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Database: tarSyr1 Primary Table: xenoRefGene Row Count: 888,233 Data last updated: 2020-09-01
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_001079635 | varchar(255) | Name of gene (usually transcript_id from GTF) |
| chrom | scaffold_51919 | varchar(255) | Reference sequence chromosome or scaffold |
| strand | - | char(1) | + or - for strand |
| txStart | 5839 | int(10) unsigned | Transcription start position (or end position for minus strand item) |
| txEnd | 8765 | int(10) unsigned | Transcription end position (or start position for minus strand item) |
| cdsStart | 5839 | int(10) unsigned | Coding region start (or end position for minus strand item) |
| cdsEnd | 8765 | int(10) unsigned | Coding region end (or start position for minus strand item) |
| exonCount | 4 | int(10) unsigned | Number of exons |
| exonStarts | 5839,6371,7807,8687, | longblob | Exon start positions (or end positions for minus strand item) |
| exonEnds | 5879,6509,7888,8765, | longblob | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | score |
| name2 | CRISP3 | 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 | 2,0,1,0, | 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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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)
tarSyr1.all_mrna.qName (via xenoRefGene.name)
tarSyr1.xenoRefFlat.name (via xenoRefGene.name)
tarSyr1.xenoRefSeqAli.qName (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_001079635 | scaffold_51919 | - | 5839 | 8765 | 5839 | 8765 | 4 | 5839,6371,7807,8687, | 5879,6509,7888,8765, | 0 | CRISP3 | incmpl | incmpl | 2,0,1,0, |
| 585 | NM_001080635 | scaffold_102294 | - | 4943 | 5057 | 4943 | 5057 | 1 | 4943, | 5057, | 0 | ldlrap1b | incmpl | incmpl | 0, |
| 585 | NM_001309148 | scaffold_234093 | + | 3295 | 3442 | 3295 | 3442 | 1 | 3295, | 3442, | 0 | LOC105380324 | cmpl | incmpl | 0, |
| 585 | NM_013214 | scaffold_382688 | - | 4290 | 4444 | 4290 | 4436 | 2 | 4290,4381, | 4335,4444, | 0 | Acot7 | cmpl | incmpl | 0,0, |
| 585 | NM_013214 | scaffold_39194 | - | 420 | 12282 | 420 | 12282 | 3 | 420,6538,12124, | 536,6630,12282, | 0 | Acot7 | incmpl | incmpl | 0,1,2, |
| 585 | NM_013214 | scaffold_438229 | - | 187 | 314 | 187 | 314 | 1 | 187, | 314, | 0 | Acot7 | incmpl | incmpl | 0, |
| 585 | NM_001261082 | scaffold_81885 | + | 4059 | 4222 | 4059 | 4222 | 1 | 4059, | 4222, | 0 | PRRG1 | incmpl | incmpl | 0, |
| 585 | NM_001261083 | scaffold_15257 | - | 18646 | 19668 | 19100 | 19668 | 5 | 18646,18694,18838,18966,19099, | 18680,18727,18926,19090,19668, | 0 | TNFAIP8 | incmpl | cmpl | -1,-1,-1,-1,2, |
| 585 | NM_001260986 | scaffold_41019 | + | 5427 | 12412 | 5454 | 12412 | 2 | 5427,12333, | 5465,12412, | 0 | AKAP8L | cmpl | incmpl | 0,2, |
| 585 | NM_001260986 | scaffold_468032 | + | 829 | 1163 | 829 | 1163 | 1 | 829, | 1163, | 0 | AKAP8L | incmpl | incmpl | 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