Schema for GENCODE V36 - GENCODE V36 |
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Database: hg38 Primary Table: knownGene Data last updated: 2021-06-20
Big Bed File: /data01/chenjy/rloopbase/ucsc/gbdb/hg38/gencode/gencodeV36.bb
Item Count: 232,184
Format description: GENCODE bigGenePred
| field | example | description |
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| chrom | chr1 | Reference sequence chromosome or scaffold | | chromStart | 166022214 | Start position in chromosome | | chromEnd | 166023027 | End position in chromosome | | name | ENST00000422100.1 | Ensembl ID | | score | 0 | Score (0-1000) | | strand | + | + or - for strand | | thickStart | 166022214 | Start of where display should be thick (start codon) | | thickEnd | 166022214 | End of where display should be thick (stop codon) | | reserved | 16724991 | RGB value (use R,G,B string in input file) | | blockCount | 1 | Number of blocks | | blockSizes | 813, | Comma separated list of block sizes | | chromStarts | 0, | Start positions relative to chromStart | | name2 | uc286ezv.1 | UCSC Genes ID | | cdsStartStat | none | Status of CDS start annotation (none, unknown, incomplete, or complete) | | cdsEndStat | none | Status of CDS end annotation (none, unknown, incomplete, or complete) | | exonFrames | -1, | Exon frame {0,1,2}, or -1 if no frame for exon | | type | none | Transcript type | | geneName | RPS3AP10 | Gene Symbol | | geneName2 | none | UniProt display ID | | geneType | none | Gene type | | transcriptClass | pseudo | Transcript Class | | source | havana_homo_sapiens | Source of transcript (from gencodeTranscriptSource) | | transcriptType | processed_pseudogene | BioType of transcript (from gencodeAttrs) | | tag | basic,pseudo_consens | symbolic tags (from gencodeTags) | | level | 1 | support level, tsl1 is strongest support, tsl5 weakest, NA means not analyzed (from gencodeTranscriptionSupportLevel) | | tier | canonical,basic,all | Transcript Tier |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | name2 | cdsStartStat | cdsEndStat | exonFrames | type | geneName | geneName2 | geneType | transcriptClass | source | transcriptType | tag | level | tier |
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| chr1 | 166022214 | 166023027 | ENST00000422100.1 | 0 | + | 166022214 | 166022214 | 16724991 | 1 | 813, | 0, | uc286ezv.1 | none | none | -1, | none | RPS3AP10 | none | none | pseudo | havana_homo_sapiens | processed_pseudogene | basic,pseudo_consens | 1 | canonical,basic,all |
| chr1 | 166042243 | 166042350 | ENST00000384611.1 | 0 | + | 166042243 | 166042243 | 16724991 | 1 | 107, | 0, | uc057mzt.1 | none | none | -1, | none | RNA5SP64 | none | none | pseudo | ncrna_homo_sapiens | rRNA_pseudogene | basic | 3 | canonical,basic,all |
| chr1 | 166057425 | 166166225 | ENST00000435676.2 | 0 | - | 166070240 | 166166225 | 789624 | 3 | 3238,932,240, | 0,12406,108560, | uc057mzu.1 | none | none | -1,2,2, | none | FAM78B | H7C3M6 | none | coding | havana_homo_sapiens | nonsense_mediated_decay | alternative_3_UTR,cds_start_NF,mRNA_start_NF,ncRNA_host,not_organism_supported,overlapping_locus | 2 | all |
| chr1 | 166059688 | 166166381 | ENST00000456900.1 | 0 | - | 166070240 | 166166248 | 789624 | 3 | 975,929,396, | 0,10146,106297, | uc057mzv.1 | none | none | -1,2,0, | none | FAM78B | Q5VT40 | none | coding | havana_homo_sapiens | nonsense_mediated_decay | CCDS,alternative_3_UTR,ncRNA_host,not_organism_supported,overlapping_locus | 2 | all |
| chr1 | 166059900 | 166166234 | ENST00000441649.1 | 0 | - | 166070240 | 166166234 | 789624 | 3 | 763,1252,249, | 0,9611,106085, | uc057mzw.1 | none | none | -1,2,2, | none | FAM78B | H7C075 | none | coding | havana_homo_sapiens | nonsense_mediated_decay | alternative_3_UTR,cds_start_NF,mRNA_start_NF,ncRNA_host,not_organism_supported,overlapping_locus | 2 | all |
| chr1 | 166069298 | 166167001 | ENST00000354422.4 | 0 | - | 166070240 | 166166248 | 789624 | 2 | 1465,1016, | 0,96687, | uc021pef.3 | none | none | 2,0, | none | FAM78B | Q5VT40 | none | coding | havana_homo_sapiens | protein_coding | CCDS,MANE_Select,appris_principal_1,basic,ncRNA_host,overlapping_locus | 2 | canonical,basic,all |
| chr1 | 166070019 | 166166969 | ENST00000338353.3 | 0 | - | 166070240 | 166166248 | 789624 | 3 | 744,734,119, | 0,95966,96831, | uc057mzx.1 | none | none | 2,0,-1, | none | FAM78B | Q5VT40 | none | coding | ensembl_homo_sapiens | protein_coding | CCDS,appris_principal_1,basic,ncRNA_host,overlapping_locus | 3 | basic,all |
| chr1 | 166081182 | 166087483 | ENST00000366136.2 | 0 | + | 166081182 | 166081182 | 25600 | 3 | 70,127,397, | 0,1422,5904, | uc057mzy.1 | none | none | -1,-1,-1, | none | FAM78B-AS1 | none | none | nonCoding | havana_homo_sapiens | lncRNA | basic,exp_conf | 1 | canonical,basic,all |
| chr1 | 166147781 | 166165095 | ENST00000451784.1 | 0 | - | 166147781 | 166147781 | 25600 | 2 | 178,306, | 0,17008, | uc057mzz.1 | none | none | -1,-1, | none | AL596087.3 | none | none | nonCoding | havana_homo_sapiens | lncRNA | basic,ncRNA_host,overlapping_locus | 2 | canonical,basic,all |
| chr1 | 166154742 | 166154798 | ENST00000401133.1 | 0 | - | 166154742 | 166154742 | 25600 | 1 | 56, | 0, | uc021peg.1 | none | none | -1, | none | MIR921 | none | none | nonCoding | ncrna_homo_sapiens | miRNA | basic | 3 | canonical,basic,all |
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GENCODE V36 (knownGene) Track Description
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Track description in UCSC
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