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Database: mm39 Primary Table: ncbiRefSeq Row Count: 136,261   Data last updated: 2024-02-20
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 609 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XR_004936710.1 | 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 | 3172238 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 3172348 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 3172348 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 3172348 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 3172238, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 3172348, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | Gm26206 | 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, | 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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609 | XR_004936710.1 | chr1 | + | 3172238 | 3172348 | 3172348 | 3172348 | 1 | 3172238, | 3172348, | 0 | Gm26206 | none | none | -1, |
76 | XM_006495550.5 | chr1 | - | 3269955 | 3741733 | 3286244 | 3741571 | 4 | 3269955,3283661,3491924,3740774, | 3277540,3287191,3492124,3741733, | 0 | Xkr4 | cmpl | cmpl | -1,1,2,0, |
76 | NM_001011874.1 | chr1 | - | 3284704 | 3741721 | 3286244 | 3741571 | 3 | 3284704,3491924,3740774, | 3287191,3492124,3741721, | 0 | Xkr4 | cmpl | cmpl | 1,2,0, |
76 | XR_004935518.1 | chr1 | + | 3363895 | 3448035 | 3448035 | 3448035 | 6 | 3363895,3365063,3396935,3436479,3438010,3438564, | 3364050,3365091,3397056,3436728,3438060,3448035, | 0 | Gm53491 | none | none | -1,-1,-1,-1,-1,-1, |
76 | XM_011238395.4 | chr1 | - | 3393038 | 3741733 | 3393969 | 3741571 | 3 | 3393038,3491924,3740774, | 3393983,3492124,3741733, | 0 | Xkr4 | cmpl | cmpl | 1,2,0, |
76 | XM_036152287.1 | chr1 | - | 3420931 | 3741733 | 3422507 | 3741571 | 3 | 3420931,3491924,3740774, | 3422536,3492124,3741733, | 0 | Xkr4 | cmpl | cmpl | 1,2,0, |
611 | XR_004935517.1 | chr1 | + | 3422902 | 3448035 | 3448035 | 3448035 | 2 | 3422902,3438564, | 3438060,3448035, | 0 | Gm53491 | none | none | -1,-1, |
9 | XM_030252325.2 | chr1 | - | 4185895 | 4479489 | 4186157 | 4479410 | 25 | 4185895,4189890,4190237,4212834,4218034,4218834,4234077,4240427,4267756,4276882,4296833,4298665,4301275,4313355,4313639,4313765, ... | 4186171,4189935,4190296,4212989,4218186,4218967,4234164,4240627,4267864,4277060,4297046,4298842,4301367,4313485,4313671,4313842, ... | 0 | Rp1 | cmpl | cmpl | 1,1,2,0,1,0,0,1,1,0,0,0,1,0,1,2,1,0,1,0,0,1,0,0,0, |
9 | NM_001370921.1 | chr1 | - | 4190088 | 4430526 | 4190226 | 4423048 | 23 | 4190088,4212834,4218034,4218834,4234077,4240427,4267756,4276882,4296833,4298665,4301275,4313355,4313639,4313765,4315253,4331749, ... | 4190296,4212989,4218186,4218967,4234164,4240627,4267864,4277060,4297046,4298842,4301367,4313485,4313671,4313842,4315329,4331828, ... | 0 | Rp1 | cmpl | cmpl | 2,0,1,0,0,1,1,0,0,0,1,0,1,2,1,0,1,0,0,1,0,0,-1, |
77 | NM_001195662.2 | chr1 | - | 4361068 | 4479508 | 4363203 | 4479410 | 4 | 4361068,4422132,4422424,4479392, | 4363235,4422304,4423060,4479508, | 0 | Rp1 | cmpl | cmpl | 1,0,0,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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