Schema for ncbiRefSeqCurated
|
|
Database: panPan2 Primary Table: ncbiRefSeqCurated Row Count: 143   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 | 1 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | NM_001293718.1 | 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 | 33550139 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 33589402 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 33551275 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 33589052 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 12 | int(10) unsigned | range | Number of exons |
exonStarts | 33550139,33550413,33550626,... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 33550320,33550534,33550838,... | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | AZIN2 | 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 | -1,-1,-1,0,0,0,2,2,0,1,0,2, | 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 |
---|
1 | NM_001293718.1 | chr1 | + | 33550139 | 33589402 | 33551275 | 33589052 | 12 | 33550139,33550413,33550626,33551203,33552970,33561068,33562300,33563556,33565713,33567073,33586771,33588913, | 33550320,33550534,33550838,33551380,33553144,33561241,33562435,33563722,33565876,33567186,33586986,33589402, | 0 | AZIN2 | cmpl | cmpl | -1,-1,-1,0,0,0,2,2,0,1,0,2, |
1090 | NR_106556.1 | chr1 | - | 66194649 | 66194724 | 66194724 | 66194724 | 1 | 66194649, | 66194724, | 0 | MIR101 | none | none | -1, |
1136 | NR_106538.1 | chr1 | - | 72273840 | 72273926 | 72273926 | 72273926 | 1 | 72273840, | 72273926, | 0 | MIR186 | none | none | -1, |
1433 | NR_106586.1 | chr1 | + | 111204126 | 111204201 | 111204201 | 111204201 | 1 | 111204126, | 111204201, | 0 | MIR197 | none | none | -1, |
1582 | NM_001290340.1 | chr1 | + | 130765002 | 130773974 | 130765289 | 130773859 | 6 | 130765002,130769316,130769378,130770210,130772811,130773716, | 130765321,130769377,130769453,130770386,130772897,130773974, | 0 | OAZ3 | cmpl | cmpl | 0,2,0,0,2,1, |
1582 | NM_001301415.1 | chr1 | + | 130768808 | 130773974 | 130768875 | 130773859 | 6 | 130768808,130769316,130769378,130770210,130772811,130773716, | 130769042,130769377,130769453,130770386,130772897,130773974, | 0 | OAZ3 | cmpl | cmpl | 0,2,0,0,2,1, |
1647 | NM_001302655.1 | chr1 | - | 139224138 | 139226614 | 139224138 | 139226614 | 4 | 139224138,139224739,139225779,139226568, | 139224344,139225008,139226125,139226614, | 0 | SLAMF9 | cmpl | cmpl | 1,2,1,0, |
1647 | NM_001302656.1 | chr1 | - | 139224138 | 139226614 | 139224138 | 139226614 | 4 | 139224138,139224739,139225779,139226568, | 139224344,139225008,139226125,139226614, | 0 | SLAMF9 | cmpl | cmpl | 1,2,1,0, |
1739 | NR_106578.1 | chr1 | - | 151346554 | 151346664 | 151346664 | 151346664 | 1 | 151346554, | 151346664, | 0 | MIR214 | none | none | -1, |
1739 | NR_106575.1 | chr1 | - | 151352287 | 151352397 | 151352397 | 151352397 | 1 | 151352287, | 151352397, | 0 | MIR199A | none | none | -1, |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|