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Database: bosTau2 Primary Table: mgcGenes Row Count: 11,743   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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | BC140629 | 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 | 27253 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 39541 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 27660 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 39523 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 5 | int(10) unsigned | range | Number of exons |
exonStarts | 27253,28469,31254,36300,39183, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 27741,28566,31377,36367,39541, | 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 | 0,2,2,1,0, | 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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585 | BC140629 | chr1 | - | 27253 | 39541 | 27660 | 39523 | 5 | 27253,28469,31254,36300,39183, | 27741,28566,31377,36367,39541, | 0 | | cmpl | cmpl | 0,2,2,1,0, |
587 | BC110223 | chr1 | - | 313819 | 325445 | 314011 | 325217 | 7 | 313819,314411,316030,317469,320866,322633,325078, | 314122,314507,316162,317628,320934,322801,325445, | 0 | | cmpl | cmpl | 0,0,0,0,1,1,0, |
588 | BC120358 | chr1 | - | 431415 | 451991 | 431544 | 444526 | 12 | 431415,432922,434707,438881,439320,440136,440917,442146,444235,444437,447978,451671, | 431662,433077,434854,438948,439397,440258,441062,442346,444351,444537,448119,451991, | 0 | | cmpl | cmpl | 2,0,0,2,0,1,0,1,2,0,-1,-1, |
594 | BC102794 | chr1 | - | 1193992 | 1230830 | 1195424 | 1212358 | 7 | 1193992,1198912,1201745,1208822,1210174,1212259,1230729, | 1195470,1198970,1201838,1208890,1210287,1212399,1230830, | 0 | | cmpl | cmpl | 2,1,1,2,0,0,-1, |
594 | BC122573 | chr1 | - | 1264445 | 1290444 | 1265036 | 1287667 | 22 | 1264445,1265310,1266083,1266466,1267590,1268813,1270736,1271181,1272475,1273016,1273420,1275394,1278598,1278931,1279505,1280670, ... | 1265228,1265426,1266225,1266597,1267728,1269020,1270889,1271433,1272674,1273126,1273515,1275626,1278767,1279017,1279593,1280796, ... | 0 | | cmpl | cmpl | 0,1,0,1,1,1,1,1,0,1,2,1,0,1,0,0,0,2,1,1,0,-1, |
595 | BC133573 | chr1 | - | 1322505 | 1332510 | 1323173 | 1332493 | 10 | 1322505,1324486,1325878,1326923,1327136,1327841,1329233,1330314,1331203,1332317, | 1323311,1324699,1326077,1327028,1327218,1328020,1329412,1330518,1331285,1332510, | 0 | | cmpl | cmpl | 0,0,2,2,1,2,0,0,2,0, |
595 | BC118422 | chr1 | - | 1333244 | 1366327 | 1333539 | 1357598 | 13 | 1333244,1334179,1336611,1337745,1339522,1341877,1343115,1351418,1353165,1355250,1355884,1357532,1366271, | 1333639,1334225,1336717,1337867,1339621,1341989,1343249,1351487,1353210,1355323,1355962,1357604,1366327, | 0 | | cmpl | cmpl | 2,1,0,1,1,0,1,1,1,0,0,0,-1, |
597 | BC102204 | chr1 | - | 1696540 | 1703896 | 1696607 | 1703868 | 7 | 1696540,1696998,1698310,1699105,1701388,1702445,1703832, | 1696721,1697085,1698423,1699235,1701499,1702496,1703896, | 0 | | cmpl | cmpl | 0,0,1,0,0,0,0, |
599 | BC123561 | chr1 | - | 1840483 | 1868986 | 1841256 | 1868926 | 8 | 1840483,1841099,1847342,1854931,1860095,1861758,1866394,1868877, | 1841049,1841406,1847500,1855079,1860262,1861916,1866518,1868986, | 0 | | cmpl | cmpl | -1,0,1,0,1,2,1,0, |
606 | BC102432 | chr1 | + | 2823053 | 2831731 | 2823146 | 2831414 | 5 | 2823053,2826817,2828690,2829587,2831306, | 2823218,2826908,2828760,2829705,2831731, | 0 | | cmpl | cmpl | 0,0,1,2,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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