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Database: eriEur1 Primary Table: xenoRefGene Row Count: 935,974 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_001324041 | varchar(255) | Name of gene (usually transcript_id from GTF) |
| chrom | scaffold_377779 | varchar(255) | Reference sequence chromosome or scaffold |
| strand | - | char(1) | + or - for strand |
| txStart | 34272 | int(10) unsigned | Transcription start position (or end position for minus strand item) |
| txEnd | 38981 | int(10) unsigned | Transcription end position (or start position for minus strand item) |
| cdsStart | 34272 | int(10) unsigned | Coding region start (or end position for minus strand item) |
| cdsEnd | 38981 | int(10) unsigned | Coding region end (or start position for minus strand item) |
| exonCount | 3 | int(10) unsigned | Number of exons |
| exonStarts | 34272,34674,38864, | longblob | Exon start positions (or end positions for minus strand item) |
| exonEnds | 34506,34854,38981, | longblob | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | score |
| name2 | ZNF75A | 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 | 0,0,0, | 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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eriEur1.all_mrna.qName (via xenoRefGene.name)
eriEur1.xenoRefFlat.name (via xenoRefGene.name)
eriEur1.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_001324041 | scaffold_377779 | - | 34272 | 38981 | 34272 | 38981 | 3 | 34272,34674,38864, | 34506,34854,38981, | 0 | ZNF75A | incmpl | incmpl | 0,0,0, |
| 585 | NM_001092728 | scaffold_342941 | + | 42982 | 46465 | 42982 | 46465 | 5 | 42982,43627,44159,46160,46303, | 43097,43674,44207,46187,46465, | 0 | atp1b2.S | incmpl | incmpl | 0,1,0,0,0, |
| 585 | NM_001092727 | scaffold_139328 | + | 63 | 168 | 63 | 168 | 1 | 63, | 168, | 0 | sccpdh.2.L | incmpl | incmpl | 0, |
| 585 | NM_001092727 | scaffold_181916 | - | 363 | 471 | 363 | 471 | 1 | 363, | 471, | 0 | sccpdh.2.L | incmpl | incmpl | 0, |
| 585 | NM_001092727 | scaffold_280108 | - | 738 | 3344 | 738 | 3344 | 3 | 738,889,3248, | 759,1009,3344, | 0 | sccpdh.2.L | incmpl | incmpl | 1,0,0, |
| 585 | NM_001092726 | scaffold_373877 | + | 69899 | 99683 | 69899 | 99683 | 4 | 69899,84726,93314,99572, | 70120,84852,93431,99683, | 0 | alcam.S | incmpl | incmpl | 0,0,0,0, |
| 585 | NM_001092725 | scaffold_347326 | - | 49722 | 49841 | 49722 | 49841 | 1 | 49722, | 49841, | 0 | rdh5.L | incmpl | incmpl | 1, |
| 585 | NM_001092725 | scaffold_378881 | - | 3577 | 6822 | 3577 | 6822 | 4 | 3577,4041,6218,6663, | 3763,4188,6467,6822, | 0 | rdh5.L | incmpl | incmpl | 0,0,0,0, |
| 585 | NM_001102724 | scaffold_292974 | - | 21900 | 39117 | 21900 | 39117 | 2 | 21900,38949, | 21984,39117, | 0 | setdb2 | incmpl | incmpl | 0,0, |
| 585 | NM_212489 | scaffold_179119 | + | 7580 | 7796 | 7580 | 7796 | 1 | 7580, | 7796, | 0 | Btnl8 | 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