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Database: panTro6 Primary Table: refFlat Row Count: 2,829   Data last updated: 2018-07-25
Format description: A gene prediction with additional geneName field. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
geneName | INTS11 | varchar(255) | values | Name of gene as it appears in genome browser. |
name | NM_001280424 | varchar(255) | values | Name of gene |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 353 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 12299 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 353 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 12249 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 10 | int(10) unsigned | range | Number of exons |
exonStarts | 353,579,1170,1759,2339,2455... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 439,769,1235,1898,2374,2554... | longblob | | Exon end positions (or start positions for minus strand item) |
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Connected Tables and Joining Fields
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Sample Rows
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geneName | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds |
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INTS11 | NM_001280424 | chr1 | - | 353 | 12299 | 353 | 12249 | 10 | 353,579,1170,1759,2339,2455,6196,7387,7927,12221, | 439,769,1235,1898,2374,2554,6425,7461,8025,12299, |
LHX1 | NM_001033916 | chr17 | - | 19607809 | 19612746 | 19607809 | 19612746 | 5 | 19607809,19608575,19610053,19610424,19612576, | 19608189,19608741,19610331,19610651,19612746, |
DRD3 | NM_001033912 | chr3 | - | 112335658 | 112378682 | 112335658 | 112378682 | 6 | 112335658,112338228,112346090,112353979,112366491,112378412, | 112335855,112338511,112346287,112354122,112366604,112378682, |
CSNK1G1 | NM_001280254 | chr15 | - | 42608404 | 42755922 | 42608707 | 42739403 | 12 | 42608404,42617113,42639755,42641111,42641535,42644148,42650603,42653266,42690764,42698444,42739222,42755867, | 42608762,42617220,42639863,42641260,42641620,42644234,42650838,42653418,42690834,42698485,42739627,42755922, |
CCDC27 | NM_001279930 | chr1 | + | 2349905 | 2369109 | 2349936 | 2368987 | 13 | 2349905,2351577,2352916,2354193,2358735,2360074,2360562,2360754,2361160,2364005,2364695,2367243,2368864, | 2350254,2351701,2353027,2354351,2358885,2360167,2360661,2360929,2361291,2364083,2364908,2367348,2369109, |
VAMP3 | NM_001246583 | chr1 | + | 6479136 | 6489280 | 6479233 | 6487489 | 5 | 6479136,6481302,6485012,6485971,6487469, | 6479235,6481372,6485171,6486023,6489280, |
SLC2A5 | NM_001246591 | chr1 | - | 7735172 | 7786078 | 7735814 | 7767166 | 14 | 7735172,7736122,7736656,7737053,7737778,7738026,7738290,7740011,7745772,7755775,7756485,7767133,7782651,7786018, | 7736018,7736250,7736732,7737155,7737889,7738214,7738416,7740164,7745897,7755936,7756584,7767224,7782804,7786078, |
MIR32 | NR_032006 | chr9 | - | 81262004 | 81262074 | 81262074 | 81262074 | 1 | 81262004, | 81262074, |
MIR31 | NR_032004 | chr9 | - | 21512494 | 21512565 | 21512565 | 21512565 | 1 | 21512494, | 21512565, |
MIR30A | NR_032002 | chr6 | - | 68842861 | 68842932 | 68842932 | 68842932 | 1 | 68842861, | 68842932, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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