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Database: hg16 Primary Table: mgcGenes Row Count: 31,100   Data last updated: 2020-01-27
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 588 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | BC137547 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 407502 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 408497 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 407521 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 408460 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 407502, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 408497, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | 0, | 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. |
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Connected Tables and Joining Fields
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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588 | BC137547 | chr1 | + | 407502 | 408497 | 407521 | 408460 | 1 | 407502, | 408497, | 0 | | cmpl | cmpl | 0, |
588 | BC137568 | chr1 | + | 407502 | 408497 | 407521 | 408460 | 1 | 407502, | 408497, | 0 | | cmpl | cmpl | 0, |
590 | BC137547 | chr1 | - | 660921 | 661916 | 660958 | 661897 | 1 | 660921, | 661916, | 0 | | cmpl | cmpl | 0, |
590 | BC137568 | chr1 | - | 660921 | 661916 | 660958 | 661897 | 1 | 660921, | 661916, | 0 | | cmpl | cmpl | 0, |
592 | BC008788 | chr1 | - | 923262 | 933514 | 925891 | 932981 | 9 | 923262,925790,926688,927315,928576,928939,931790,932909,933428, | 924425,925944,926748,927450,928642,929035,931866,933003,933514, | 0 | | cmpl | cmpl | -1,1,1,1,1,1,0,0,-1, |
592 | BC126152 | chr1 | + | 1021167 | 1027018 | 1021491 | 1026580 | 9 | 1021167,1021471,1021920,1022168,1023178,1023798,1024313,1025357,1026406, | 1021291,1021778,1022039,1022298,1023253,1023884,1024485,1025529,1027018, | 0 | | cmpl | cmpl | -1,0,2,1,2,2,1,2,0, |
592 | BC126154 | chr1 | + | 1021167 | 1027018 | 1021491 | 1026580 | 9 | 1021167,1021471,1021920,1022168,1023178,1023798,1024313,1025357,1026406, | 1021291,1021778,1022039,1022298,1023253,1023884,1024485,1025529,1027018, | 0 | | cmpl | cmpl | -1,0,2,1,2,2,1,2,0, |
592 | BC156964 | chr1 | - | 1045029 | 1048010 | 1045029 | 1048009 | 4 | 1045029,1045836,1046807,1047822, | 1045398,1045924,1046930,1048010, | 0 | | incmpl | cmpl | 2,1,1,0, |
592 | BC156102 | chr1 | - | 1045030 | 1048010 | 1045031 | 1048009 | 4 | 1045030,1045836,1046807,1047822, | 1045398,1045924,1046930,1048010, | 0 | | incmpl | cmpl | 2,1,1,0, |
592 | BC152381 | chr1 | - | 1045283 | 1048010 | 1045283 | 1048009 | 5 | 1045283,1045471,1045836,1046807,1047822, | 1045406,1045674,1045924,1046930,1048010, | 0 | | incmpl | cmpl | 1,2,1,1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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