+The GENCODE Genes track (version 48, April 2025) shows high-quality manual +annotations merged with evidence-based automated annotations across the entire +human genome generated by the +GENCODE project. +By default, only the basic gene set is +displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts +that GENCODE believes will be useful to the majority of users.
+ ++The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes +are not displayed by default. It contains annotations on the reference chromosomes as well as +assembly patches and alternative loci (haplotypes).
+ ++The v48 release was derived from the GTF file that contains annotations only on the main +chromosomes. Statistics for this build and information on how they were generated can be found on +the GENCODE site.
+ ++For more information on the different gene tracks, see our Genes FAQ.
+ ++By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. +It includes options to display the entire GENCODE set and pseudogenes. To customize these +options, the respective boxes can be checked or unchecked at the top of this description page. + +
+This track also includes a variety of labels which identify the transcripts when visibility is set +to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but +additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID +(uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene +and transcript names can be found in our +FAQ.
+ ++This track, in general, follows the display conventions for gene prediction tracks. The exons for +putative non-coding genes and untranslated regions are represented by relatively thin blocks, while +those for coding open reading frames are thicker. +
Coloring for the gene annotations is mostly based on the annotation type:
++This track contains an optional codon coloring feature that allows users to +quickly validate and compare gene predictions. There is also an option to display the data as +a density graph, which +can be helpful for visualizing the distribution of items over a region.
+ + ++Within a gene using the pack display mode, transcripts below a specified rank will be +condensed into a view similar to squish mode. The transcript ranking approach is +preliminary and will change in future releases. The transcripts rankings are defined by the +following criteria for protein-coding and non-coding genes:
+Protein_coding genes +
+The GENCODE v48 track was built from the GENCODE downloads file
+gencode.v48.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
+were correlated with the GENCODE data to build association tables.
+The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a +downloadable +file. + +
+One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list +is then available on the table menu. + + +
+GENCODE Genes and its associated tables can be explored interactively using the +REST API, the +Table Browser or the +Data Integrator. +The genePred format files for hg38 are available from our + +downloads directory or in our + +GTF download directory. +All the tables can also be queried directly from our public MySQL +servers, with more information available on our +help page as well as on +our blog.
+ ++The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a +computational pipeline developed by Jim Kent and Brian Raney. This version of the track was +generated by Jonathan Casper.
+ ++Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, +Barnes I, Bennett R et al. + +GENCODE 2025: reference gene annotation for human and mouse. +Nucleic Acids Res. 2025 Jan 6;53(D1):D966-D975. +PMID: 39565199; PMC: PMC11701607 +
+ +A full list of GENCODE publications is available +at The GENCODE +Project web site. +
+ +GENCODE data are available for use without restrictions.