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Database: calMil1 Primary Table: ncbiRefSeq Row Count: 30,695   Data last updated: 2020-04-01
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 | XR_489181.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | AAVX02039917 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 43042 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 47028 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 47028 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 47028 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 2 | int(10) unsigned | range | Number of exons |
exonStarts | 43042,46899, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 43198,47028, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC103190692 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | -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 | XR_489181.1 | AAVX02039917 | - | 43042 | 47028 | 47028 | 47028 | 2 | 43042,46899, | 43198,47028, | 0 | LOC103190692 | none | none | -1,-1, |
585 | XM_007911773.1 | AAVX02040487 | + | 8731 | 56295 | 22599 | 54428 | 23 | 8731,13871,22597,26713,27400,28962,29989,32508,33342,33634,34478,36022,38654,41182,43654,44675,45951,46994,47803,50386,51982,537 ... | 9328,14033,22693,26797,27573,29147,30092,32635,33452,33747,34597,36078,38861,41306,43813,44849,46062,47170,47941,50491,52075,538 ... | 0 | LOC103190869 | cmpl | cmpl | -1,-1,0,1,1,0,2,0,1,0,2,1,0,0,1,1,1,1,0,0,0,0,2, |
585 | XM_007911910.1 | AAVX02040794 | + | 2442 | 55346 | 2442 | 54944 | 16 | 2442,2874,13346,15182,24028,26746,27640,28722,29052,29213,30604,31847,33806,35432,36087,52986, | 2511,3103,13402,15308,24184,26841,27767,28969,29108,29296,30753,31986,34004,35669,36244,55346, | 0 | LOC103190984 | cmpl | cmpl | 1,1,2,1,1,1,0,1,2,1,0,2,0,0,0,1, |
585 | XM_007912056.1 | AAVX02041197 | - | 4089 | 13283 | 7229 | 12554 | 6 | 4089,6742,9711,11261,12113,13266, | 4099,7475,9879,11789,12572,13283, | 0 | LOC103191103 | cmpl | cmpl | -1,0,0,0,0,-1, |
585 | XM_007912054.1 | AAVX02041197 | - | 4089 | 16421 | 7229 | 12554 | 6 | 4089,6742,9711,11261,12113,16261, | 4099,7475,9879,11789,12572,16421, | 0 | LOC103191103 | cmpl | cmpl | -1,0,0,0,0,-1, |
585 | XM_007912055.1 | AAVX02041197 | - | 5976 | 16421 | 7229 | 12554 | 5 | 5976,9711,11261,12113,16261, | 7475,9879,11789,12572,16421, | 0 | LOC103191103 | cmpl | cmpl | 0,0,0,0,-1, |
585 | XM_007912057.1 | AAVX02041197 | - | 26026 | 34273 | 26576 | 31394 | 5 | 26026,28805,29641,30953,34062, | 26846,28970,30169,31412,34273, | 0 | LOC103191104 | cmpl | cmpl | 0,0,0,0,-1, |
585 | XM_007912103.1 | AAVX02041304 | - | 19320 | 31395 | 20334 | 30395 | 4 | 19320,22982,30347,31225, | 21650,23148,30424,31395, | 0 | LOC103191140 | cmpl | cmpl | 1,0,0,-1, |
585 | XM_007912102.1 | AAVX02041304 | - | 19320 | 32060 | 20334 | 30395 | 4 | 19320,22982,30347,31988, | 21650,23148,30424,32060, | 0 | LOC103191140 | cmpl | cmpl | 1,0,0,-1, |
585 | XM_007912101.1 | AAVX02041304 | + | 32193 | 42289 | 40294 | 41626 | 3 | 32193,35817,40290, | 32254,35904,42289, | 0 | leng9 | cmpl | cmpl | -1,-1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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