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Database: dipOrd1 Primary Table: xenoRefGene Row Count: 666,567 Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| name | NM_001171286 | varchar(255) | Name of gene (usually transcript_id from GTF) |
| chrom | scaffold_61833 | varchar(255) | Reference sequence chromosome or scaffold |
| strand | + | char(1) | + or - for strand |
| txStart | 5534 | int(10) unsigned | Transcription start position (or end position for minus strand item) |
| txEnd | 5659 | int(10) unsigned | Transcription end position (or start position for minus strand item) |
| cdsStart | 5534 | int(10) unsigned | Coding region start (or end position for minus strand item) |
| cdsEnd | 5659 | int(10) unsigned | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | Number of exons |
| exonStarts | 5534, | longblob | Exon start positions (or end positions for minus strand item) |
| exonEnds | 5659, | longblob | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | score |
| name2 | SERPINB7 | varchar(255) | Alternate name (e.g. gene_id from GTF) |
| cdsStartStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | Status of CDS start annotation (none, unknown, incomplete, or complete) |
| cdsEndStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | Status of CDS end annotation (none, unknown, incomplete, or complete) |
| exonFrames | 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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dipOrd1.all_mrna.qName (via xenoRefGene.name)
dipOrd1.xenoMrna.qName (via xenoRefGene.name)
dipOrd1.xenoRefFlat.name (via xenoRefGene.name)
dipOrd1.xenoRefSeqAli.qName (via xenoRefGene.name)
hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
hgFixed.gbSeq.acc (via xenoRefGene.name)
hgFixed.gbWarn.acc (via xenoRefGene.name)
hgFixed.imageClone.acc (via xenoRefGene.name)
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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 | NM_001171286 | scaffold_61833 | + | 5534 | 5659 | 5534 | 5659 | 1 | 5534, | 5659, | 0 | SERPINB7 | incmpl | incmpl | 1, |
| 585 | NM_001012821 | scaffold_3049 | - | 84138 | 84468 | 84138 | 84468 | 1 | 84138, | 84468, | 0 | ZFP92 | incmpl | incmpl | 0, |
| 585 | NM_001012821 | scaffold_3049 | - | 84149 | 84552 | 84149 | 84552 | 1 | 84149, | 84552, | 0 | ZFP92 | incmpl | incmpl | 0, |
| 585 | NM_001081466 | scaffold_23654 | + | 1448 | 1771 | 1448 | 1771 | 2 | 1448,1711, | 1531,1771, | 0 | Gtf2ird1 | incmpl | incmpl | 1,0, |
| 585 | NM_001097189 | scaffold_77104 | - | 3768 | 3951 | 3768 | 3951 | 1 | 3768, | 3951, | 0 | cnot1 | incmpl | incmpl | 0, |
| 585 | NM_001122636 | scaffold_57694 | - | 6875 | 7000 | 6875 | 7000 | 1 | 6875, | 7000, | 0 | GALNT9 | incmpl | incmpl | 2, |
| 585 | NM_001163898 | scaffold_2479 | - | 15688 | 22262 | 15688 | 22262 | 4 | 15688,17253,19179,22199, | 15751,17298,19344,22262, | 0 | Notch | incmpl | incmpl | 0,0,0,0, |
| 585 | NM_152701 | scaffold_9659 | + | 10758 | 51912 | 10776 | 51912 | 4 | 10758,36240,36920,51829, | 10845,36334,37044,51912, | 0 | ABCA13 | cmpl | incmpl | 0,0,1,2, |
| 585 | NM_152688 | scaffold_992 | - | 18063 | 18193 | 18063 | 18193 | 1 | 18063, | 18193, | 0 | KHDRBS2 | incmpl | incmpl | 2, |
| 585 | NM_152688 | scaffold_9360 | - | 39986 | 44976 | 39986 | 44976 | 2 | 39986,44848, | 40185,44976, | 0 | KHDRBS2 | incmpl | incmpl | 2,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server