< knownGeneArchive | This super track contains previous versions of the GENCODE primary gene set. < knownGeneArchive | 41566,42711d41559 < knownGeneV36 | html < knownGeneV36 |
< knownGeneV36 | The GENCODE Genes track (version 36, Oct 2020) shows high-quality manual < knownGeneV36 | annotations merged with evidence-based automated annotations across the entire < knownGeneV36 | human genome generated by the < knownGeneV36 | GENCODE project. < knownGeneV36 | By default, only the basic gene set is < knownGeneV36 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV36 | that GENCODE believes will be useful to the majority of users.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV36 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV36 | assembly patches and alternative loci (haplotypes).
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | The following table provides statistics for the v36 release derived from the GTF file that contains < knownGeneV36 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV36 | in the GENCODE site.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 |
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 |
< knownGeneV36 | GENCODE v36 Release Stats < knownGeneV36 | Genes Observed Transcripts Observed < knownGeneV36 | Protein-coding genes 19,965 Protein-coding transcripts 83,986 < knownGeneV36 | Long non-coding RNA genes 17,910 - full length protein-coding 57,935 < knownGeneV36 | Small non-coding RNA genes 7,576 - partial length protein-coding 26,051 < knownGeneV36 | Pseudogenes 14,749 Nonsense mediated decay transcripts 15,811 < knownGeneV36 | Immunoglobulin/T-cell receptor gene segments 645 Long non-coding RNA loci transcripts 48,351
< knownGeneV36 |
< knownGeneV36 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV36 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV36 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV36 | < knownGeneV36 |
< knownGeneV36 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV36 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV36 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV36 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV36 | and transcript names can be found in our < knownGeneV36 | FAQ.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV36 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV36 | those for coding open reading frames are thicker. < knownGeneV36 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV36 |< knownGeneV36 | This track contains an optional codon coloring feature that allows users to < knownGeneV36 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV36 | a density graph, which < knownGeneV36 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV36 | < knownGeneV36 |
< knownGeneV36 | The GENCODE v36 track was built from the GENCODE downloads file
< knownGeneV36 | gencode.v36.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV36 | were correlated with the GENCODE data to build association tables.
< knownGeneV36 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV36 | downloadable < knownGeneV36 | file. < knownGeneV36 | < knownGeneV36 |
< knownGeneV36 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV36 | is then available on the table menu. < knownGeneV36 | < knownGeneV36 | < knownGeneV36 |
< knownGeneV36 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV36 | REST API, the < knownGeneV36 | Table Browser or the < knownGeneV36 | Data Integrator. < knownGeneV36 | The genePred format files for hg38 are available from our < knownGeneV36 | < knownGeneV36 | downloads directory or in our < knownGeneV36 | < knownGeneV36 | GTF download directory. < knownGeneV36 | All the tables can also be queried directly from our public MySQL < knownGeneV36 | servers, with more information available on our < knownGeneV36 | help page as well as on < knownGeneV36 | our blog.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV36 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneV36 | A, Searle S et al. < knownGeneV36 | < knownGeneV36 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneV36 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneV36 | PMID: 22955987; PMC: PMC3431492 < knownGeneV36 |
< knownGeneV36 | < knownGeneV36 |< knownGeneV36 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneV36 | Swarbreck D et al. < knownGeneV36 | < knownGeneV36 | GENCODE: producing a reference annotation for ENCODE. < knownGeneV36 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneV36 | PMID: 16925838; PMC: PMC1810553 < knownGeneV36 |
< knownGeneV36 | < knownGeneV36 |A full list of GENCODE publications is available < knownGeneV36 | at The GENCODE < knownGeneV36 | Project web site. < knownGeneV36 |
< knownGeneV36 | < knownGeneV36 |GENCODE data are available for use without restrictions.
< knownGeneV36 | < knownGeneV38 | html < knownGeneV38 |< knownGeneV38 | The GENCODE Genes track (version 38, May 2021) shows high-quality manual < knownGeneV38 | annotations merged with evidence-based automated annotations across the entire < knownGeneV38 | human genome generated by the < knownGeneV38 | GENCODE project. < knownGeneV38 | By default, only the basic gene set is < knownGeneV38 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV38 | that GENCODE believes will be useful to the majority of users.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV38 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV38 | assembly patches and alternative loci (haplotypes).
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | The following table provides statistics for the v38 release derived from the GTF file that contains < knownGeneV38 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV38 | in the GENCODE site.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 |
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 |
< knownGeneV38 | GENCODE v38 Release Stats < knownGeneV38 | Genes Observed Transcripts Observed < knownGeneV38 | Protein-coding genes 19,955 Protein-coding transcripts 86,757 < knownGeneV38 | Long non-coding RNA genes 17,944 - full length protein-coding 61,015 < knownGeneV38 | Small non-coding RNA genes 7,567 - partial length protein-coding 25,742 < knownGeneV38 | Pseudogenes 14,773 Nonsense mediated decay transcripts 18,881 < knownGeneV38 | Immunoglobulin/T-cell receptor gene segments 409 Long non-coding RNA loci transcripts 48,752
< knownGeneV38 |
< knownGeneV38 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV38 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV38 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV38 | < knownGeneV38 |
< knownGeneV38 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV38 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV38 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV38 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV38 | and transcript names can be found in our < knownGeneV38 | FAQ.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV38 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV38 | those for coding open reading frames are thicker. < knownGeneV38 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV38 |< knownGeneV38 | This track contains an optional codon coloring feature that allows users to < knownGeneV38 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV38 | a density graph, which < knownGeneV38 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV38 | < knownGeneV38 |
< knownGeneV38 | The GENCODE v38 track was built from the GENCODE downloads file
< knownGeneV38 | gencode.v38.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV38 | were correlated with the GENCODE data to build association tables.
< knownGeneV38 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV38 | downloadable < knownGeneV38 | file. < knownGeneV38 | < knownGeneV38 |
< knownGeneV38 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV38 | is then available on the table menu. < knownGeneV38 | < knownGeneV38 | < knownGeneV38 |
< knownGeneV38 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV38 | REST API, the < knownGeneV38 | Table Browser or the < knownGeneV38 | Data Integrator. < knownGeneV38 | The genePred format files for hg38 are available from our < knownGeneV38 | < knownGeneV38 | downloads directory or in our < knownGeneV38 | < knownGeneV38 | GTF download directory. < knownGeneV38 | All the tables can also be queried directly from our public MySQL < knownGeneV38 | servers, with more information available on our < knownGeneV38 | help page as well as on < knownGeneV38 | our blog.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV38 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneV38 | A, Searle S et al. < knownGeneV38 | < knownGeneV38 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneV38 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneV38 | PMID: 22955987; PMC: PMC3431492 < knownGeneV38 |
< knownGeneV38 | < knownGeneV38 |< knownGeneV38 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneV38 | Swarbreck D et al. < knownGeneV38 | < knownGeneV38 | GENCODE: producing a reference annotation for ENCODE. < knownGeneV38 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneV38 | PMID: 16925838; PMC: PMC1810553 < knownGeneV38 |
< knownGeneV38 | < knownGeneV38 |A full list of GENCODE publications is available < knownGeneV38 | at The GENCODE < knownGeneV38 | Project web site. < knownGeneV38 |
< knownGeneV38 | < knownGeneV38 |GENCODE data are available for use without restrictions.
< knownGeneV38 | < knownGeneV39 | html < knownGeneV39 |< knownGeneV39 | The GENCODE Genes track (version 39, December 2021) shows high-quality manual < knownGeneV39 | annotations merged with evidence-based automated annotations across the entire < knownGeneV39 | human genome generated by the < knownGeneV39 | GENCODE project. < knownGeneV39 | By default, only the basic gene set is < knownGeneV39 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV39 | that GENCODE believes will be useful to the majority of users.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV39 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV39 | assembly patches and alternative loci (haplotypes).
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | The following table provides statistics for the v39 release derived from the GTF file that contains < knownGeneV39 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV39 | in the GENCODE site.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 |
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 |
< knownGeneV39 | GENCODE v39 Release Stats < knownGeneV39 | Genes Observed Transcripts Observed < knownGeneV39 | Protein-coding genes 19,982 Protein-coding transcripts 87,151 < knownGeneV39 | Long non-coding RNA genes 18,811 - full length protein-coding 61,516 < knownGeneV39 | Small non-coding RNA genes 7,567 - partial length protein-coding 25,635 < knownGeneV39 | Pseudogenes 14,763 Nonsense mediated decay transcripts 19,762 < knownGeneV39 | Immunoglobulin/T-cell receptor gene segments 409 Long non-coding RNA loci transcripts 53,009
< knownGeneV39 |
< knownGeneV39 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV39 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV39 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV39 | < knownGeneV39 |
< knownGeneV39 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV39 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV39 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV39 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV39 | and transcript names can be found in our < knownGeneV39 | FAQ.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV39 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV39 | those for coding open reading frames are thicker. < knownGeneV39 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV39 |< knownGeneV39 | This track contains an optional codon coloring feature that allows users to < knownGeneV39 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV39 | a density graph, which < knownGeneV39 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV39 | < knownGeneV39 |
< knownGeneV39 | The GENCODE v39 track was built from the GENCODE downloads file
< knownGeneV39 | gencode.v39.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV39 | were correlated with the GENCODE data to build association tables.
< knownGeneV39 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV39 | downloadable < knownGeneV39 | file. < knownGeneV39 | < knownGeneV39 |
< knownGeneV39 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV39 | is then available on the table menu. < knownGeneV39 | < knownGeneV39 | < knownGeneV39 |
< knownGeneV39 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV39 | REST API, the < knownGeneV39 | Table Browser or the < knownGeneV39 | Data Integrator. < knownGeneV39 | The genePred format files for hg38 are available from our < knownGeneV39 | < knownGeneV39 | downloads directory or in our < knownGeneV39 | < knownGeneV39 | GTF download directory. < knownGeneV39 | All the tables can also be queried directly from our public MySQL < knownGeneV39 | servers, with more information available on our < knownGeneV39 | help page as well as on < knownGeneV39 | our blog.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV39 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneV39 | A, Searle S et al. < knownGeneV39 | < knownGeneV39 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneV39 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneV39 | PMID: 22955987; PMC: PMC3431492 < knownGeneV39 |
< knownGeneV39 | < knownGeneV39 |< knownGeneV39 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneV39 | Swarbreck D et al. < knownGeneV39 | < knownGeneV39 | GENCODE: producing a reference annotation for ENCODE. < knownGeneV39 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneV39 | PMID: 16925838; PMC: PMC1810553 < knownGeneV39 |
< knownGeneV39 | < knownGeneV39 |A full list of GENCODE publications is available < knownGeneV39 | at The GENCODE < knownGeneV39 | Project web site. < knownGeneV39 |
< knownGeneV39 | < knownGeneV39 |GENCODE data are available for use without restrictions.
< knownGeneV39 | < knownGeneV43 | html < knownGeneV43 |< knownGeneV43 | The GENCODE Genes track (version 43, February 2023) shows high-quality manual < knownGeneV43 | annotations merged with evidence-based automated annotations across the entire < knownGeneV43 | human genome generated by the < knownGeneV43 | GENCODE project. < knownGeneV43 | By default, only the basic gene set is < knownGeneV43 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV43 | that GENCODE believes will be useful to the majority of users.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV43 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV43 | assembly patches and alternative loci (haplotypes).
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | The following table provides statistics for the v43 release derived from the GTF file that contains < knownGeneV43 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV43 | in the GENCODE site.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 |
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 |
< knownGeneV43 | GENCODE v43 Release Stats < knownGeneV43 | Genes Observed Transcripts Observed < knownGeneV43 | Protein-coding genes 19,393 Protein-coding transcripts 89,411 < knownGeneV43 | Long non-coding RNA genes 19,928 - full length protein-coding 64,004 < knownGeneV43 | Small non-coding RNA genes 7,566 - partial length protein-coding 25,407 < knownGeneV43 | Pseudogenes 14,737 Nonsense mediated decay transcripts 21,354 < knownGeneV43 | Immunoglobulin/T-cell receptor gene segments 410 Long non-coding RNA loci transcripts 58,023 < knownGeneV43 | Total No of distinct translations 65,519 Genes that have more than one distinct translations 13,618
< knownGeneV43 |
< knownGeneV43 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV43 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV43 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV43 | < knownGeneV43 |
< knownGeneV43 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV43 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV43 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV43 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV43 | and transcript names can be found in our < knownGeneV43 | FAQ.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV43 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV43 | those for coding open reading frames are thicker. < knownGeneV43 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV43 |< knownGeneV43 | This track contains an optional codon coloring feature that allows users to < knownGeneV43 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV43 | a density graph, which < knownGeneV43 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV43 | < knownGeneV43 | < knownGeneV43 |< knownGeneV43 | Within a gene using the pack display mode, transcripts below a specified rank will be < knownGeneV43 | condensed into a view similar to squish mode. The transcript ranking approach is < knownGeneV43 | preliminary and will change in future releases. The transcripts rankings are defined by the < knownGeneV43 | following criteria for protein-coding and non-coding genes:
< knownGeneV43 | Protein_coding genes < knownGeneV43 |
< knownGeneV43 | The GENCODE v43 track was built from the GENCODE downloads file
< knownGeneV43 | gencode.v43.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV43 | were correlated with the GENCODE data to build association tables.
< knownGeneV43 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV43 | downloadable < knownGeneV43 | file. < knownGeneV43 | < knownGeneV43 |
< knownGeneV43 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV43 | is then available on the table menu. < knownGeneV43 | < knownGeneV43 | < knownGeneV43 |
< knownGeneV43 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV43 | REST API, the < knownGeneV43 | Table Browser or the < knownGeneV43 | Data Integrator. < knownGeneV43 | The genePred format files for hg38 are available from our < knownGeneV43 | < knownGeneV43 | downloads directory or in our < knownGeneV43 | < knownGeneV43 | GTF download directory. < knownGeneV43 | All the tables can also be queried directly from our public MySQL < knownGeneV43 | servers, with more information available on our < knownGeneV43 | help page as well as on < knownGeneV43 | our blog.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV43 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneV43 | A, Searle S et al. < knownGeneV43 | < knownGeneV43 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneV43 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneV43 | PMID: 22955987; PMC: PMC3431492 < knownGeneV43 |
< knownGeneV43 | < knownGeneV43 |< knownGeneV43 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneV43 | Swarbreck D et al. < knownGeneV43 | < knownGeneV43 | GENCODE: producing a reference annotation for ENCODE. < knownGeneV43 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneV43 | PMID: 16925838; PMC: PMC1810553 < knownGeneV43 |
< knownGeneV43 | < knownGeneV43 |A full list of GENCODE publications is available < knownGeneV43 | at The GENCODE < knownGeneV43 | Project web site. < knownGeneV43 |
< knownGeneV43 | < knownGeneV43 |GENCODE data are available for use without restrictions.
< knownGeneV43 | < knownGeneV44 | html < knownGeneV44 |< knownGeneV44 | The GENCODE Genes track (version 44, July 2023) shows high-quality manual < knownGeneV44 | annotations merged with evidence-based automated annotations across the entire < knownGeneV44 | human genome generated by the < knownGeneV44 | GENCODE project. < knownGeneV44 | By default, only the basic gene set is < knownGeneV44 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV44 | that GENCODE believes will be useful to the majority of users.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV44 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV44 | assembly patches and alternative loci (haplotypes).
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | The following table provides statistics for the v44 release derived from the GTF file that contains < knownGeneV44 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV44 | in the GENCODE site.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 |
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 |
< knownGeneV44 | GENCODE v44 Release Stats < knownGeneV44 | Genes Observed Transcripts Observed < knownGeneV44 | Protein-coding genes 19,396 Protein-coding transcripts 89,067 < knownGeneV44 | Long non-coding RNA genes 19,922 - full length protein-coding 63,968 < knownGeneV44 | Small non-coding RNA genes 7,566 - partial length protein-coding 25,099 < knownGeneV44 | Pseudogenes 14,735 Nonsense mediated decay transcripts 21,384 < knownGeneV44 | Immunoglobulin/T-cell receptor gene segments 647 Long non-coding RNA loci transcripts 58,246 < knownGeneV44 | Total No of distinct translations 65,342 Genes that have more than one distinct translations 13,594
< knownGeneV44 |
< knownGeneV44 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV44 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV44 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV44 | < knownGeneV44 |
< knownGeneV44 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV44 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV44 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV44 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV44 | and transcript names can be found in our < knownGeneV44 | FAQ.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV44 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV44 | those for coding open reading frames are thicker. < knownGeneV44 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV44 |< knownGeneV44 | This track contains an optional codon coloring feature that allows users to < knownGeneV44 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV44 | a density graph, which < knownGeneV44 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV44 | < knownGeneV44 | < knownGeneV44 |< knownGeneV44 | Within a gene using the pack display mode, transcripts below a specified rank will be < knownGeneV44 | condensed into a view similar to squish mode. The transcript ranking approach is < knownGeneV44 | preliminary and will change in future releases. The transcripts rankings are defined by the < knownGeneV44 | following criteria for protein-coding and non-coding genes:
< knownGeneV44 | Protein_coding genes < knownGeneV44 |
< knownGeneV44 | The GENCODE v44 track was built from the GENCODE downloads file
< knownGeneV44 | gencode.v44.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV44 | were correlated with the GENCODE data to build association tables.
< knownGeneV44 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV44 | downloadable < knownGeneV44 | file. < knownGeneV44 | < knownGeneV44 |
< knownGeneV44 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV44 | is then available on the table menu. < knownGeneV44 | < knownGeneV44 | < knownGeneV44 |
< knownGeneV44 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV44 | REST API, the < knownGeneV44 | Table Browser or the < knownGeneV44 | Data Integrator. < knownGeneV44 | The genePred format files for hg38 are available from our < knownGeneV44 | < knownGeneV44 | downloads directory or in our < knownGeneV44 | < knownGeneV44 | GTF download directory. < knownGeneV44 | All the tables can also be queried directly from our public MySQL < knownGeneV44 | servers, with more information available on our < knownGeneV44 | help page as well as on < knownGeneV44 | our blog.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV44 | computational pipeline developed by Jim Kent and Brian Raney. This version of the track was < knownGeneV44 | generated by Jonathan Casper.
< knownGeneV44 | < knownGeneV44 |< knownGeneV44 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, < knownGeneV44 | Arnan C, Barnes I et al. < knownGeneV44 | < knownGeneV44 | GENCODE: reference annotation for the human and mouse genomes in 2023. < knownGeneV44 | Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. < knownGeneV44 | PMID: 36420896; PMC: PMC9825462 < knownGeneV44 |
< knownGeneV44 | < knownGeneV44 |A full list of GENCODE publications is available < knownGeneV44 | at The GENCODE < knownGeneV44 | Project web site. < knownGeneV44 |
< knownGeneV44 | < knownGeneV44 |GENCODE data are available for use without restrictions.
< knownGeneV44 | < knownGeneV45 | html < knownGeneV45 |< knownGeneV45 | The GENCODE Genes track (version 45, January 2024) shows high-quality manual < knownGeneV45 | annotations merged with evidence-based automated annotations across the entire < knownGeneV45 | human genome generated by the < knownGeneV45 | GENCODE project. < knownGeneV45 | By default, only the basic gene set is < knownGeneV45 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV45 | that GENCODE believes will be useful to the majority of users.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV45 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV45 | assembly patches and alternative loci (haplotypes).
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | The following table provides statistics for the v45 release derived from the GTF file that contains < knownGeneV45 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneV45 | in the GENCODE site.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 |
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 |
< knownGeneV45 | GENCODE v45 Release Stats < knownGeneV45 | Genes Observed Transcripts Observed < knownGeneV45 | Protein-coding genes 19,395 Protein-coding transcripts 89,110 < knownGeneV45 | Long non-coding RNA genes 20,424 - full length protein-coding 64,028 < knownGeneV45 | Small non-coding RNA genes 7,565 - partial length protein-coding 25,082 < knownGeneV45 | Pseudogenes 14,719 Nonsense mediated decay transcripts 21,427 < knownGeneV45 | Immunoglobulin/T-cell receptor gene segments 648 Long non-coding RNA loci transcripts 59,719 < knownGeneV45 | Total No of distinct translations 65,357 Genes that have more than one distinct translations 13,600
< knownGeneV45 |
< knownGeneV45 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV45 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV45 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV45 | < knownGeneV45 |
< knownGeneV45 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV45 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV45 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV45 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV45 | and transcript names can be found in our < knownGeneV45 | FAQ.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV45 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV45 | those for coding open reading frames are thicker. < knownGeneV45 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneV45 |< knownGeneV45 | This track contains an optional codon coloring feature that allows users to < knownGeneV45 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV45 | a density graph, which < knownGeneV45 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV45 | < knownGeneV45 | < knownGeneV45 |< knownGeneV45 | Within a gene using the pack display mode, transcripts below a specified rank will be < knownGeneV45 | condensed into a view similar to squish mode. The transcript ranking approach is < knownGeneV45 | preliminary and will change in future releases. The transcripts rankings are defined by the < knownGeneV45 | following criteria for protein-coding and non-coding genes:
< knownGeneV45 | Protein_coding genes < knownGeneV45 |
< knownGeneV45 | The GENCODE v45 track was built from the GENCODE downloads file
< knownGeneV45 | gencode.v45.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV45 | were correlated with the GENCODE data to build association tables.
< knownGeneV45 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV45 | downloadable < knownGeneV45 | file. < knownGeneV45 | < knownGeneV45 |
< knownGeneV45 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV45 | is then available on the table menu. < knownGeneV45 | < knownGeneV45 | < knownGeneV45 |
< knownGeneV45 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV45 | REST API, the < knownGeneV45 | Table Browser or the < knownGeneV45 | Data Integrator. < knownGeneV45 | The genePred format files for hg38 are available from our < knownGeneV45 | < knownGeneV45 | downloads directory or in our < knownGeneV45 | < knownGeneV45 | GTF download directory. < knownGeneV45 | All the tables can also be queried directly from our public MySQL < knownGeneV45 | servers, with more information available on our < knownGeneV45 | help page as well as on < knownGeneV45 | our blog.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV45 | computational pipeline developed by Jim Kent and Brian Raney. This version of the track was < knownGeneV45 | generated by Jonathan Casper.
< knownGeneV45 | < knownGeneV45 |< knownGeneV45 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, < knownGeneV45 | Arnan C, Barnes I et al. < knownGeneV45 | < knownGeneV45 | GENCODE: reference annotation for the human and mouse genomes in 2023. < knownGeneV45 | Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. < knownGeneV45 | PMID: 36420896; PMC: PMC9825462 < knownGeneV45 |
< knownGeneV45 | < knownGeneV45 |A full list of GENCODE publications is available < knownGeneV45 | at The GENCODE < knownGeneV45 | Project web site. < knownGeneV45 |
< knownGeneV45 | < knownGeneV45 |GENCODE data are available for use without restrictions.
< knownGeneV45 | < knownGeneV46 | html < knownGeneV46 |< knownGeneV46 | The GENCODE Genes track (version 46, May 2024) shows high-quality manual < knownGeneV46 | annotations merged with evidence-based automated annotations across the entire < knownGeneV46 | human genome generated by the < knownGeneV46 | GENCODE project. < knownGeneV46 | By default, only the basic gene set is < knownGeneV46 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneV46 | that GENCODE believes will be useful to the majority of users.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneV46 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneV46 | assembly patches and alternative loci (haplotypes).
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | The v46 release was derived from the GTF file that contains annotations only on the main < knownGeneV46 | chromosomes. Statistics for this build and information on how they were generated can be found on < knownGeneV46 | the GENCODE site.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneV46 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneV46 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneV46 | < knownGeneV46 |
< knownGeneV46 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneV46 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneV46 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneV46 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneV46 | and transcript names can be found in our < knownGeneV46 | FAQ.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneV46 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneV46 | those for coding open reading frames are thicker. < knownGeneV46 |
Coloring for the gene annotations is mostly based on the annotation type:
< knownGeneV46 |< knownGeneV46 | This track contains an optional codon coloring feature that allows users to < knownGeneV46 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneV46 | a density graph, which < knownGeneV46 | can be helpful for visualizing the distribution of items over a region.
< knownGeneV46 | < knownGeneV46 | < knownGeneV46 |< knownGeneV46 | Within a gene using the pack display mode, transcripts below a specified rank will be < knownGeneV46 | condensed into a view similar to squish mode. The transcript ranking approach is < knownGeneV46 | preliminary and will change in future releases. The transcripts rankings are defined by the < knownGeneV46 | following criteria for protein-coding and non-coding genes:
< knownGeneV46 | Protein_coding genes < knownGeneV46 |
< knownGeneV46 | The GENCODE v46 track was built from the GENCODE downloads file
< knownGeneV46 | gencode.v46.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneV46 | were correlated with the GENCODE data to build association tables.
< knownGeneV46 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneV46 | downloadable < knownGeneV46 | file. < knownGeneV46 | < knownGeneV46 |
< knownGeneV46 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneV46 | is then available on the table menu. < knownGeneV46 | < knownGeneV46 | < knownGeneV46 |
< knownGeneV46 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneV46 | REST API, the < knownGeneV46 | Table Browser or the < knownGeneV46 | Data Integrator. < knownGeneV46 | The genePred format files for hg38 are available from our < knownGeneV46 | < knownGeneV46 | downloads directory or in our < knownGeneV46 | < knownGeneV46 | GTF download directory. < knownGeneV46 | All the tables can also be queried directly from our public MySQL < knownGeneV46 | servers, with more information available on our < knownGeneV46 | help page as well as on < knownGeneV46 | our blog.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneV46 | computational pipeline developed by Jim Kent and Brian Raney. This version of the track was < knownGeneV46 | generated by Jonathan Casper.
< knownGeneV46 | < knownGeneV46 |< knownGeneV46 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, < knownGeneV46 | Arnan C, Barnes I et al. < knownGeneV46 | < knownGeneV46 | GENCODE: reference annotation for the human and mouse genomes in 2023. < knownGeneV46 | Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. < knownGeneV46 | PMID: 36420896; PMC: PMC9825462 < knownGeneV46 |
< knownGeneV46 | < knownGeneV46 |A full list of GENCODE publications is available < knownGeneV46 | at The GENCODE < knownGeneV46 | Project web site. < knownGeneV46 |
< knownGeneV46 | < knownGeneV46 |GENCODE data are available for use without restrictions.
< knownGeneV46 |