|
|
Database: danRer7 Primary Table: mgcGenes Row Count: 18,264   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 | BC157389 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | Zv9_NA110 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 3369 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 25536 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 3426 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 25536 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 15 | int(10) unsigned | range | Number of exons |
exonStarts | 3369,4371,5127,7177,8049,11... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 3564,4476,5209,7306,8102,11... | 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 | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | 0,0,0,1,1,0,2,2,0,2,1,1,2,0,2, | 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 |
---|
585 | BC157389 | Zv9_NA110 | + | 3369 | 25536 | 3426 | 25536 | 15 | 3369,4371,5127,7177,8049,11127,13688,13992,14258,15888,16240,19924,20951,22766,25415, | 3564,4476,5209,7306,8102,11318,13754,14047,14338,16022,16315,20096,21168,22831,25536, | 0 | | cmpl | incmpl | 0,0,0,1,1,0,2,2,0,2,1,1,2,0,2, |
585 | BC048878 | Zv9_NA119 | - | 1161 | 3883 | 1161 | 3883 | 4 | 1161,1983,3095,3815, | 1712,2099,3224,3883, | 0 | | incmpl | incmpl | 2,0,0,1, |
585 | BC165814 | Zv9_NA122 | - | 0 | 12938 | 0 | 12937 | 3 | 0,6871,12901, | 56,6998,12938, | 0 | | incmpl | cmpl | 1,0,0, |
585 | BC045451 | Zv9_NA122 | - | 0 | 13196 | 0 | 12937 | 3 | 0,6871,12901, | 56,6998,13196, | 0 | | incmpl | cmpl | 1,0,0, |
585 | BC065661 | Zv9_NA122 | - | 0 | 13201 | 0 | 12937 | 3 | 0,6871,12901, | 56,6998,13201, | 0 | | incmpl | cmpl | 1,0,0, |
585 | BC142829 | Zv9_NA123 | - | 39150 | 44920 | 39447 | 44906 | 3 | 39150,41107,44692, | 40274,41251,44920, | 0 | | cmpl | cmpl | 1,1,0, |
585 | BC100007 | Zv9_NA15 | + | 18564 | 21757 | 21676 | 21757 | 2 | 18564,21675, | 18677,21757, | 0 | | cmpl | incmpl | -1,0, |
585 | BC154641 | Zv9_NA154 | - | 29657 | 32056 | 30038 | 32030 | 1 | 29657, | 32056, | 0 | | cmpl | cmpl | 0, |
585 | BC171687 | Zv9_NA154 | - | 29809 | 32054 | 30038 | 32030 | 1 | 29809, | 32054, | 0 | | cmpl | cmpl | 0, |
585 | BC171691 | Zv9_NA154 | - | 29809 | 32054 | 30038 | 32030 | 1 | 29809, | 32054, | 0 | | cmpl | cmpl | 0, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|