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Database: otoGar3 Primary Table: ncbiRefSeq Row Count: 38,532   Data last updated: 2020-04-08
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XM_003803761.3 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | AAQR03191568 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 3234 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 3809 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 3357 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 3768 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 3234, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 3809, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC100962662 | 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, | 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 | XM_003803761.3 | AAQR03191568 | - | 3234 | 3809 | 3357 | 3768 | 1 | 3234, | 3809, | 0 | LOC100962662 | cmpl | cmpl | 0, |
585 | XM_012814027.2 | AAQR03191568 | - | 4723 | 5442 | 4846 | 5239 | 1 | 4723, | 5442, | 0 | LOC105888424 | cmpl | cmpl | 0, |
585 | XM_003803762.3 | AAQR03191568 | + | 5528 | 6076 | 5590 | 5971 | 1 | 5528, | 6076, | 0 | LOC100962970 | cmpl | cmpl | 0, |
585 | XM_003803763.3 | AAQR03191568 | - | 11327 | 12763 | 12320 | 12701 | 1 | 11327, | 12763, | 0 | LOC100963288 | cmpl | cmpl | 0, |
585 | XM_012814028.2 | AAQR03191568 | + | 12849 | 13568 | 13052 | 13445 | 1 | 12849, | 13568, | 0 | LOC100963921 | cmpl | cmpl | 0, |
585 | XM_003803764.3 | AAQR03191568 | + | 14482 | 15057 | 14523 | 14934 | 1 | 14482, | 15057, | 0 | LOC100963606 | cmpl | cmpl | 0, |
585 | XM_003803767.1 | AAQR03191595 | + | 15722 | 17516 | 15722 | 17516 | 4 | 15722,16565,16799,17364, | 15909,16670,16853,17516, | 0 | LOC100964543 | cmpl | cmpl | 0,1,1,1, |
585 | XM_012814031.1 | AAQR03191690 | - | 5428 | 9690 | 6023 | 9444 | 8 | 5428,7106,7246,7973,8468,9158,9434,9623, | 6161,7122,7353,8125,8843,9242,9521,9690, | 0 | LOC100966443 | cmpl | cmpl | 0,2,0,1,1,1,0,-1, |
585 | XM_012814033.2 | AAQR03191848 | + | 5722 | 6674 | 5722 | 6674 | 2 | 5722,6497, | 6496,6674, | 0 | LOC100944283 | cmpl | cmpl | 0,0, |
585 | XM_003803776.1 | AAQR03191862 | - | 6034 | 6979 | 6034 | 6979 | 1 | 6034, | 6979, | 0 | LOC100944607 | cmpl | cmpl | 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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