Schema for ncbiRefSeqCurated |
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Database: hg19 Primary Table: ncbiRefSeqCurated Row Count: 99,517 Data last updated: 2024-09-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | NR_046018.2 | 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 | 11873 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 14409 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 14409 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 14409 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 3 | int(10) unsigned | range | Number of exons |
| exonStarts | 11873,12612,13220, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 12227,12721,14409, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | DDX11L1 | 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,-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 | NR_046018.2 | chr1 | + | 11873 | 14409 | 14409 | 14409 | 3 | 11873,12612,13220, | 12227,12721,14409, | 0 | DDX11L1 | none | none | -1,-1,-1, |
| 585 | NR_024540.1 | chr1 | - | 14361 | 29370 | 29370 | 29370 | 11 | 14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320, | 14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370, | 0 | WASH7P | none | none | -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, |
| 585 | NR_106918.1 | chr1 | - | 17368 | 17436 | 17436 | 17436 | 1 | 17368, | 17436, | 0 | MIR6859-1 | none | none | -1, |
| 585 | NR_036051.1 | chr1 | + | 30365 | 30503 | 30503 | 30503 | 1 | 30365, | 30503, | 0 | MIR1302-2 | none | none | -1, |
| 585 | NR_026818.1 | chr1 | - | 34610 | 36081 | 36081 | 36081 | 3 | 34610,35276,35720, | 35174,35481,36081, | 0 | FAM138A | none | none | -1,-1,-1, |
| 585 | NM_001005484.2 | chr1 | + | 65418 | 71585 | 65564 | 70008 | 3 | 65418,65519,69036, | 65433,65573,71585, | 0 | OR4F5 | cmpl | cmpl | -1,0,0, |
| 586 | NR_039983.2 | chr1 | - | 134772 | 140566 | 140566 | 140566 | 3 | 134772,139789,140074, | 139696,139847,140566, | 0 | LOC729737 | none | none | -1,-1,-1, |
| 73 | NR_182075.1 | chr1 | - | 232469 | 266063 | 266063 | 266063 | 4 | 232469,238417,259016,265966, | 237955,238567,259121,266063, | 0 | LOC127239154 | none | none | -1,-1,-1,-1, |
| 73 | NR_182076.1 | chr1 | - | 232469 | 266063 | 266063 | 266063 | 3 | 232469,238417,265966, | 237955,238567,266063, | 0 | LOC127239154 | none | none | -1,-1,-1, |
| 73 | NR_182074.1 | chr1 | - | 232469 | 267255 | 267255 | 267255 | 4 | 232469,238417,259016,267095, | 237955,238567,259121,267255, | 0 | LOC127239154 | none | none | -1,-1,-1,-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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US Server