## Description

This track shows selected non-coding Affy transcribed fragments (transfrags) and Yale transcriptionally-active regions (TARs) from the Affy Transfrags and Yale TAR annotation tracks, grouped into subsets based on their proximity to the transcript-coding and exon-coding regions of Gencode genes. The transfrags/TARs are divided into four categories:

- Intergenic distal subtracks: Transfrags/TARS in the intergenic ENCODE areas, i.e. outside the transcript-coding region of any Gencode gene and at least 5000 base pairs distant from any Gencode gene exon-coding region.
- Intergenic proximal subtracks: Transfrags/TARS in the intergenic ENCODE regions that are close to Gencode genes, i.e. outside the transcript-coding region of any Gencode gene, but within 5000 bases of a Gencode gene exon-coding region.
- Intronic distal subtracks: Transfrags/TARS within Gencode genes introns, i.e. within the transcript-coding region of a Gencode gene, but at least 5000 base pairs distant from the exon-coding region of any Gencode gene.
- Intronic proximal subtracks: Transfrags/TARS within Gencode genes introns that are close to Gencode genes exons, i.e. within the transcript-coding region of a Gencode gene and also within 5000 bases of a Gencode gene exon-coding region.

## Display Conventions and Configuration

This annotation track is comprised of subtracks that show different aspects of the displayed data. The complete list of subtracks is displayed near the top of the track description page.

To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. The "Select subtracks" section allows you to select or unselect entire groups of subtracks based on a particular data characteristic, such as distance and region, cell type, data source, etc. To add or remove an entire subgroup of data from the graphical display, click the appropriate add or clear button.

Color differences among the subtracks are arbitrary. They provide a visual cue for distinguishing among the different data sets and subgroups.

## Methods

This annotation track was derived from data contained in the Yale TAR and Affy Transfrags annotation tracks using the UCSC Table Browser. See the description pages associated with these annotation tracks for more information about the data sets.

## Credits

This annotation was generated by Hiram Clawson of the UCSC Genome Bioinformatics Group.