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Database: xenTro9 Primary Table: ncbiRefSeq Row Count: 43,724   Data last updated: 2021-02-11
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 586 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XM_012956089.1 | 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 | 133269 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 152620 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 133269 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 152620 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 6 | int(10) unsigned | range | Number of exons |
exonStarts | 133269,140925,143199,146034... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 134186,141049,143418,146880... | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC100490505 | 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 | 1,0,0,0,2,0, | 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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586 | XM_012956089.1 | chr1 | - | 133269 | 152620 | 133269 | 152620 | 6 | 133269,140925,143199,146034,151249,152381, | 134186,141049,143418,146880,151541,152620, | 0 | LOC100490505 | cmpl | cmpl | 1,0,0,0,2,0, |
586 | XM_018090860.1 | chr1 | - | 158469 | 174433 | 158469 | 174433 | 5 | 158469,160350,162164,170432,174037, | 159374,160474,162386,171221,174433, | 0 | LOC100490675 | cmpl | cmpl | 1,0,0,0,0, |
586 | XM_012956191.2 | chr1 | - | 192349 | 195109 | 192518 | 195011 | 2 | 192349,194935, | 193426,195109, | 0 | LOC100489075 | cmpl | cmpl | 1,0, |
586 | XM_002941730.2 | chr1 | - | 211482 | 212022 | 211482 | 212022 | 1 | 211482, | 212022, | 0 | LOC100488911 | cmpl | cmpl | 0, |
586 | XM_012956192.2 | chr1 | + | 218227 | 243623 | 218227 | 243623 | 5 | 218227,233350,235322,238854,242715, | 218478,233453,235619,238978,243623, | 0 | LOC100488739 | cmpl | cmpl | 0,2,0,0,1, |
587 | XM_012956193.2 | chr1 | + | 286313 | 303509 | 286313 | 303509 | 4 | 286313,289920,291982,303393, | 286394,290044,292879,303509, | 0 | LOC105946480 | cmpl | cmpl | 0,0,1,1, |
588 | XM_012956142.2 | chr1 | + | 435241 | 461138 | 435254 | 461138 | 6 | 435241,448180,453999,456506,459382,460233, | 435499,448472,454833,456725,459506,461138, | 0 | LOC100487968 | cmpl | cmpl | 0,2,0,0,0,1, |
588 | XM_012956143.1 | chr1 | - | 510429 | 522960 | 510429 | 522960 | 6 | 510429,512239,517796,518541,521348,522766, | 511337,512363,518024,519342,521640,522960, | 0 | LOC105946420 | cmpl | cmpl | 1,0,0,0,2,0, |
589 | XM_018090861.1 | chr1 | + | 563921 | 579424 | 563921 | 579424 | 5 | 563921,569617,571441,577976,578522, | 564046,569753,572263,578100,579424, | 0 | LOC108645644 | cmpl | cmpl | 0,2,0,0,1, |
589 | XM_018090862.1 | chr1 | + | 587221 | 615857 | 587221 | 615857 | 7 | 587221,590379,592510,608841,610756,612068,615393, | 587457,590671,593335,609069,610961,612974,615857, | 0 | LOC100498444 | cmpl | cmpl | 0,2,0,0,0,1,1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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