and filtered out. Alignments of greater than 97% identity may represent mouse contamination of human or vice versa.
-- | Display conventions: This track follows the display conventions for BLAT tracks.
-- | Track details: Clicking on an item will show details on mouse sequence fragment and alignment details.
-- | Table details: To view a text version of the data set, select the blatMouse positional table in the Table Browser. To view the table definition, click here.
Mouse Chain This track shows mouse genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Mouse Cons This track displays the conservation between the human and mouse genomes for 50bp windows in the human genome that have at least 15bp aligned to mouse. The score for a window reflects the probability that the level of observed conservation in that 50bp region would occur by chance under neutral evolution. It is given on a logarithmic scale, and thus it is called the "L-score". An L-score of 1 means there is a 1/10 probability that the observed conservation level would occur by chance, an L-score of 2 means a 1/100 probability, an L-score of 3 means a 1/1000 probability, etc. The L-scores display as "mountain ranges".
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show human genome position information for the window, as well as position information for the corresponding region in the mouse genome. The details page provides links to the underlying sequence for the alignment and to the sequence underlying the individual alignment windows. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the humMusL positional table in the Table Browser. To view the table definition, click here.
Mouse Ecores This track shows Mouse evolutionary conserved regions (ecores) computed against the selected assembly genome by the Exofish program at Genoscope. For information on this track, see the Human Ecores track description. Mouse ESTs This track shows alignments between mouse Expressed Sequence Tags (ESTs) - spliced and unspliced - in GenBank and the genome. This track was generated by aligning mouse ESTs from GenBank against the genome using the BLAT program. Note that the maximum intron length allowed by BLAT is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within 1% of the best are kept. Alignments must also have at least 93% base identity to be kept.
-- | Display conventions: This track uses the display conventions for EST tracks. As with other EST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an individual EST entry will show basic track information, the accession number, GenBank highlights, and links to EST/Genomic Alignments.
-- | Table details: To view a text version of the data set, select the all_est positional table in the Table Browser. To view the table definition, click here.
Mouse mRNAs See the description for Human mRNAs. Mouse Net This track shows the best mouse chain for every part of the selected genome. See the Human Net track description for more information. Mouse Synteny (hg13+) This track shows syntenous (corresponding) regions between human and mouse chromosomes. The track was created by passing a 100k non-overlapping window over the genome and using the blastz best in mouse genome alignments to look for high-scoring regions where at least 40% of the bases aligned with the same region in mouse. 100k segments were joined together if they agreed in direction and were within 500kb of each other in the human genome and within 4mb of each other in the mouse. Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with synteny (direction and mouse location). The syntenic block was extended to include these areas.
-- | Display conventions: This track uses the display conventions for synteny tracks.
-- | Track details: Clicking on an item in full display mode shows details of the mouse-human correspondence and provides a link to the genomic sequence for this feature.
-- | Table details: To view a text version of the data set, select the syntenyMouse positional table in the Table Browser. To view the table definition, click here.
Mouse Synteny (hg12 only) This track shows orthologous (syntenic) regions between mouse and human chromosomes based on data from Michael Kamal at the Whitehead Institute.
-- | Display conventions: This track uses the display conventions for synteny tracks.
Track details: Clicking on an item in full display mode will show details of the mouse-human correspondence, as well links to genomic dotplots, additional information, and an alternative synteny map based on orthologous genes.
-- | Table details: To view a text version of the data set, select the mouseSynWhd positional table in the Table Browser. To view the table definition, click here.
Multiz Yeast This track displays multiz multiple alignments of seven species of the genus Saccharomyces. The graphic display shows the alignment projected onto S. cerevisiae.
-- | Display conventions: In full display mode, the track displays pairwise alignments of several species aligned to the S. cerevisiae genome. The pairwise alignments are displayed in standard UCSC browser "dense" mode using a grey-scale density gradient. When zoomed-in to the base-display level, the track shows the base composition of each alignment. The numbers and symbols on the "hidden gap" line indicate the lengths of gaps in the S. cerevisiae sequence at those alignment positions. If the gap size is greater than 9, the "+" symbol is displayed. The track must be zoomed-in to 30,000 or fewer bases to access detailed information about the alignments at a specific position.
-- | Track details: Clicking on an entry in full display mode will show detailed alignment information for each of the organisms.
-- | Table details: To view a text version of the data set, select the multizYeast positional table in the Table Browser. To view the table definition, click here.
NIA Genes This track displays alignments of the National Institute on Aging (NIA) Mouse Gene Index (Version 3) against the mouse genome.
-- | Display conventions: This track uses the display conventions for Blat alignment tracks.
-- | Track details: Clicking on an individual track item in full mode displays a page with alignment details and a link to the corresponding NIA Mouse Gene Index entry.
-- | Table details: To view a text version of the data set, select the NIAGene positional table in the Table Browser. To view the table definition, click here.
NCI60 This track displays cDNA expression data for a micro-array of 8,000 genes for 60 cell lines used in an NCI cancer drug screen.
-- | Display conventions: To understand the track, experiment with it set to full mode but other tracks (except known genes) hidden, while reading its filter page. Each column of colored boxes represents variation in transcript levels for a given cDNA across array experiments; each row represents the measured transcript levels for all genes in a single sample. The saturation of a color corresponds to the magnitude of transcript variation. Black indicates an undetectable change in expression; gray shows missing data.
-- | Track configuration: The track description page contains a filter to limit the tissue types displayed and change the color scheme of the display.
Track details: Clicking on an individual track item in full mode opens a rich details page. The exon probe and experiment selected are highlighted in blue under item name.
-- | Table details: To view a text version of the data set, select the nci60 positional table in the Table Browser. To view the table definition, click here.
Non-A. gambiae mRNAs See the description for Non-Human mRNAs. Non-A. mel. mRNAs mRNAs of organisms other than A. mellifera. See the description for Non-Human mRNAs. Non-Chicken mRNAs See the description for Non-Human mRNAs. Non-Chicken RefSeq This track shows known protein-coding genes from organisms other than chicken, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the Non-Dog RefSeq track for more information. Non-Chimp ESTs See the description for Non-Human ESTs. Non-Chimp mRNAs See the description for Non-Human mRNAs. Non-C. intestinalis mRNAs See the description for Non-Human mRNAs. Non-Ciona mRNAs See the description for Non-Human mRNAs. Non-Ciona RefSeq This track shows known protein-coding genes from organisms other than C. intestinalis, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the Non-Dog RefSeq track for more information. Non-Dog RefSeq This track shows known protein-coding genes from organisms other than dog, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, and related links to external databases.
-- | Track configuration: The track description page contains configuration options to change the feature label to display the gene name (default), the accession name, both the gene and accession names, or no label at all.
-- | Table details: To view a text version of the data set, select the xenoRefGene positional table in the Table Browser. To view the table definition, click here.
Non-D. anan. mRNAs mRNAs of organisms other than D. ananassae. See the description for Non-Human mRNAs. Non-D. anan. RefSeq This track shows known protein-coding genes from organisms other than D. ananassae, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the description for Non-Human mRNAs. Non-D. melanogaster mRNAs See the description for Non-Human mRNAs. Non-D. moj. mRNAs mRNAs of organisms other than D. mojavensis. See the description for Non-Human mRNAs. Non-D. moj. RefSeq This track shows known protein-coding genes from organisms other than D. mojavensis, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the description for Non-Human mRNAs. Non-D. pseudo. mRNAs mRNAs of organisms other than D. pseudoobscura. See the description for Non-Human mRNAs. Non-D. pseudo. RefSeq This track shows known protein-coding genes from organisms other than D. pseudoobscura, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the description for Non-Human mRNAs. Non-D. vir. mRNAs mRNAs of organisms other than D. virilis. See the description for Non-Human mRNAs. Non-D. vir. RefSeq This track shows known protein-coding genes from organisms other than D. virilis, taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the description for Non-Human mRNAs. Non-D. yakuba mRNAs See the description for Non-Human mRNAs. Non-Fugu mRNAs See the description for Non-Human mRNAs. Non-Human ESTs This track displays translated BLAT alignments of non-human vertebrate ESTs from GenBank. The alignments were passed through a piecewise near-best-in-genome filter. In cases where ESTs align to multiple places in the genome, only the near-best are retained. Matches help validate human exon identification.
-- | Display conventions: This track uses the display conventions for EST tracks. As with other EST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an item in full display will show a summary of the GenBank entry, a hyperlink to the full record, PubMed links by gene name, product, and author, and mRNA/genomic alignment information.
-- | Table details: To view a text version of the data set, select the xenoEst positional table in the Table Browser. To view the table definition, click here.
Non-Human mRNAs This track displays translated BLAT alignments of vertebrate and invertebrate mRNA (other than that from the selected genome) from GenBank. The alignments were passed through a near-best-in-genome filter. Some mRNAs align to multiple places but only the near-best are retained. For a distant vertebrate, alignment requires a fairly slowly evolving gene. Matches are often plausible ortholog candidates.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track configuration: The track description page contains a filter to restrict the display to only those entries that match certain keywords and to change the color of the selected entries.
-- | Track details: Clicking on an entry in full display mode will show a summary of the GenBank entry on that mRNA, convenient hyperlinks to major databases, and base-by-base mRNA/genomic alignments.
-- | Table details: To view a text version of the data set, select the xenoMrna positional table in the Table Browser. To view the table definition, click here.
Non-Mouse ESTs See the description for Non-Human ESTs. Non-Mouse mRNAs See the description for Non-Human mRNAs. Non-Opossum mRNAs See the description for Non-Human mRNAs. Non-Rat ESTs See the description for Non-Human ESTs. Non-Rat mRNAs See the description for Non-Human mRNAs. Non-Tetraodon mRNAs See the description for Non-Human mRNAs. Non-Zebrafish mRNAs See the description for Non-Human mRNAs. Opossum Chain This track shows opossum genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Opossum mRNAs See the description for Human mRNAs. Opossum Net This track shows the best opossum chain for every part of the selected genome. See the Human Net track description for more information. Overlap SNPs (older archived versions only) This track shows single nucleotide polymorphisms found on overlapping contigs. Overlap SNPs are useful markers in mapping genes and diseases. This data was provided by the SNP Consortium.
-- | Display conventions: SNP locations are indicated by thin grey vertical lines.
-- | Track details: Clicking in full mode brings up a location description and dbSNP link.
-- | Table details: To view a text version of the data set, select the snpNih positional table in the Table Browser. To view the table definition, click here.
Parsimony P-Values (Zoo) This track displays the level of conservation of Zoo sequences at any given position. More precisely, it computes the p-value of observing a certain parsimony score for a given column of the multiple alignment under the null model of neutral evolution.
-- | Display conventions: This track uses the display conventions for wiggle tracks.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on one of the peaks in the track when in full display mode will show genome position information for the window and a link to the underlying DNA sequence. In full mode in a zoomed-out display, detailed information may not be accessible for an individual feature. In this case, zoom in and try again.
-- | Table details: To view a text version of the data set, select the parsPValues positional table in the Table Browser. To view the table definition, click here.
Perlegen (chr21 only) This track shows haplotype blocks derived from common single nucleotide polymorphisms (SNPs) on Chromosome 21 by Perlegen Sciences, as described in Patil N et. al. (2001), "Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning", Science 294:1719-1723. General information on the blocks is available from Perlegen's Chromosome 21 Haplotype Browser.
-- | Display conventions: The location of each haplotype block is represented by a blue horizontal line with tall vertical blue bars at the first and last SNPs of the block. Blocks are displayed as starting at the first SNP and ending at the last SNP of the block. This is slightly different from the representation on the Perlegen web site in which blocks are stretched until they abut each other. The shade of the blue indicates the minimum number of SNPs required to discriminate between haplotype patterns that account for at least 80% of genotyped chromosomes. Darker colors indicate fewer SNPs are necessary. Individual SNPs are denoted by smaller black vertical bars. At multi-megabase resolution in dense display mode, clusters of tall blue bars may indicate hotspots for recombination.
-- | Track details: Clicking on an entry in full display mode will show basic position information, SNP information for the block, and a link to sequence information for the feature. To view additional information on a particular block, click on Outside Link on the item's details page.
-- | Table details: To view a text version of the data set, select the perlegen positional table in the Table Browser. To view the table definition, click here.
QTL This track shows approximate positions of quantititive trait loci (QTL) based on reported peak LOD scores taken from Jackson Lab's Mouse Genome Informatics (MGI) Database.
-- | Display conventions: QTL locations are indicated by thin vertical bars.
-- | Track details: Clicking on an item in full mode provides a link to the MGI record for the selected QTL, information about the QTL, and position information.
-- | Table details: To view a text version of the data set, select the jaxQTL positional table in the Table Browser. To view the table definition, click here.
Quality Scores This track shows the sequencing quality score (between 0 and 100) of each base in the assembly.
-- | Display conventions: The height at each position of the track indicates the quality of the base. When zoomed out to a large range, the heights reflect the averaged scores. Scores of 40 or higher reflect high confidence in the sequence (with an error rate of less than 1/10,000); scores of 20 or higher reflect reasonable confidence (of working draft quality).
-- | Table details: To view a text version of the data set, select the quality positional table in the Table Browser. To view the table definition, click here.
Radiation Hybrid Map (Zebrafish) This track shows alignments between zebrafish Radiation Hybrid (RH) map sequences (consisting of ESTs and other genetic markers) and the genome.
-- | Display conventions: This track uses the display conventions for EST tracks.
-- | Track details: Clicking in full display mode provides a link to the genomic alignment.
-- | Table details: To view a text version of the data set, select the rhMap positional table in the Table Browser. To view the table definition, click here.
Random SNPs (older archived versions only) This track displays single nucleotide polymorphisms (SNPs)found by random sequencing. Random SNPs are useful markers in mapping genes and complex traits. Because these SNPs are detected from random reads, they are useful for evolutionary studies. This data was provided by the SNP Consortium.
-- | Display conventions: SNP locations are indicated by thin grey vertical lines.
-- | Track details: Clicking in full mode brings up a location description and dbSNP link.
-- | Table details: To view a text version of the data set, select the snpTsc positional table in the Table Browser. To view the table definition, click here.
Rat Chain This track shows rat genomic alignment to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Rat Ecores This track shows rat evolutionary conserved regions (ecores) computed against the selected assembly genome by the Exofish program at Genoscope. For information on this track, see the Human Ecores track description. Rat ESTs See the description for the Human ESTs track. Rat mRNAs See the description for the Human mRNAs track. Rat Net This track shows the best rat chain for every part of the selected genome. See the Human Net track description for more information. Rat Synteny This track shows syntenous (corresponding) regions between human and rat chromosomes. The track was created by passing a 100k non-overlapping window over the genome and using the blastz best in mouse genome alignments to look for high-scoring regions where at least 40% of the bases aligned with the same region in rat. 100k segments were joined together if they agreed in direction and were within 500kb of each other in the human genome and within 4mb of each other in the rat. Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with synteny (direction and rat location). The syntenic block was extended to include these areas.
-- | Display conventions: This track uses the display conventions for synteny tracks.
-- | Track details: Clicking on an item in full display mode shows details of the rat-human correspondence and provides a link to the genomic sequence for this feature.
-- | Table details: To view a text version of the data set, select the syntenyRat positional table in the Table Browser. To view the table definition, click here.
Recomb Rate This track shows calculated sex-averaged rates of recombination based on either the deCODE, Marshfield, or Genethon genetic maps. The deCODE map rates are displayed by default.
-- | Display conventions: Each 1Mb window represents the average recombination rate of the bases contained within that window. Darker shades of gray correspond to higher recombination rates.
-- | Track configuration: The track description page contains a filter to map distances (sex-averaged distance, female distance, or male distance) for the 3 different types of maps.
-- | Track details: Clicking in full mode shows position information and a list of all the recombination rate values for that 1Mb window.
-- | Table details: To view a text version of the data set, select the recombRate positional table in the Table Browser. To view the table definition, click here.
RefSeq Genes The RefSeq Gene track shows known protein coding genes taken from the mRNA reference sequences collection (RefSeq) compiled at NCBI. Refseq mRNAs are aligned against the genome using the BLAT program. When a single mRNA aligns in multiple places, only the best alignments are kept. Alignments must also have at least 98% sequence identity to be kept.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks. Non-coding RNA genes have their own track in some assemblies. The color shading indicates the level of review that the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, and related links to outside databases.
-- | Track configuration: The track description page contains configuration options to change the feature label to display the gene name (default), the accession name, both the gene and accession names, or no label at all.
-- | Table details: To view a text version of the data set, select the refGene positional table in the Table Browser. To view the table definition, click here.
Reg. CHIP/CHIP This track shows the location of the probes spotted on a slide in the chromatin immunoprecipitation/microarray hybridization (CHIP/CHIP) experiments described in Harbison, C.T. et al., Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004), 99-104 (2004). See also the "Regulatory Code" track for the position of the individual motifs.
-- | Display conventions: Black boxes indicate the probe locations.
-- | Track details: Clicking on an entry in full display mode shows position information, as well as which transcription factors pulled down DNA that is enriched for the probe sequence, which transcription factor binding site motifs are present in the probe, and whether these motifs are conserved in related yeast species.
-- | Table details: To view a text version of the data set, select the transRegCodeProbe positional table in the Table Browser. To view the table definition, click here.
Regulatory Code This track shows putative regulatory elements in S. cerevisiae that are supported by cross-species evidence, as described in (Harbison, C.T. et al., Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004), 99-104 (2004)). The authors performed a genome-wide location analysis with 203 known DNA-binding transcriptional regulators (some under multiple environmental conditions) and identified 11,000 high-confidence interactions between regulators and promoter regions. They then compiled a compendium of motifs for 102 transcriptional regulators based on a combination of their experimental results, cross-species conservation data for four species of yeast, and motifs from the literature, and finally, they mapped these motifs to the S. cerevisiae genome. This track shows positions at which these motifs matched the genome with high confidence and at which the matching sequence was well conserved across yeast species. See the "Reg. CHIP/CHIP" track for additional related information.
-- | Display conventions: Regulatory elements are represented by rectangular blocks. The darker the shade of the block, the stronger the evidence supporting it.
-- | Track details: Clicking on an entry in full display mode shows the sequence at that site compared to the position-specific probability matrix for the associated transcriptional regulator (shown as both a table and a graphical logo). It also indicates whether the binding site is supported by experimental (CHIP/CHIP) results and the number of other yeast species in which it is conserved.
-- | Track configuration: The user can set the minimum unnormalized score criteria that data must meet to be displayed in the track.
-- | Table details: To view a text version of the data set, select the tranRegCode positional table in the Table Browser. To view the table definition, click here.
Regulatory Module This track shows predicted transcription factor binding sites based on sequence similarities upstream of coordinately expressed genes. Clicking on a particular predicted binding site brings up a page which indicates the sequence motif associated with the predicted transcription factor, and the sequence at the predicted binding site. Where known motifs have been identified by this method, they are named, otherwise they are assigned a Motif_ number.
-- | Display conventions: In dense display mode, gold areas indicate the extent of the area searched for binding sites; black boxes indicate the actual binding sites. In fuller display modes, the gold areas disappear and only the binding sites are displayed.
-- | Track details: Clicking on an entry in full display mode provides positional and score information about the item, and a link to display the DNA underlying the feature.
-- | Track configuration: The user can set the minimum unnormalized score criteria that data must meet to be displayed in the track.
-- | Table details: To view a text version of the data set, select the esRegGeneToMotif positional table in the Table Browser. To view the table definition, click here.
RepeatMasker The track shows dispersed repeats as determined by RepeatMasker using the Repbase Update library of repetitive sequences from the Genetic Information Research Institute. These elements include SINE, LINE, LTR, DNA, simple, low complexity, micro-satellite, tRNA, and other repeat families.
-- | Display conventions: Darker gray boxes indicates a more recent age (as dated by alignment to a canonical repeat). In dense mode for large chromosomal regions, the black boxes representing repeats may merge into misleading single blocks in the display. Full display mode shows 9 tracks representing the major repeat classes.
-- | Table details: To view a text version of the data set, select the rmsk positional table in the Table Browser. To view the table definition, click here.
Retroposed Genes This track shows processed mRNAs that have been inserted back into the genome after the mouse/human split. Retrogenes can be functional genes that have acquired a promoter from a neighboring gene, non-functional pseudogenes, or transcribed pseudogenes.
-- | Display conventions: This track follows the display conventions used by gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show detailed information about the pseudogene's characteristics, alignment links, and Genome Browser annotation links for the gene locus that spawned the retrogene.
-- | Table details: To view a text version of the data set, select the pseudoGeneLink positional table in the Table Browser. To view the table definition, click here.
RGD ESTs This track shows alignments expressed sequence tags (ESTs) from the Rat Genome Database (RGD).
-- | Display conventions: This track uses the display conventions for EST tracks. As with other EST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an individual EST entry will show basic track information, the accession number, GenBank highlights, links to EST/genomic alignments, and an external link to the RGD EST report.
-- | Table details: To view a text version of the data set, select the rgdEst positional table in the Table Browser. To view the table definition, click here.
RGD Genes This track shows RefSeq genes curated by the Rat Genome Database (RGD).
-- | Display conventions: This track follows the display conventions used by gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will display position information, links to sequence displays, and links to outside sources showing additional information.
-- | Track configuration: The track description page contains a filter that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the rgdGene positional table in the Table Browser. To view the table definition, click here.
RGD QTL This track shows quantitative trait loci (QTLs) curated by the Rat Genome Database (RGD).
-- | Display conventions: Loci positions are represented by blocks.
-- | Track details: Clicking on an entry in full display mode will display genomic information and a link to the corresponding entry in the RGD.
-- | Table details: To view a text version of the data set, select the rgdQtl positional table in the Table Browser. To view the table definition, click here.
RGD SSLP This track shows simple sequence length polymorphisms (SSLPs), also known as microsatellite DNA, from the Rat Genome Database (RGD). SSLPs consist of 1 - 6 simple nucleotide repeat sequences, highly polymorphic in repeat length among strains. They are often used as genetic markers for genotyping.
-- | Display conventions: SSLP positions are represented by thin blocks.
-- | Track details: Clicking on an entry in full display mode will display genomic information and a link to the corresponding entry in the RGD.
-- | Table details: To view a text version of the data set, select the rgdSslp positional table in the Table Browser. To view the table definition, click here.
Rinn Sex Exp This track shows gene expression differences between adult male and female tissues as described in Rinn, JL et al. (2004) Major Molecular Differences between Mammalian Sexes Are Involved in Drug Metabolism and Renal Function. Developmental Cell 6:791-800.
-- | Display conventions: This track follows display conventions similar to PSL alignment tracks.
-- | Track details: In dense or packed display mode, the track shows averages of related tissues. In full display mode, all tissues are displayed. Click on an individual tissue entry to show a gene expression map for all tissues in the experiment.
-- | Table details: To view a text version of the data set, select the rinnSex positional table in the Table Browser. To view the table definition, click here.
RNA Genes This track shows human non-protein-coding RNA genes and RNA pseudogenes. This includes tRNAs, rRNAs, SRPs, methylation guide snoRNAs, U2-U6 RNA-like, and similar elements both known and predicted (by tRNAscanSE etc). The density of these elements can range from 1-4 per million bp in some chromosomes. Protein coding genes are displayed elsewhere in the RefSeq Genes track.
-- | Display conventions: RNA genes are represented by light-colored blocks. Pseudogenes are represented by darker blocks.
-- | Track details: Clicking on an entry in full display mode will display feature classification, method of prediction, location, reliability score, and a link to DNA sequence for the feature.
-- | Table details: To view a text version of the data set, select the rnaGene positional table in the Table Browser. To view the table definition, click here.
Rosetta This track displays microarray tissue expression data provided by Rosetta Inpharmatics. It helps catalogue genes and transcriptome, complements computational gene predictions, and seeks to define gene boundaries via co-regulated expression of nearby exons.
-- | Display conventions: The data is stratified by various tissue and disease-specific conditions of gene expression. Confirmed and predicted exons are placed in separate tracks. Click on the mini-button to the left of the track to display a track description page containing more information.
-- | Track configuration: The track description page contains a filter to fine-tune the track display. The following display options are configurable: o Reference Sample: Determines which of the 69 different experiments are displayed, based on the reference sample used. o Exons Shown: Determines whether data is shown for probes corresponding to confirmed, predicted, or all exons. o Color Scheme: Data are presented using two color false display. The default colors can be changed for those who are colorblind. Gray values indicate missing data.
-- | Track details: Clicking on a Rosetta exon in full display mode will show an averaged display that can be expanded via checkboxes to a graph of actual intensities for an individual experiment.
-- | Table details: To view a text version of the data set, select the rosetta positional table in the Table Browser. To view the table definition, click here.
Sanger 22 and Sanger 22 Pseudo These tracks contain the Sanger Centre annotations of chromosome 22.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on the track while in full display mode will show details of the methods used to construct this track as well as the contributors.
-- | Table details: To view a text version of the data set, select the sanger22 positional table in the Table Browser. To view the table definition, click here.
S. cerevisiae ESTs See the Human ESTs track description. S. cerevisiae mRNAs See the Human mRNAs track description. Scaffolds (Chimp) This track shows the chromosome-based version of the November 2003 Arachne chimp assembly (panTro1) from the Chimp Genome Sequencing Consortium.
-- | Display conventions: In dense display mode, this track depicts in alternating gold and brown the individual scaffolds used to create the assembled sequence. Where gaps exist in the path, spaces are shown between the gold and brown blocks. Relative order and orientation of the scaffolds, as determined from the human/chimp alignments, is implied for the non-random chromosomes. The display must be sufficiently zoomed in to view the gap features.
-- | Track details: Clicking on an item in full display mode will show information about the scaffold fragment and bases and position information.
-- | Table details: To view a text version of the data set, select the gold positional table in the Chimp Table Browser. To view the table definition, click here.
Scaffolds (Fugu, Zebrafish, Tetraodon) This track shows the draft and finished clones that comprise the assembly.
-- | Display conventions: In dense display mode, this track depicts in alternating gold and brown the individual clones used to create the assembled sequence. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If the relative order and orientation of the contigs between the two blocks is known, a line is drawn to bridge the blocks. The display must be sufficiently zoomed in to view the gap features.
-- | Track details: Clicking on an item in full display mode will show contig and position information.
-- | Table details: To view a text version of the data set, select the gold positional table in the Fugu or Zebrafish Table Browser. To view the table definition, click here.
Segmental Duplications This track shows regions detected as putative genomic duplications within the golden path. For a description of the 'fuguization' detection method, see Bailey JA et. al. (2001). "Segmental duplications: organization and impact within the current human genome project assembly". Genome Res 11:1005-17.
-- | Display conventions: Orange, yellow, dark-light gray represent similarities of greater than 99%, 99-98% and 98-90% respectively. Duplications greater than 98% similarity that lack sufficient SDD evidence (likely missed overlaps) are shown as red. Cut off values were at least 1 kb of total sequence aligned (containing at least 500 bp non-RepeatMasked sequence) and at least 90% sequence identity.
-- | Track details: Clicking on an entry in full display mode provides position, filter, and alignment information as well as links to the corresponding genomic sequence.
-- | Table details: To view a text version of the data set, select the genomicSuperDups positional table in the Table Browser. To view the table definition, click here.
Self Chain This track shows alignments of the selected genome with itself using blastz and axtChain.
-- | Display conventions: This track uses the display conventions for chain tracks.
-- | Track details: Clicking on an item in full display mode shows position information, the chain ID and score, and provides links to view details of parts of the chain or to open the browser to the corresponding aligning position.
-- | Table details: To view a text version of the data set, select the chainSelf positional table in the Table Browser. To view the table definition, click here.
SGD Genes This track shows annotated genes and open reading frames (ORFs) of Saccharomyces cerevisiae obtained from the Saccharomyces Genome Database (SGD).
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode provides a wealth of genomic, mRNA, and protein information about the gene as well as links to several associated external sites.
-- | Table details: To view a text version of the data set, select the sgdGene positional table in the Table Browser. To view the table definition, click here.
SGD Other This track shows a variety of features in the Saccharomyces cerevisiae genome, including tRNAs, transposons, centromeres, and open reading frames (ORFs) classified as dubious. The data was downloaded from the Saccharomyces Genome Database (SGD).
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode provides genomic information and a link to view the DNA underlying the track.
-- | Table details: To view a text version of the data set, select the sgdOther positional table in the Table Browser. To view the table definition, click here.
SGP Genes This track shows gene predictions from the SGP program, which is being developed at the Grup de Recerca en Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona. To predict genes in a genomic query, SGP combines geneid predictions with tblastx comparisons of the genomic query against other genomic sequences.
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode provides position information as well as links to the corresponding protein, mRNA, genomic, and comparative sequences.
-- | Table details: To view a text version of the data set, select the sgpGene positional table in the Table Browser. To view the table definition, click here.
Short Match This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly.
-- | Display conventions: Perfect matches are indicated by a solid rectangle. In full display mode, each occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the "+" strand is shown.
-- | Track details: Clicking on an entry in full display mode provides position information about the match.
-- | Track configuration: The track may be configured to search for any short sequence of 2-30 bases in length. To change the sequence, type a new sequence into the text box at the top of the track description page.
-- | Table details: Unlike most annotations in the Genome Browser, this track is not table-based.
Simple Repeats This track displays simple tandem repeats (possibly imperfect) located by Tandem Repeats Finder, which is specialized to this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases.
-- | Display conventions: Repeats are represented by block boxes that indicate location in the assembly.
-- | Track details: Clicking on an item in full display mode will show the simple repeat sequence, copy number, and quality of match statistics.
-- | Table details: To view a text version of the data set, select the simpleRepeats positional table in the Table Browser. To view the table definition, click here.
Slam Human, Slam Mouse, Slam Rat These tracks predict coding exons and conserved noncoding regions in a pair of homologous DNA sequences, incorporating both statistical sequence properties and the degree of conservation in making the predictions. The model is symmetric: the same gene structure (with possibly different exon lengths) is predicted in both sequences.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, plus links to the predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the appropriate slam positional table in the Table Browser (e.g. slamHuman, slamMouse, slamRat). To view the table definition, click here.
SlamHumanNonCoding, SlamMouseNonCoding, SlamRatNonCoding These tables show slam predictions of conserved noncoding regions in homologous DNA sequences.
-- | Display conventions: The data in these tables are displayed as part of the Slam Human, Slam Mouse, and Slam Rat tracks. See the track descriptions for these tracks for display information.
-- | Table details: To view a text version of the data set, select the appropriate slamNonCoding positional table in the Table Browser (e.g. slamHumanNonCoding, slamMouseNonCoding, slamRatNonCoding). To view the table definition, click here.
SNAP Genes (C. intestinalis) This track shows gene predictions determined by SNAP (Semi-HMM-based Nucleic Acid Parser), a general purpose gene-finding program written by Ian Korf. SNAP is suitable for both eukaryotic and prokaryotic genomes. For this set of gene predictions, it was trained on gene annotations from the DOE Joint Genome Institute (JGI).
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode brings up basic track information, plus links to the translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the snapGene positional table in the Table Browser. To view the table definition, click here.
Sno/miRNA This track displays positions of four different types of RNA in the human genome: microRNAs from the miRNA Registry at the Wellcome Trust Sanger Institute, small nucleolar RNAs (C/D box and H/ACA box snoRNAs) and Cajal body-specific RNAs (scaRNAs) from the snoRNA-LBME-DB maintained at the Laboratoire de Biologie Moléculaire Eucaryote. C/D box and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation, respectively, of rRNAs and snRNAs, although many of them have no documented target RNA. The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase II, and often contain both C/D and H/ACA domains.
-- | Display conventions: Mature miRNAs (miRs) are represented by thick red blocks; the predicted stem-loop portions of the primary transcripts are indicated by thinner blocks. When a single precursor produces two mature miRs from its 5' and 3' parts, both positions of the mature miRNA are individually displayed. C/D box, H/ACA box snoRNAs and scaRNAs are represented by blue, green and magenta blocks, respectively. At a zoomed-in resolution, arrows superimposed on the blocks indicate the sense orientation of the snoRNAs.
-- | Track details: Clicking on an entry in full display mode provides a link to the miRNA Registry, the RNA type, position information, and a link to the DNA sequence associated with the feature.
-- | Table details: To view a text version of the data set, select the wgRna positional table in the Table Browser. To view the table definition, click here.
SNPs (Human assemblies hg17 and later) This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that can be mapped against the current genome assembly. These data were obtained from dbSNP and commercially-available genotyping arrays and include known point mutations (Single Nucleotide Polymorphisms), insertions, deletions, multiple See the track description page for more information about the SNP classifications. These data were provided by the SNP Consortium and Affymetric, Inc..
-- | Display conventions: Variants are drawn a single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases.
-- | Track details: Clicking in full mode brings up position information about the reference sequence, detailed information about the variant, and a link to the record in dbSNP.
-- | Track configuration: The colors of variants may be changed to highlight their source, molecule type, variant class, validation status, or functional classification. Variants can be excluded from the display based on these same criteria or if they fall below the user-specified minimum average heterozygosity.
-- | Table details: To view a text version of the data set, select the snp positional table in the Table Browser. To view the table definition, click here.
SNPs (Human assemblies prior to hg17) This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that can be mapped against the current genome assembly. These include known point mutations (Single Nucleotide Polymorphisms), insertions, deletions, and segmental mutations from the current build of dbSnp (shown in the Genome Browser release log). See the track description page for more information about major cases that are not mapped. These data were provided by the SNP Consortium.
-- | Display conventions: SNP locations are indicated by thin grey vertical lines.
-- | Track details: Clicking in full mode brings up a location description and dbSNP link.
-- | Table details: To view a text version of the data set, select the snpMap positional table in the Table Browser. To view the table definition, click here.
Spliced ESTs The Spliced EST track displays the subset of Expressed Sequence Tags (ESTs) from GenBank that show signs of splicing when aligned against the genome. ESTs are single read (typically approximately 500 base) sequences that usually represent fragments of transcribed genes. By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. This track may also suggest alternate splices. The GT-AG splice donor/acceptor rule has not been applied. For a display of all ESTs (including unspliced), see the Human EST track. This track was generated by aligning human ESTs from GenBank against the genome using the BLAT program. Note that the maximum intron length allowed by BLAT is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within 1% of the best are kept. Alignments must also have at least 93% base identity to be kept.
-- | Display conventions: This track uses the display conventions for EST tracks As with other EST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an individual EST entry will show basic track information, the accession number, GenBank highlights, and links to translated protein, predicted mRNA, and genomic sequences.
-- | Table details: To view a text version of the data set, select the intronEst positional table in the Table Browser. To view the table definition, click here.
STS Markers (human) This track shows the locations of Sequence Tagged Site (STS) markers along the draft assembly. The STS markers have been mapped using either genetic (Genethon and Marshfield maps), radiation hybridization (the Stanford, Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map) techniques. In releases prior to August 2001, this track also shows the approximate position of FISH mapped clones. Starting with the August 2001 assembly, the FISH clones have been moved into a separate track.
-- | Display conventions: Genetic map markers are shown in blue, and radiation hybrid map markers are shown in black. When a marker maps to multiple positions in the genome, it is shown in a lighter color.
-- | Track details: Clicking on a specific marker in full display mode will show synonyms, position information, primers, YAC map position, and uniSTS and GDB links.
-- | Table details: To view a text version of the data set, select the stsMap positional table in the Table Browser. To view the table definition, click here.
STS Markers (mouse) This track shows the locations of Sequence Tagged Site (STS) markers along the draft assembly of the mouse genome. These STS markers appear on the MGI consensus mouse genetic map. Information about the genetic map and STS marker primer sequences are provided by the Mouse Genome Informatics database group at The Jackson Laboratory.
-- | Display conventions: Genetic map markers are shown as thin black boxes.
-- | Track details: Clicking on a specific marker in full display mode will show position information, primers, genetic map position, genomic alignments, and MGI links.
-- | Table details: To view a text version of the data set, select the stsMapMouse positional table in the Table Browser. To view the table definition, click here.
STS Markers (rat) This track shows locations of Sequence Tagged Site (STS) markers along the draft assembly of the rat genome. These STSs have been mapped using either genetic (rat FHH x ACI F2 intercross genetic map, rat SHRSP x BN F2 intercross genetic map) or radiation hybridization (RH map.2.2).
-- | Display conventions: Genetic map markers are shown as thin black boxes.
-- | Track details: Clicking on a specific marker in full display mode will show position information, primers, genetic map position, and links to the corresponding UniSTS and RGD entries.
-- | Table details: To view a text version of the data set, select the stsMapRat positional table in the Table Browser. To view the table definition, click here.
Superfamily The Superfamily track shows proteins having homologs with known structures or functions. Each entry in the track shows the coding region of a gene (based on Ensembl gene prediction). The label, shown in Full mode at the left hand side of each entry, consists of the names of all known protein domains coded by this gene. This usually contains structural and/or function descriptions that provide valuable information for getting a quick grasp of the biological significance for the gene.
-- | Display conventions: Coding regions are indicated by red blocks.
-- | Track details: Clicking on an entry in full display mode will show the Superfamily domains of the corresponding protein and provide a link to the Superfamily database entry.
-- | Table details: To view a text version of the data set, select the superfamily positional table in the Table Browser. To view the table definition, click here.
Tetraodon Chain This track shows Tetraodon genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Tetraodon Ecores This track shows Tetraodon evolutionary conserved regions (ecores) computed against the selected assembly genome by the Exofish program at Genoscope. For information on this track, see the Human Ecores track description. Tetraodon Net This track shows the best Tetraodon chain for every part of the selected genome. See the Human Net track description for more information. TFBS Conserved This tracks shows the location and score of transcription factor binding sites (TFBSs) conserved in a multiple species alignment. A binding site is considered to be conserved across the alignment if its score meets the threshold score for that binding site in all aligned species. The score and threshold are computed with the Transfac Matrix Database created by Biobase. The data are purely computational, and as such not all binding sites listed here are biologically functional binding sites.
-- | Display conventions: TFBSs are represented by thin blocks. The darker the shading, the better the match of the binding site.
-- | Track details: Clicking on a block in full display mode will show the the entry's Transfac ID, positional information, and a link to its Transfac Matrix (free registration with Transfac is required).
-- | Table details: To view a text version of the data set, select the tfbsCons positional table in the Table Browser. To view the table definition, click here.
Tight Mouse This track displays Blastz alignments of the specified mouse draft assembly to the human genome, filtered by axtBest and subsetAxt with very stringent constraints. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show human and mouse position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzTightMouse positional table in the Table Browser. To view the table definition, click here.
Tight Rat This track displays Blastz alignments of the Nov. 2002 rat draft assembly to the mouse genome, filtered by axtBest and subsetAxt with very stringent constraints. See the track's description page for more details.
-- | Display conventions: This track uses the display conventions for cross-species synteny tracks.
-- | Track details: Clicking on an entry in full display mode will show mouse and rat position information, alignment details, and a link to a detailed view of parts of the alignment.
-- | Track configuration: The track description page contains a filter that can be used to turn on the chromosome color track or to filter the display output by chromosome.
-- | Table details: To view a text version of the data set, select the blastzTightRat positional table in the Table Browser. To view the table definition, click here.
Tigr Gene Index This track displays alignments of the TIGR Gene Index (TGI) against the human genome. The TGI is based largely on assemblies of EST sequences from the public databases and TIGR. Entries are actual assemblies providing a consensus sequence, not simply clusters of overlapping sequences, but generally don't predict whole genes. Gene indices for mouse, rat, cow, and pig also contribute to this track.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, links to the predicted mRNA and genomic sequences, and a link to supporting information in the TIGR Human Gene Index.
-- | Table details: To view a text version of the data set, select the tigrGeneIndex positional table in the Table Browser. To view the table definition, click here.
Transcriptome This track shows transcriptome data for chromosomes 21 and 22 from Affymetrix, as described in "Large-Scale Transcriptional Activity in Chromosomes 21 and 22", Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S, Strausberg, R. L., Fodor, S.P.A. and Gingeras, T.R.. In general, the data presented is the perfect match - mismatch value. Different experiments were normalized by setting the average value to be the same for each chip.
-- | Display conventions: This track uses the display conventions for wiggle tracks. To present a more interpretable display when zoomed out, averages have been precalculated over the chromosome at two different resolutions in addition to the raw data. For example, when zoomed out, there may appear to be a peak at the center of a gene rather than a signal at every exon. Zooming in will reveal the raw data for that region.
-- | Track details: In dense mode (or at the top of the track in full mode), the transcriptome wiggle track displays the maximum value over all experiments for that probe, the idea being to paint as many transcribed regions as possible. In full mode, the track displays a separate wiggle track for each cell type, showing the data produced by averaging together replicates for that cell type. Clicking on an individual data point will show positional information and a link to view the sequence for the feature.
-- | Table details: To view a text version of the data set, select the affyTranscriptome positional table in the Table Browser. To view the table definition, click here.
Twinscan Gene Predictions This track displays Twinscan gene predictions. Twinscan predicts genes in a manner similar to Genscan, except that Twinscan takes advantage of genome comparison to improve gene prediction accuracy. More information and a web server can be found at the Washington University St. Louis Twinscan web page.
-- | Display conventions: This track uses the display conventions for gene predictions tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, links to the predicted protein, predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the twinscan positional table in the Table Browser. To view the table definition, click here.
UCSC Synteny (hg12) See description for Mouse Synteny (hg13+). UniGene This track shows UniGene clusters of ESTs aligned to the genome using BLAT. This data imperfectly indicates exon/intron boundaries and to a lesser extent genes. The Serial Analysis of Gene Expression (SAGE) project at NCBI - a quantitative measurement of gene expression in various tissues and disease states - mapped small 10bp bar-coded expression markers onto these UniGene clusters in the SageMap project. The Genome Browser uses this mapping to provide access to the SAGE data associated with the UniGene track in the assembled and annotated genome.
-- | Display conventions: This track uses the display conventions for PSL alignment tracks.
-- | Track details: Clicking on a UniGene feature will show an elaborate display of tabular and graphical data from the SAGE project relevant to that cluster.
-- | Table details: To view a text version of the data set, select the uniGene positional table in the Table Browser. To view the table definition, click here.
Vega Genes (selected human chromosomes only) This track shows genes from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, a link to the Vega web page for the item, and links to the predicted protein, predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the vegaGene positional table in the Table Browser. To view the table definition, click here.
Vega Pseudogenes (selected human chromosomes only) This track shows annotated pseudogenes and immunoglobulin segments from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show basic track information, a link to the Vega web page for the item, and links to the predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the vegaPseudoGene positional table in the Table Browser. To view the table definition, click here.
WashU Clones This track displays the location of clones (mostly lambda and cosmid clones) from Washington University in St. Louis using the names assigned by that group. The data was downloaded from the Saccharomyces Genome Database (SGD).
-- | Display conventions: The clone positions are shown in black.
-- | Track details: Clicking on an entry in full display mode brings up genomic information and a link to the American Type Culture Collection (ATCC) website.
-- | Table details: To view a text version of the data set, select the sgdClone positional table in the Table Browser. To view the table definition, click here.
WormBase Genes This track shows Sanger Gene predictions from the Wormbase files downloaded from the Sanger Institute FTP site. The data shown is the subset annotated with "curated", "DNA", or "RNA" followed by one of these strings: "intron", "exon", "cds", "sequence", or "transcri".
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show a wealth of information about the gene and its associated mRNA and protein, as well as links to many related external sites.
-- | Track configuration: The track description page contains a filter that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the sangerGene positional table in the Table Browser. To view the table definition, click here.
WormBase Genefinder This track shows Sanger Gene predictions from the Wormbase files downloaded from the Sanger Institute FTP site. The data shown is the subset annotated with the string "Genefinder" and found by the gene prediction program, Genefinder.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show genomic information and links to the translated protein, predicted mRNA, genomic sequence.
-- | Track configuration: The track description page contains a filter that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the sangerGenefinder positional table in the Table Browser. To view the table definition, click here.
WSSD Coverage This track represents coverage of clones that were assayed for segmental duplications using high-depth Celera reads. Absent regions were not assessed by this version of the Segmental Duplication Database (SDD). For a description of the whole-genome shotgun sequence detection (WSSD) "fuguization" method, see Bailey, JA. et al., Segmental duplications: organization and impact within the current human genome project assembly, Genome Res. 11(6), 1005-17 (2001).
-- | Display conventions: Rectangular blocks indicate the positions of clones.
-- | Track details: Clicking on an entry in full display mode will show position information and a link to the underlying DNA for the feature.
-- | Table details: To view a text version of the data set, select the celeraCoverage positional table in the Table Browser. To view the table definition, click here.
WSSD Duplication High-depth sequence reads from the Celera project were used to detect paralogy in the human genome reference sequence. This track shows confirmed segmental duplications, defined as having similarity to sequences in the Segmental Duplication Database (SDD) of greater than 90% over more than 250 bp of repeatmasked sequence. For a description of the whole-genome shotgun sequence detection (WSSD) 'fuguization' method, see Bailey, JA. et al., Segmental duplications: organization and impact within the current human genome project assembly, Genome Res. 11(6), 1005-17 (2001).
-- | Display conventions: Rectangular blocks indicate the positions of duplications.
-- | Track details: Clicking on an entry in full display mode will show the WSSD ID number, position information, and a link to the underlying DNA for the feature.
-- | Table details: To view a text version of the data set, select the celeraDupPositive positional table in the Table Browser. To view the table definition, click here.
WSSD Overlay This track shows regions detected as overlays of Celera whole-genome shotgun sequence assembly on the public human assembly.
-- | Display conventions: Regions are represented by rectangular blocks.
-- | Track details: Clicking on an entry in full display mode will show position information and a link to the underlying DNA for the feature.
-- | Table details: To view a text version of the data set, select the celeraOverlay positional table in the Table Browser. To view the table definition, click here.
X. tropicalis Chain This track shows X. tropicalis genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. X. tropicalis ESTs See the description for the Human ESTs track. X. tropicalis mRNAs See the description for the Human mRNAs track. X. tropicalis Net This track shows the best X. tropicalis chain for every part of the selected genome. See the Human Net track description for more information. Yale Pseudo This track shows pseudogenes identified in the Yale Pseudogene Database.
-- | Display conventions: This track uses the display conventions for gene prediction tracks.
-- | Track details: Clicking on an entry in full display mode will show genomic information, a link to the corresponding pseudogene entry in the Yale Pseudogene Database, and links to predicted mRNA and genomic sequence.
-- | Track configuration: The track description page provides an option to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the pseudoYale positional table in the Table Browser. To view the table definition, click here.
Zebrafish Chain This track shows zebrafish genomic alignments to the selected genome using blastz and axtChain. See the Human Chain track description for more information. Zebrafish ESTs See the Human ESTs track description. Zebrafish mRNAs See the Human mRNAs track description. Zebrafish Net This track shows the best Zebrafish chain for every part of the selected genome. See the Human Net track description for more information. Zfish WZ EST Clusters (Zebrafish) This track shows alignments between zebrafish WZ expressed sequence tags (ESTs) from WashU-Zebrafish Genome Resources and the genome. These WZ ESTs are compiled to produce longer reads by clustering together ESTs that originate from the same transcript.
-- | Display conventions: This track uses the display conventions for EST tracks. Hatch marks on the introns indicate the direction of transcription. As with otherEST tracks, it may be necessary to zoom in to display entries in full display mode due to the 300 line display limit.
-- | Track details: Clicking on an individual EST entry displays a link to the genomic alignment.
-- | Table details: To view a text version of the data set, select the wz_ests positional table in the Table Browser. To view the table definition, click here.
ZGC Genes (Zebrafish) This track shows alignments to the genome of zebrafish mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs).
-- | Display conventions: This track uses the display conventions for known genes and gene predictions tracks.
-- | Track details: Clicking on an entry in full display provides links to the corresponding protein, mRNA, and genomic sequences, and related links to outside databases.
-- | Track configuration: The track description page offers configuration options that can be used to turn on codon coloring for the track. Click the "Codon coloring help" link on the page for more information about this feature.
-- | Table details: To view a text version of the data set, select the mgcGenes positional table in the Table Browser. To view the table definition, click here.
ZooSeq (Zoo) This track displays the level of conservation for each zoo species based on blastz pair-wise alignments.
-- | Display conventions: This track uses the display conventions for wiggle tracks. Gray horizontal bars denote a mapping/sequencing gap. Percent identities of less than 50% are not shown because they fall below the minimum y-axis value.
-- | Track configuration: The track description page contains options to configure several of the graph characteristics. To read more information about each option, click the "Graph configuration help" link.
-- | Track details: Clicking on an entry in full display mode will show basic track information, a link to the Vega web page for the item, and links to the predicted mRNA, genomic sequence, and comparative sequence.
-- | Table details: To view a text version of the data set, select the zoo positional table in the Table Browser. To view the table definition, click here.
Last updated on 3 Mar. 2005. Questions and feedback welcome. |