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Database: hg38 Primary Table: orfeomeGenes Row Count: 38,840   Data last updated: 2019-03-09
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | KJ905121 | 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 | 35139 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 35736 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 35736 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 35736 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 3 | int(10) unsigned | range | Number of exons |
exonStarts | 35139,35276,35720, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 35174,35481,35736, | 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 | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | -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. |
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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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585 | KJ905121 | chr1 | - | 35139 | 35736 | 35736 | 35736 | 3 | 35139,35276,35720, | 35174,35481,35736, | 0 | | unk | unk | -1,-1,-1, |
586 | KJ904234 | chr1 | - | 185220 | 195412 | 185220 | 195411 | 10 | 185220,185490,186316,187128,187378,187754,188129,188438,188790,195262, | 185350,185559,186469,187290,187577,187890,188266,188584,188902,195412, | 0 | | incmpl | cmpl | 1,1,1,1,0,2,0,0,2,0, |
588 | KJ899668 | chr1 | - | 450741 | 451678 | 450741 | 451678 | 1 | 450741, | 451678, | 0 | | incmpl | cmpl | 0, |
590 | KJ899668 | chr1 | - | 685717 | 686654 | 685717 | 686654 | 1 | 685717, | 686654, | 0 | | incmpl | cmpl | 0, |
591 | KJ901126 | chr1 | - | 826701 | 827192 | 826701 | 827191 | 1 | 826701, | 827192, | 0 | | incmpl | cmpl | 0, |
592 | KJ905008 | chr1 | + | 939307 | 944152 | 944152 | 944152 | 8 | 939307,941143,942135,942409,942558,943252,943697,943907, | 939460,941306,942251,942488,943058,943377,943808,944152, | 0 | | unk | unk | -1,-1,-1,-1,-1,-1,-1,-1, |
592 | KJ898602 | chr1 | - | 944694 | 959241 | 944695 | 959240 | 19 | 944694,945056,945517,946172,946401,948130,948489,951126,951999,952411,953174,953781,954003,955922,956094,956893,957098,958928,95 ... | 944800,945146,945653,946286,946545,948232,948603,951238,952139,952600,953288,953892,954082,956013,956215,957025,957273,959081,95 ... | 0 | | incmpl | cmpl | 1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0, |
592 | AM393843 | chr1 | - | 944696 | 959241 | 944696 | 959240 | 19 | 944696,945056,945517,946172,946401,948130,948489,951126,951999,952411,953174,953781,954003,955922,956094,956893,957098,958928,95 ... | 944800,945146,945653,946286,946545,948232,948603,951238,952139,952600,953288,953892,954082,956013,956215,957025,957273,959081,95 ... | 0 | NOC2L | incmpl | cmpl | 1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0, |
592 | BC166618 | chr1 | + | 960693 | 965189 | 960693 | 965189 | 12 | 960693,961292,961628,961825,962354,962703,963108,963336,963919,964106,964348,964962, | 960800,961552,961750,962047,962471,962917,963253,963504,964008,964180,964530,965189, | 0 | KLHL17 | cmpl | incmpl | 0,2,1,0,0,0,1,2,2,1,0,2, |
592 | KJ904192 | chr1 | + | 961633 | 962271 | 961633 | 962270 | 2 | 961633,961825, | 961750,962271, | 0 | | cmpl | incmpl | 0,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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