Schema for ncbiRefSeqPredicted
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Database: ochPri3 Primary Table: ncbiRefSeqPredicted Row Count: 26,227   Data last updated: 2020-03-20
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_004599723.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | ALIT01119338 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | - | char(1) | values | + or - for strand |
txStart | 8906 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 14354 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 8906 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 14354 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 2 | int(10) unsigned | range | Number of exons |
exonStarts | 8906,14141, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 9092,14354, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC101532914 | 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 | 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 | XM_004599723.1 | ALIT01119338 | - | 8906 | 14354 | 8906 | 14354 | 2 | 8906,14141, | 9092,14354, | 0 | LOC101532914 | cmpl | cmpl | 1,1, |
585 | XM_004599725.1 | ALIT01119401 | - | 3680 | 23585 | 3680 | 23548 | 3 | 3680,10494,23404, | 3783,10607,23585, | 0 | LOC101533391 | cmpl | cmpl | 2,0,0, |
585 | XM_004599726.1 | ALIT01119402 | - | 8005 | 22024 | 8005 | 22024 | 5 | 8005,8895,14072,19073,21935, | 8164,9111,14408,19329,22024, | 0 | LMCD1 | cmpl | cmpl | 0,0,0,2,0, |
585 | XM_012931245.1 | ALIT01119634 | + | 10140 | 20846 | 10140 | 20846 | 6 | 10140,11729,14283,17156,17936,20765, | 10231,11893,14389,17231,17974,20846, | 0 | LOC105942638 | cmpl | cmpl | 0,1,0,1,1,0, |
585 | XM_004599732.2 | ALIT01119880 | + | 8103 | 25512 | 8159 | 25512 | 4 | 8103,20021,23488,25352, | 8225,20055,23653,25512, | 0 | LOC101536068 | cmpl | cmpl | 0,0,1,1, |
585 | XM_004599741.1 | ALIT01120075 | - | 1223 | 14080 | 1223 | 14080 | 5 | 1223,5519,7750,10710,14017, | 1581,5624,7854,10791,14080, | 0 | LOC101518198 | cmpl | cmpl | 2,2,0,0,0, |
585 | XM_012931252.1 | ALIT01120092 | - | 7359 | 8895 | 7359 | 8895 | 1 | 7359, | 8895, | 0 | LOC101518444 | cmpl | cmpl | 0, |
585 | XM_004599743.1 | ALIT01120252 | - | 467 | 7072 | 467 | 7072 | 4 | 467,1100,5696,7014, | 722,1364,6047,7072, | 0 | LOC101519416 | cmpl | cmpl | 1,1,1,0, |
585 | XM_012931254.1 | ALIT01120281 | - | 1606 | 1870 | 1606 | 1756 | 1 | 1606, | 1870, | 0 | LOC105942642 | cmpl | cmpl | 0, |
585 | XM_004599744.1 | ALIT01120286 | - | 758 | 7633 | 758 | 7633 | 5 | 758,2906,3719,6947,7538, | 815,3029,3819,7316,7633, | 0 | LOC101520153 | cmpl | cmpl | 0,0,2,2,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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