Schema for ncbiRefSeqCurated
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Database: felCat9 Primary Table: ncbiRefSeqCurated Row Count: 391   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 | 673 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | NM_001009858.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chrA1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 11563271 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 11622511 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 11563271 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 11622186 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 31 | int(10) unsigned | range | Number of exons |
exonStarts | 11563271,11565646,11571100,... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 11563338,11565871,11571209,... | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | BRCA2 | 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 | 0,1,1,2,1,0,1,0,1,1,1,2,1,0... | 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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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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673 | NM_001009858.1 | chrA1 | + | 11563271 | 11622511 | 11563271 | 11622186 | 31 | 11563271,11565646,11571100,11571829,11571975,11572208,11573064,11574005,11574951,11577487,11580062,11580070,11580082,11582017,11 ... | 11563338,11565871,11571209,11571876,11572016,11572320,11573114,11574117,11576070,11580061,11580069,11580081,11582016,11582027,11 ... | 0 | BRCA2 | cmpl | cmpl | 0,1,1,2,1,0,1,0,1,1,1,2,1,0,1,1,1,2,1,0,2,2,0,0,1,0,1,0,1,0,0, |
759 | NM_001309049.1 | chrA1 | + | 22918805 | 22920348 | 22919057 | 22920092 | 1 | 22918805, | 22920348, | 0 | LPAR6 | cmpl | cmpl | 0, |
771 | NM_001048155.1 | chrA1 | - | 24436704 | 24481859 | 24437643 | 24461268 | 9 | 24436704,24455532,24460023,24461220,24472201,24473001,24476952,24477084,24481792, | 24437754,24455610,24460161,24461330,24472274,24473055,24476989,24477174,24481859, | 0 | LRCH1 | cmpl | cmpl | 0,0,0,0,-1,-1,-1,-1,-1, |
1173 | NM_001114344.1 | chrA1 | - | 77088366 | 77130144 | 77088366 | 77130144 | 5 | 77088366,77090096,77090957,77107822,77130022, | 77088755,77090210,77091050,77108106,77130144, | 0 | EFNB2 | cmpl | cmpl | 1,1,1,2,0, |
1213 | NM_001163655.1 | chrA1 | + | 82349957 | 82367091 | 82349964 | 82366275 | 9 | 82349957,82355010,82356955,82357292,82363801,82364528,82365408,82365544,82366135, | 82350016,82355132,82357175,82357451,82363989,82364654,82365475,82365715,82367091, | 0 | LAMP1 | cmpl | cmpl | 0,1,0,1,1,0,0,1,1, |
1284 | NM_001167474.1 | chrA1 | + | 91725271 | 91726174 | 91725271 | 91726174 | 1 | 91725271, | 91726174, | 0 | FELCATV1R2 | cmpl | cmpl | 0, |
1433 | NM_001309037.1 | chrA1 | + | 111190386 | 111192290 | 111190386 | 111192290 | 4 | 111190386,111190641,111191340,111192184, | 111190545,111190683,111191466,111192290, | 0 | CSF2 | cmpl | cmpl | 0,0,0,0, |
1436 | NM_001009845.2 | chrA1 | - | 111639220 | 111641240 | 111639610 | 111641196 | 4 | 111639220,111639816,111640817,111641052, | 111639709,111639945,111640850,111641240, | 0 | IL5 | cmpl | cmpl | 0,0,0,0, |
1437 | NM_001043339.1 | chrA1 | + | 111778711 | 111787544 | 111778745 | 111787449 | 4 | 111778711,111779150,111785000,111787356, | 111778880,111779198,111785126,111787544, | 0 | IL4 | cmpl | cmpl | 0,0,0,0, |
1439 | NM_001165900.1 | chrA1 | - | 111946494 | 111949509 | 111946494 | 111949509 | 2 | 111946494,111949115, | 111947457,111949509, | 0 | GDF9 | cmpl | cmpl | 1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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