Schema for Gencode Genes - ENCODE Gencode Gene Annotations
  Database: hg18    Primary Table: wgEncodeGencodeManualV3    Row Count: 87,627   Data last updated: 2009-11-02
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name ENST00000450305varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1872int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3533int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3533int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3533int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 1872,2041,2475,2837,3083,3315,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1920,2090,2560,2915,3237,3533,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 RP11-34P13.1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-1,-1,-1,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        hg18.wgEncodeGencodeAutoV3.name (via wgEncodeGencodeManualV3.name)
      hg18.wgEncodeGencodeClassesV3.name (via wgEncodeGencodeManualV3.name)
      hg18.wgEncodeGencodePolyaV3.name (via wgEncodeGencodeManualV3.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585ENST00000450305chr1+187235333533353361872,2041,2475,2837,3083,3315,1920,2090,2560,2915,3237,3533,0RP11-34P13.1nonenone-1,-1,-1,-1,-1,-1,
585ENST00000488147chr1-4266194331943319433114266,4867,5658,6469,6720,7095,7468,7777,8130,14600,19396,4364,4901,5810,6628,6918,7231,7605,7924,8229,14754,19433,0WASH5Pnonenone-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585ENST00000473358chr1+19416209602096020960319416,20426,20838,19902,20530,20960,0AL627309.6nonenone-1,-1,-1,
585ENST00000469289chr1+20129209722097220972220129,20838,20530,20972,0AL627309.6nonenone-1,-1,
585ENST00000417324chr1-24416259442500025599324416,25139,25583,25037,25344,25944,0FAM138Acmplcmpl2,1,0,
585ENST00000461467chr1-25107259362593625936225107,25583,25344,25936,0FAM138Anonenone-1,-1,
585ENST00000492842chr1+52810537505375053750152810,53750,0OR4G11Pnonenone-1,
585ENST00000326183chr1+58917599715895359871158917,59971,0OR4F5cmplcmpl0,
585ENST00000466430chr1-79157110795110795110795479157,81953,102562,110637,81492,82103,102667,110795,0AL627309.9nonenone-1,-1,-1,-1,
585ENST00000495576chr1-79413809688096880968279413,80149,79913,80968,0AL627309.4nonenone-1,-1,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Gencode Genes (wgEncodeSangerGencode) Track Description
 

Release Notes

This release of the Gencode Genes track (Version 3c, October 2009) shows high-quality manual annotations in the ENCODE regions generated by the GENCODE project.

Version 3 of the Gencode gene set presents a full merge between HAVANA and ENSEMBL, giving priority to the manually curated Havana objects and using ENSEMBL objects where they are different or fall into un-annotated regions. The annotation was carried out on genome assembly GRCh37 (hg19), features are projected back to NCBI36 (hg18) where possible. Gencode 3c is a small update of version 3b (July 09 freeze) mainly for chromosomes 3 & 4 for which the latest annotation was held back and QC'ed again to be used in the RNASeq Genome Annotation Assessment Project. Statistics about this release can be found here.

Display Conventions and Configuration

The annotations are divided into separate tracks based on source/confidence. The Gencode project recommends that the annotations from level 1 & 2 be used as the reference gene annotation, level 3 was added to fill gaps for methods that analyze the entire genome and require a full set.

  • Level 1: validated
At this time only pseudogene loci, that were predicted by the analysis-pipelines from YALE, UCSC as well as by HAVANA manual annotation from WTSI.
  • Level 2: manual annotation
HAVANA manual annotation from WTSI.
The following regions are considered "fully annotated" and contain level 2 annotation from HAVANA only, although they will still be updated: chromosomes 1, 2, 6, 9, 10, 13, 20, 21, 22, X, Y, ENCODE pilot regions, chr11:2353995-3878750.
  • Level 3: automated annotation
ENSEMBL loci in regions where no HAVANA annotation can be found.

NOTE: The release cycles for Gencode, Havana and Ensembl differ. Users are cautioned to compare release dates to determine which annotation is most current.

The gene annotations are colored based on the HAVANA annotation type and the confidence level. See the table below for the color key, as well as more detail about the transcript and feature types.

Class Color Description Transcript Types (see Vega Transcript Types)
Validated_coding Dark Orange Level 1 Validated:
coding regions 		protein_coding
Validated_processed Light Orange Level 1 Validated:
processed 		processed_transcript
Validated_processed_pseudogene Dark Pink Level 1 Validated:
processed pseudogenes 		processed_pseudogene, processed_transcript, transcribed_processed_pseudogene
Validated_unprocessed_pseudogeneMedium Pink Level 1 Validated:
unprocessed pseudogenes 		transcribed_unprocessed_pseudogene, unprocessed_pseudogene
Validated_pseudogene Light Pink Level 1 Validated:
pseudogenes 		IG_pseudogene, polymorphic_pseudogene, pseudogene, retrotransposed, unitary_pseudogene
Havana_coding Dark Orange Level 2 Manual annotation:
coding 		IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,protein_coding
Havana_nonsense Medium OrangeLevel 2 Manual annotation:
nonsense 		nonsense_mediated_decay
Havana_non_coding Light Orange Level 2 Manual annotation:
non-coding 		ambiguous_orf, antisense, non_coding, processed_transcript, retained_intron
Havana_polyA Black Level 2 Manual annotation:
polyA 		polyA_signal, polyA_site, pseudo_polyA
Havana_processed_pseudogene Dark Pink Level 2 Manual annotation:
processed pseudogene 		processed_pseudogene, transcribed_processed_pseudogene
Havana_unprocessed_pseudogene Medium Pink Level 2 Manual annotation:
unprocessed pseudogene 		transcribed_unprocessed_pseudogene, unprocessed_pseudogene
Havana_pseudogene Light Pink Level 2 Manual annotation:
pseudogene 		IG_pseudogene, TR_pseudogene, polymorphic_pseudogene, pseudogene, retrotransposed, unitary_pseudogene
Havana_TEC Grey Level 2 Manual annotation:
TEC 		TEC, artifact
Ensembl_coding Dark Red Level 3 Automated annotation:
coding 		IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, protein_coding
Ensembl_non_coding Light Orange Level 3 Automated annotation:
non-coding 		antisense, non_coding, processed_transcript, retained_intron
Ensembl_pseudogene Dark Pink Level 3 Automated annotation:
pseudogene 		IG_pseudogene, miRNA_pseudogene, misc_RNA_pseudogene, pseudogene, retrotransposed, unitary_pseudogene
Ensembl_processed_pseudogene Medium Pink Level 3 Automated annotation:
processed pseudogene 		processed_pseudogene
Ensembl_unprocessed_pseudogene Light Pink Level 3 Automated annotation:
unprocessed pseudogene		unprocessed_pseudogene
Ensembl_RNA Light Red Level 3 Automated annotation:
RNA transcripts 		Mt_rRNA, Mt_tRNA, Mt_tRNA_pseudogene, miRNA, misc_RNA, rRNA, rRNA_pseudogene, scRNA_pseudogene, snRNA, snRNA_pseudogene, snoRNA, snoRNA_pseudogene, tRNA_pseudogene, tRNAscan
2way_consensus_pseudogene Dark Purple Level 3 Automated annotation:
pseudogenes 		pseudogenes

This track uses filtering by category to select subsets of transcripts and has additional advanced features. Help with these features can be found here.

Methods

We aim to annotate all evidence-based gene features at high accuracy on the human reference sequence. This includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. We integrate computational approaches (including comparative methods), manual annotation and targeted experimental verification.

For a detailed description of the methods and references used, see Harrow et al (2006).

Verification

See Harrow et al. (2006) for information on verification techniques.

Credits

This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: Felix Kokocinski)

Lab/Institution
 Contributors
HAVANA annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Adam Frankish, James Gilbert, Jennifer Harrow, Felix Kokocinski, Stephen Trevanion, Tim Hubbard (GENCODE Principal Investigator)
Genome Bioinformatics Lab (CRG), Barcelona, Spain Thomas Derrien, Tyler Alioto, Roderic Guigó
Genome Bioinformatics, University of California Santa Cruz (UCSC), USA Rachel Harte, Mark Diekhans, Robert Baertsch, David Haussler
Comp. Genomics Lab, Washington University St. Louis (WUSTL), USA Jeltje van Baren, Charlie Comstock, David Lu, Michael Brent
Computer Science and Artificial Intelligence Lab, Broad Institute of MIT and Harvard, USA Mike Lin, Manolis Kellis
Bioinformatics, Yale University (Yale), USA Philip Cayting, Mark Gerstein
Center for Integrative Genomics, University of Lausanne, Switzerland Cedric Howald, Alexandre Reymond
ENSEMBL genebuild group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Bronwen Aken, Julio Fernandez Banet, Stephen Searle
Structural Computational Biology Group, Centro Natcional de Investigaciones Oncologicas (CNIO), Madrid, Spain Manuel Rodríguez José, Jan-Jaap Wesselink, Michael Tress, Alfonso Valencia

References

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, et al. The GENCODE exome: sequencing the complete human exome. European Journal of Human Genetics. March 2011;19 827-831. [Epub ahead of print]

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9.

Data Release Policy

GENCODE data are available for use without restrictions. The full data release policy for ENCODE is available here.