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Database: danRer10 Primary Table: mgcGenes Row Count: 16,938   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 | BC059530 | 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 | 6647 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 11761 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 6679 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 11755 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 6 | int(10) unsigned | range | Number of exons |
exonStarts | 6647,6891,9557,10080,11549,... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 6760,6955,9694,10191,11625,... | 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 | 0,2,0,0,2,0, | 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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585 | BC059530 | chr1 | - | 6647 | 11761 | 6679 | 11755 | 6 | 6647,6891,9557,10080,11549,11750, | 6760,6955,9694,10191,11625,11761, | 0 | | cmpl | cmpl | 0,2,0,0,2,0, |
585 | BC053114 | chr1 | + | 11986 | 16373 | 11997 | 15963 | 11 | 11986,12372,12794,13033,13211,13503,14031,14289,14698,15351,15675, | 12034,12521,12953,13128,13332,13667,14190,14402,15137,15427,16373, | 0 | | cmpl | cmpl | 0,1,0,0,2,0,2,2,1,2,0, |
585 | BC153556 | chr1 | + | 27827 | 34330 | 27835 | 34247 | 12 | 27827,29800,30079,31228,31399,31658,31813,32109,32377,32982,33505,34120, | 27955,29953,30172,31294,31525,31740,31905,32243,32483,33141,33579,34330, | 0 | | cmpl | cmpl | 0,0,0,0,0,0,1,0,2,0,0,2, |
585 | BC093351 | chr1 | + | 27843 | 34330 | 27886 | 34247 | 12 | 27843,29800,30079,31228,31399,31658,31813,32109,32377,32982,33505,34120, | 27955,29953,30172,31294,31525,31740,31905,32243,32483,33141,33579,34330, | 0 | | cmpl | cmpl | 0,0,0,0,0,0,1,0,2,0,0,2, |
585 | BC164450 | chr1 | + | 27886 | 34245 | 27886 | 34245 | 12 | 27886,29800,30079,31228,31399,31658,31813,32109,32377,32982,33505,34120, | 27955,29953,30172,31294,31525,31740,31905,32243,32483,33141,33579,34245, | 0 | | cmpl | incmpl | 0,0,0,0,0,0,1,0,2,0,0,2, |
585 | BC092729 | chr1 | + | 36733 | 39191 | 36848 | 39035 | 6 | 36733,37983,38492,38757,38980,39079, | 36878,38221,38644,38876,39067,39191, | 0 | | cmpl | cmpl | 0,0,1,0,2,-1, |
585 | BC056707 | chr1 | - | 39324 | 44525 | 39821 | 43400 | 10 | 39324,39447,40318,40796,41250,41933,42172,42478,43287,44331, | 39435,40061,40439,40984,41572,42088,42256,42701,43430,44525, | 0 | | cmpl | cmpl | -1,0,2,0,2,0,0,2,0,-1, |
585 | BC053314 | chr1 | - | 44838 | 49831 | 45511 | 49692 | 8 | 44838,45787,47420,47660,47952,48434,48889,49637, | 45550,46371,47549,47807,48072,48584,49060,49831, | 0 | | cmpl | cmpl | 0,1,1,1,1,1,1,0, |
585 | BC139693 | chr1 | + | 109797 | 119138 | 109843 | 117618 | 10 | 109797,110643,111175,111530,112244,115047,115237,117070,117731,118302, | 109928,110807,111200,111644,112391,115139,115358,117717,117956,119138, | 0 | | cmpl | cmpl | 0,1,0,1,1,1,0,1,-1,-1, |
585 | BC095023 | chr1 | + | 119959 | 125246 | 119975 | 124755 | 8 | 119959,120112,120863,120961,121701,122110,122328,124204, | 120036,120276,120888,121078,121842,122232,122449,125246, | 0 | | cmpl | cmpl | 0,1,0,1,1,1,0,1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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