|
|
Database: xenTro7 Primary Table: mgcGenes Row Count: 8,980   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 | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | BC159143 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | KB021649 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 27473 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 761927 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 761927 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 761927 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 4 | int(10) unsigned | range | Number of exons |
exonStarts | 27473,27663,386798,761462, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 27570,27889,386990,761927, | 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 | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | unk | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | -1,-1,-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. |
|
| |
|
|
Connected Tables and Joining Fields
|
|
Sample Rows
|
|
bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
---|
73 | BC159143 | KB021649 | - | 27473 | 761927 | 761927 | 761927 | 4 | 27473,27663,386798,761462, | 27570,27889,386990,761927, | 0 | | unk | unk | -1,-1,-1,-1, |
585 | BC158298 | KB021649 | - | 36911 | 60823 | 37125 | 60789 | 6 | 36911,39691,42987,46525,46757,60681, | 37300,39909,43106,46663,46884,60823, | 0 | | cmpl | cmpl | 2,0,1,1,0,0, |
73 | BC088522 | KB021649 | - | 116442 | 150860 | 116604 | 150829 | 26 | 116442,116993,117367,120070,123411,125436,125892,127032,128024,129305,129593,129821,130550,131112,131368,141195,141603,142420,14 ... | 116754,117095,117568,120160,123536,125534,126045,127196,128179,129423,129731,129897,130699,131235,131546,141273,141705,142479,14 ... | 0 | | cmpl | cmpl | 0,0,0,0,1,2,2,0,1,0,0,2,0,0,2,0,0,1,0,1,1,0,0,0,0,0, |
586 | BC124046 | KB021649 | + | 180511 | 206093 | 181145 | 204912 | 6 | 180511,180951,198873,200179,203020,204692, | 180558,181322,198960,200277,203155,206093, | 0 | | cmpl | cmpl | -1,0,0,0,2,2, |
73 | BC061422 | KB021649 | - | 254345 | 266565 | 255023 | 266459 | 4 | 254345,254863,263572,266396, | 254854,255183,263827,266565, | 0 | | cmpl | cmpl | -1,2,0,0, |
587 | BC075356 | KB021649 | + | 302785 | 311145 | 302792 | 310277 | 6 | 302785,304033,305246,308050,309356,310136, | 302826,304158,306140,308239,309458,311145, | 0 | | cmpl | cmpl | 0,1,0,0,0,0, |
587 | BC075503 | KB021649 | + | 338519 | 341230 | 338533 | 339698 | 2 | 338519,339366, | 338666,341230, | 0 | | cmpl | cmpl | 0,1, |
587 | BC153746 | KB021649 | - | 376590 | 378296 | 376590 | 378246 | 2 | 376590,378178, | 376827,378296, | 0 | | incmpl | cmpl | 2,0, |
589 | BC074716 | KB021649 | - | 536053 | 548037 | 536740 | 547924 | 17 | 536053,537380,537686,538135,538530,538960,539165,539410,539618,539898,540393,540749,541390,542083,543197,543501,547907, | 536843,537535,537842,538444,538743,539083,539330,539523,539754,540032,540496,540881,541521,542226,543370,543613,548037, | 0 | | cmpl | cmpl | 2,0,0,0,0,0,0,1,0,1,0,0,1,2,0,2,0, |
589 | BC159311 | KB021649 | - | 550520 | 573700 | 550783 | 573593 | 14 | 550520,552363,559993,560587,563004,564359,565035,566265,567378,568302,570287,571001,571887,573530, | 550898,552496,560155,560628,563300,564426,565202,566412,567509,568459,570481,571133,571978,573700, | 0 | | cmpl | cmpl | 2,1,1,2,0,2,0,0,1,0,1,1,0,0, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|