Description

This track shows genomic regions grouped into subsets based on their locations relative to the transcript-coding and exon-coding regions of Gencode genes. The data are divided into four region types:

• Gencode distal intronic: regions between Gencode gene exons that are located more than 5000 base pairs away from any exon.
• Gencode proximal intronic: regions between Gencode gene exons that are located no more than 5000 base pairs from an exon.
• Gencode distal intergenic: regions outside of all Gencode gene extents that are located more than 5000 base pairs from a gene extent.
• Gencode proximal intergenic: regions outside of all Gencode gene extents that are located within 5000 base pairs of a gene extent.

In this context, a gene extent is defined as the region between transcript start and transcript end.

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.

Methods

The Gencode reference gene set is comprised of the following gene types: Known, Novel_CDS, Novel_transcript_gencode_conf, and Putative_gencode_conf. The exons of this gene set were extracted using the UCSC Table Browser to define the set of Gencode intronic regions. Similarly, the transcript start and stop coordinates of this gene set were extracted to define the Gencode intergenic regions. There is some ambiguity associated with these classifications due to the presence of isoforms and overlapping transcripts.

Credits

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