< knownGeneArchive | This super track contains previous versions of the GENCODE primary gene set. < knownGeneArchive | < knownGeneVM27 | html < knownGeneVM27 |
< knownGeneVM27 | The GENCODE Genes track (version M27, Dec 2020) shows high-quality manual < knownGeneVM27 | annotations merged with evidence-based automated annotations across the entire < knownGeneVM27 | human genome generated by the < knownGeneVM27 | GENCODE project. < knownGeneVM27 | By default, only the basic gene set is < knownGeneVM27 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneVM27 | that GENCODE believes will be useful to the majority of users.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneVM27 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneVM27 | assembly patches and alternative loci (haplotypes).
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | The following table provides statistics for the VM27 release derived from the GTF file that contains < knownGeneVM27 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneVM27 | in the GENCODE site.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 |
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 |
< knownGeneVM27 | GENCODE VM27 Release Stats < knownGeneVM27 | Genes Observed Transcripts Observed < knownGeneVM27 | Protein-coding genes 21,834 Protein-coding transcripts 59,135 < knownGeneVM27 | Long non-coding RNA genes 13,188 - full length protein-coding 45,373 < knownGeneVM27 | Small non-coding RNA genes 6,105 - partial length protein-coding 13,762 < knownGeneVM27 | Pseudogenes 13,737 Nonsense mediated decay transcripts 18,838 < knownGeneVM27 | Immunoglobulin/T-cell receptor gene segments 701 Long non-coding RNA loci transcripts 18,838,351
< knownGeneVM27 |
< knownGeneVM27 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneVM27 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneVM27 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneVM27 | < knownGeneVM27 |
< knownGeneVM27 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneVM27 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneVM27 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneVM27 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneVM27 | and transcript names can be found in our < knownGeneVM27 | FAQ.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneVM27 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneVM27 | those for coding open reading frames are thicker. < knownGeneVM27 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneVM27 |< knownGeneVM27 | This track contains an optional codon coloring feature that allows users to < knownGeneVM27 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneVM27 | a density graph, which < knownGeneVM27 | can be helpful for visualizing the distribution of items over a region.
< knownGeneVM27 | < knownGeneVM27 |
< knownGeneVM27 | The GENCODE VM27 track was built from the GENCODE downloads file
< knownGeneVM27 | gencode.vM27.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneVM27 | were correlated with the GENCODE data to build association tables.
< knownGeneVM27 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneVM27 | downloadable < knownGeneVM27 | file. < knownGeneVM27 | < knownGeneVM27 |
< knownGeneVM27 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneVM27 | is then available on the table menu. < knownGeneVM27 | < knownGeneVM27 | < knownGeneVM27 |
< knownGeneVM27 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneVM27 | REST API, the < knownGeneVM27 | Table Browser or the < knownGeneVM27 | Data Integrator. < knownGeneVM27 | The genePred format files for mm39 are available from our < knownGeneVM27 | < knownGeneVM27 | downloads directory or in our < knownGeneVM27 | < knownGeneVM27 | GTF download directory. < knownGeneVM27 | All the tables can also be queried directly from our public MySQL < knownGeneVM27 | servers, with more information available on our < knownGeneVM27 | help page as well as on < knownGeneVM27 | our blog.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneVM27 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneVM27 | A, Searle S et al. < knownGeneVM27 | < knownGeneVM27 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneVM27 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneVM27 | PMID: 22955987; PMC: PMC3431492 < knownGeneVM27 |
< knownGeneVM27 | < knownGeneVM27 |< knownGeneVM27 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneVM27 | Swarbreck D et al. < knownGeneVM27 | < knownGeneVM27 | GENCODE: producing a reference annotation for ENCODE. < knownGeneVM27 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneVM27 | PMID: 16925838; PMC: PMC1810553 < knownGeneVM27 |
< knownGeneVM27 | < knownGeneVM27 |A full list of GENCODE publications is available < knownGeneVM27 | at The GENCODE < knownGeneVM27 | Project web site. < knownGeneVM27 |
< knownGeneVM27 | < knownGeneVM27 |GENCODE data are available for use without restrictions.
< knownGeneVM27 | < knownGeneVM30 | html < knownGeneVM30 |< knownGeneVM30 | The GENCODE Genes track (version M30, Dec 2020) shows high-quality manual < knownGeneVM30 | annotations merged with evidence-based automated annotations across the entire < knownGeneVM30 | human genome generated by the < knownGeneVM30 | GENCODE project. < knownGeneVM30 | By default, only the basic gene set is < knownGeneVM30 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneVM30 | that GENCODE believes will be useful to the majority of users.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneVM30 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneVM30 | assembly patches and alternative loci (haplotypes).
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | The following table provides statistics for the VM30 release derived from the GTF file that contains < knownGeneVM30 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneVM30 | in the GENCODE site.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 |
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 |
< knownGeneVM30 | GENCODE VM30 Release Stats < knownGeneVM30 | Genes Observed Transcripts Observed < knownGeneVM30 | Protein-coding genes 21,668 Protein-coding transcripts 59,116 < knownGeneVM30 | Long non-coding RNA genes 14,525 - full length protein-coding 45,378 < knownGeneVM30 | Small non-coding RNA genes 6,105 - partial length protein-coding 13,738 < knownGeneVM30 | Pseudogenes 13,647 Nonsense mediated decay transcripts 7,209 < knownGeneVM30 | Immunoglobulin/T-cell receptor gene segments 701 Long non-coding RNA loci transcripts 25,419
< knownGeneVM30 |
< knownGeneVM30 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneVM30 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneVM30 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneVM30 | < knownGeneVM30 |
< knownGeneVM30 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneVM30 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneVM30 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneVM30 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneVM30 | and transcript names can be found in our < knownGeneVM30 | FAQ.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneVM30 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneVM30 | those for coding open reading frames are thicker. < knownGeneVM30 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneVM30 |< knownGeneVM30 | This track contains an optional codon coloring feature that allows users to < knownGeneVM30 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneVM30 | a density graph, which < knownGeneVM30 | can be helpful for visualizing the distribution of items over a region.
< knownGeneVM30 | < knownGeneVM30 |
< knownGeneVM30 | The GENCODE VM30 track was built from the GENCODE downloads file
< knownGeneVM30 | gencode.vM30.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneVM30 | were correlated with the GENCODE data to build association tables.
< knownGeneVM30 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneVM30 | downloadable < knownGeneVM30 | file. < knownGeneVM30 | < knownGeneVM30 |
< knownGeneVM30 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneVM30 | is then available on the table menu. < knownGeneVM30 | < knownGeneVM30 | < knownGeneVM30 |
< knownGeneVM30 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneVM30 | REST API, the < knownGeneVM30 | Table Browser or the < knownGeneVM30 | Data Integrator. < knownGeneVM30 | The genePred format files for mm39 are available from our < knownGeneVM30 | < knownGeneVM30 | downloads directory or in our < knownGeneVM30 | < knownGeneVM30 | GTF download directory. < knownGeneVM30 | All the tables can also be queried directly from our public MySQL < knownGeneVM30 | servers, with more information available on our < knownGeneVM30 | help page as well as on < knownGeneVM30 | our blog.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneVM30 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneVM30 | A, Searle S et al. < knownGeneVM30 | < knownGeneVM30 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneVM30 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneVM30 | PMID: 22955987; PMC: PMC3431492 < knownGeneVM30 |
< knownGeneVM30 | < knownGeneVM30 |< knownGeneVM30 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneVM30 | Swarbreck D et al. < knownGeneVM30 | < knownGeneVM30 | GENCODE: producing a reference annotation for ENCODE. < knownGeneVM30 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneVM30 | PMID: 16925838; PMC: PMC1810553 < knownGeneVM30 |
< knownGeneVM30 | < knownGeneVM30 |A full list of GENCODE publications is available < knownGeneVM30 | at The GENCODE < knownGeneVM30 | Project web site. < knownGeneVM30 |
< knownGeneVM30 | < knownGeneVM30 |GENCODE data are available for use without restrictions.
< knownGeneVM30 | < knownGeneVM32 | html < knownGeneVM32 |< knownGeneVM32 | The GENCODE Genes track (version M32, Feb 2023) shows high-quality manual < knownGeneVM32 | annotations merged with evidence-based automated annotations across the entire < knownGeneVM32 | human genome generated by the < knownGeneVM32 | GENCODE project. < knownGeneVM32 | By default, only the basic gene set is < knownGeneVM32 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneVM32 | that GENCODE believes will be useful to the majority of users.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneVM32 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneVM32 | assembly patches and alternative loci (haplotypes).
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | The following table provides statistics for the VM32 release derived from the GTF file that contains < knownGeneVM32 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneVM32 | in the GENCODE site.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 |
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 |
< knownGeneVM32 | GENCODE VM32 Release Stats < knownGeneVM32 | Genes Observed Transcripts Observed < knownGeneVM32 | Protein-coding genes 21,565 Protein-coding transcripts 58,913 < knownGeneVM32 | Long non-coding RNA genes 14,834 - full length protein-coding 45,219 < knownGeneVM32 | Small non-coding RNA genes 6,105 - partial length protein-coding 13,694 < knownGeneVM32 | Pseudogenes 13,722 Nonsense mediated decay transcripts 7,211 < knownGeneVM32 | Immunoglobulin/T-cell receptor gene segments 701 Long non-coding RNA loci transcripts 26,421 < knownGeneVM32 | Total No of distinct translations 45,163 Genes that have more than one distinct translations 10,914
< knownGeneVM32 |
< knownGeneVM32 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneVM32 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneVM32 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneVM32 | < knownGeneVM32 |
< knownGeneVM32 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneVM32 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneVM32 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID < knownGeneVM32 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene < knownGeneVM32 | and transcript names can be found in our < knownGeneVM32 | FAQ.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneVM32 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneVM32 | those for coding open reading frames are thicker. < knownGeneVM32 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneVM32 |< knownGeneVM32 | This track contains an optional codon coloring feature that allows users to < knownGeneVM32 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneVM32 | a density graph, which < knownGeneVM32 | can be helpful for visualizing the distribution of items over a region.
< knownGeneVM32 | < knownGeneVM32 |
< knownGeneVM32 | The GENCODE VM32 track was built from the GENCODE downloads file
< knownGeneVM32 | gencode.vM32.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneVM32 | were correlated with the GENCODE data to build association tables.
< knownGeneVM32 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneVM32 | downloadable < knownGeneVM32 | file. < knownGeneVM32 | < knownGeneVM32 |
< knownGeneVM32 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneVM32 | is then available on the table menu. < knownGeneVM32 | < knownGeneVM32 | < knownGeneVM32 |
< knownGeneVM32 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneVM32 | REST API, the < knownGeneVM32 | Table Browser or the < knownGeneVM32 | Data Integrator. < knownGeneVM32 | The genePred format files for mm39 are available from our < knownGeneVM32 | < knownGeneVM32 | downloads directory or in our < knownGeneVM32 | < knownGeneVM32 | GTF download directory. < knownGeneVM32 | All the tables can also be queried directly from our public MySQL < knownGeneVM32 | servers, with more information available on our < knownGeneVM32 | help page as well as on < knownGeneVM32 | our blog.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneVM32 | computational pipeline developed by Jim Kent and Brian Raney.
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa < knownGeneVM32 | A, Searle S et al. < knownGeneVM32 | < knownGeneVM32 | GENCODE: the reference human genome annotation for The ENCODE Project. < knownGeneVM32 | Genome Res. 2012 Sep;22(9):1760-74. < knownGeneVM32 | PMID: 22955987; PMC: PMC3431492 < knownGeneVM32 |
< knownGeneVM32 | < knownGeneVM32 |< knownGeneVM32 | Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, < knownGeneVM32 | Swarbreck D et al. < knownGeneVM32 | < knownGeneVM32 | GENCODE: producing a reference annotation for ENCODE. < knownGeneVM32 | Genome Biol. 2006;7 Suppl 1:S4.1-9. < knownGeneVM32 | PMID: 16925838; PMC: PMC1810553 < knownGeneVM32 |
< knownGeneVM32 | < knownGeneVM32 |A full list of GENCODE publications is available < knownGeneVM32 | at The GENCODE < knownGeneVM32 | Project web site. < knownGeneVM32 |
< knownGeneVM32 | < knownGeneVM32 |GENCODE data are available for use without restrictions.
< knownGeneVM32 | < knownGeneVM33 | html < knownGeneVM33 |< knownGeneVM33 | The GENCODE Genes track (version M33, Jul 2023) shows high-quality manual < knownGeneVM33 | annotations merged with evidence-based automated annotations across the entire < knownGeneVM33 | human genome generated by the < knownGeneVM33 | GENCODE project. < knownGeneVM33 | By default, only the basic gene set is < knownGeneVM33 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneVM33 | that GENCODE believes will be useful to the majority of users.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneVM33 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneVM33 | assembly patches and alternative loci (haplotypes).
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | The following table provides statistics for the VM33 release derived from the GTF file that contains < knownGeneVM33 | annotations only on the main chromosomes. More information on how they were generated can be found < knownGeneVM33 | in the GENCODE site.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 |
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 |
< knownGeneVM33 | GENCODE VM33 Release Stats < knownGeneVM33 | Genes Observed Transcripts Observed < knownGeneVM33 | Protein-coding genes 21,403 Protein-coding transcripts 58,750 < knownGeneVM33 | Long non-coding RNA genes 14,842 - full length protein-coding 45,112 < knownGeneVM33 | Small non-coding RNA genes 6,105 - partial length protein-coding 13,638 < knownGeneVM33 | Pseudogenes 13,809 Nonsense mediated decay transcripts 7,218 < knownGeneVM33 | Immunoglobulin/T-cell receptor gene segments 701 Long non-coding RNA loci transcripts 26,564 < knownGeneVM33 | Total No of distinct translations 44,993 Genes that have more than one distinct translations 10,893
< knownGeneVM33 |
< knownGeneVM33 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneVM33 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneVM33 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneVM33 | < knownGeneVM33 |
< knownGeneVM33 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneVM33 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneVM33 | additional options include GENCODE Transcript ID (ENSMUST00000052204.6), UCSC Known Gene ID < knownGeneVM33 | (uc009hdu.3), UniProt Display ID (Q8BHK1). Additional information about gene < knownGeneVM33 | and transcript names can be found in our < knownGeneVM33 | FAQ.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneVM33 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneVM33 | those for coding open reading frames are thicker. < knownGeneVM33 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneVM33 |< knownGeneVM33 | This track contains an optional codon coloring feature that allows users to < knownGeneVM33 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneVM33 | a density graph, which < knownGeneVM33 | can be helpful for visualizing the distribution of items over a region.
< knownGeneVM33 | < knownGeneVM33 |
< knownGeneVM33 | The GENCODE VM33 track was built from the GENCODE downloads comprehensive gene annotation (all regions) file
< knownGeneVM33 | gencode.vM33.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneVM33 | were correlated with the GENCODE data to build association tables.
< knownGeneVM33 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneVM33 | downloadable < knownGeneVM33 | file. < knownGeneVM33 | < knownGeneVM33 |
< knownGeneVM33 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneVM33 | is then available on the table menu. < knownGeneVM33 | < knownGeneVM33 | < knownGeneVM33 |
< knownGeneVM33 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneVM33 | REST API, the < knownGeneVM33 | Table Browser or the < knownGeneVM33 | Data Integrator. < knownGeneVM33 | The genePred format files for mm39 are available from our < knownGeneVM33 | < knownGeneVM33 | downloads directory or in our < knownGeneVM33 | < knownGeneVM33 | GTF download directory. < knownGeneVM33 | All the tables can also be queried directly from our public MySQL < knownGeneVM33 | servers, with more information available on our < knownGeneVM33 | help page as well as on < knownGeneVM33 | our blog.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneVM33 | computational pipeline developed by Jim Kent and Brian Raney. This version of the track < knownGeneVM33 | was generated by Jonathan Casper.
< knownGeneVM33 | < knownGeneVM33 |< knownGeneVM33 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, < knownGeneVM33 | Arnan C, Barnes I et al. < knownGeneVM33 | < knownGeneVM33 | GENCODE: reference annotation for the human and mouse genomes in 2023. < knownGeneVM33 | Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. < knownGeneVM33 | PMID: 36420896; PMC: PMC9825462 < knownGeneVM33 |
< knownGeneVM33 | < knownGeneVM33 |A full list of GENCODE publications is available < knownGeneVM33 | at The GENCODE < knownGeneVM33 | Project web site. < knownGeneVM33 |
< knownGeneVM33 | < knownGeneVM33 |GENCODE data are available for use without restrictions.
< knownGeneVM33 | < knownGeneVM35 | html < knownGeneVM35 |< knownGeneVM35 | The GENCODE Genes track (version M35, May 2024) shows high-quality manual < knownGeneVM35 | annotations merged with evidence-based automated annotations across the entire < knownGeneVM35 | human genome generated by the < knownGeneVM35 | GENCODE project. < knownGeneVM35 | By default, only the basic gene set is < knownGeneVM35 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts < knownGeneVM35 | that GENCODE believes will be useful to the majority of users.
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes < knownGeneVM35 | are not displayed by default. It contains annotations on the reference chromosomes as well as < knownGeneVM35 | assembly patches and alternative loci (haplotypes).
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | The VM35 release was derived from the GTF file that contains annotations only on the main < knownGeneVM35 | chromosomes. Statistics for this build and information on how they were generated can be found on < knownGeneVM35 | the GENCODE site. < knownGeneVM35 | < knownGeneVM35 |
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | For more information on the different gene tracks, see our Genes FAQ.
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. < knownGeneVM35 | It includes options to display the entire GENCODE set and pseudogenes. To customize these < knownGeneVM35 | options, the respective boxes can be checked or unchecked at the top of this description page. < knownGeneVM35 | < knownGeneVM35 |
< knownGeneVM35 | This track also includes a variety of labels which identify the transcripts when visibility is set < knownGeneVM35 | to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but < knownGeneVM35 | additional options include GENCODE Transcript ID (ENSMUST00000052204.6), UCSC Known Gene ID < knownGeneVM35 | (uc009hdu.3), UniProt Display ID (Q8BHK1). Additional information about gene < knownGeneVM35 | and transcript names can be found in our < knownGeneVM35 | FAQ.
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | This track, in general, follows the display conventions for gene prediction tracks. The exons for < knownGeneVM35 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while < knownGeneVM35 | those for coding open reading frames are thicker. < knownGeneVM35 |
Coloring for the gene annotations is based on the annotation type:
< knownGeneVM35 |< knownGeneVM35 | This track contains an optional codon coloring feature that allows users to < knownGeneVM35 | quickly validate and compare gene predictions. There is also an option to display the data as < knownGeneVM35 | a density graph, which < knownGeneVM35 | can be helpful for visualizing the distribution of items over a region.
< knownGeneVM35 | < knownGeneVM35 |
< knownGeneVM35 | The GENCODE VM35 track was built from the GENCODE downloads comprehensive gene annotation (all regions) file
< knownGeneVM35 | gencode.vM35.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources
< knownGeneVM35 | were correlated with the GENCODE data to build association tables.
< knownGeneVM35 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a < knownGeneVM35 | downloadable < knownGeneVM35 | file. < knownGeneVM35 | < knownGeneVM35 |
< knownGeneVM35 | One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list < knownGeneVM35 | is then available on the table menu. < knownGeneVM35 | < knownGeneVM35 | < knownGeneVM35 |
< knownGeneVM35 | GENCODE Genes and its associated tables can be explored interactively using the < knownGeneVM35 | REST API, the < knownGeneVM35 | Table Browser or the < knownGeneVM35 | Data Integrator. < knownGeneVM35 | The genePred format files for mm39 are available from our < knownGeneVM35 | < knownGeneVM35 | downloads directory or in our < knownGeneVM35 | < knownGeneVM35 | GTF download directory. < knownGeneVM35 | All the tables can also be queried directly from our public MySQL < knownGeneVM35 | servers, with more information available on our < knownGeneVM35 | help page as well as on < knownGeneVM35 | our blog.
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a < knownGeneVM35 | computational pipeline developed by Jim Kent and Brian Raney. This version of the track < knownGeneVM35 | was generated by Jonathan Casper.
< knownGeneVM35 | < knownGeneVM35 |< knownGeneVM35 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, < knownGeneVM35 | Arnan C, Barnes I et al. < knownGeneVM35 | < knownGeneVM35 | GENCODE: reference annotation for the human and mouse genomes in 2023. < knownGeneVM35 | Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. < knownGeneVM35 | PMID: 36420896; PMC: PMC9825462 < knownGeneVM35 |
< knownGeneVM35 | < knownGeneVM35 |A full list of GENCODE publications is available < knownGeneVM35 | at The GENCODE < knownGeneVM35 | Project web site. < knownGeneVM35 |
< knownGeneVM35 | < knownGeneVM35 |GENCODE data are available for use without restrictions.
< knownGeneVM35 |