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Database: rn6 Primary Table: ncbiRefSeq Row Count: 69,456   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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XR_001835498.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 53395 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 56311 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 56311 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 56311 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 3 | int(10) unsigned | range | Number of exons |
exonStarts | 53395,55034,55623, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 53701,55222,56311, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC108349478 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | -1,-1,-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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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 | XR_001835498.1 | chr1 | - | 53395 | 56311 | 56311 | 56311 | 3 | 53395,55034,55623, | 53701,55222,56311, | 0 | LOC108349478 | none | none | -1,-1,-1, |
585 | XR_589829.2 | chr1 | - | 56565 | 60411 | 60411 | 60411 | 3 | 56565,57198,60297, | 56705,58679,60411, | 0 | LOC103690911 | none | none | -1,-1,-1, |
586 | XR_589830.2 | chr1 | - | 197017 | 211255 | 211255 | 211255 | 3 | 197017,208010,209269, | 197038,208188,211255, | 0 | LOC103690912 | none | none | -1,-1,-1, |
586 | XM_017589816.1 | chr1 | - | 237908 | 241172 | 237908 | 240959 | 3 | 237908,238456,240806, | 238120,239525,241172, | 0 | LOC108349479 | cmpl | cmpl | 1,0,0, |
586 | XM_017589815.1 | chr1 | - | 237908 | 243880 | 237908 | 243717 | 6 | 237908,238739,239591,241812,243322,243554, | 238067,239310,239595,242580,243364,243880, | 0 | LOC108349479 | cmpl | cmpl | 0,2,1,1,1,0, |
73 | XM_017589810.1 | chr1 | - | 249305 | 269871 | 249991 | 269759 | 4 | 249305,252825,253077,269756, | 251705,252886,253204,269871, | 0 | LOC102556098 | cmpl | cmpl | 2,1,0,0, |
587 | XM_017589809.1 | chr1 | + | 318092 | 329799 | 318153 | 329799 | 8 | 318092,321195,321931,322406,323589,327631,328914,329760, | 318359,321478,322405,322736,323814,327755,329759,329799, | 0 | LOC103690072 | cmpl | cmpl | 0,2,0,0,0,0,1,0, |
73 | XM_008758586.2 | chr1 | + | 390868 | 396476 | 391447 | 396476 | 5 | 390868,394636,395353,395594,396362, | 391653,395027,395516,395893,396476, | 0 | LOC103690913 | cmpl | cmpl | 0,2,0,1,0, |
588 | NM_001099457.1 | chr1 | + | 400255 | 409676 | 400351 | 409676 | 4 | 400255,401911,403344,408792, | 401059,402136,403468,409676, | 0 | Vom2r2 | cmpl | cmpl | 0,0,0,1, |
588 | XM_008758588.2 | chr1 | - | 515556 | 519170 | 515653 | 518955 | 5 | 515556,515926,517244,518558,518810, | 515680,517160,517331,518619,519170, | 0 | LOC103690914 | cmpl | cmpl | 0,2,2,1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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