Schema for ncbiRefSeqPredicted
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Database: panPan2 Primary Table: ncbiRefSeqPredicted Row Count: 59,202   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 | 591 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XM_014343994.1 | 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 | 823526 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 843433 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 824894 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 843008 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 12 | int(10) unsigned | range | Number of exons |
exonStarts | 823526,824874,828949,829835... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 823817,824966,829131,829886... | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | SAMD11 | 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 | -1,0,0,2,2,1,1,1,2,1,0,0, | 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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591 | XM_014343994.1 | chr1 | + | 823526 | 843433 | 824894 | 843008 | 12 | 823526,824874,828949,829835,833690,836810,837045,839962,841590,842110,842552,842762, | 823817,824966,829131,829886,833815,836900,837183,840125,841901,842235,842663,843433, | 0 | SAMD11 | cmpl | cmpl | -1,0,0,2,2,1,1,1,2,1,0,0, |
591 | XM_003804574.2 | chr1 | - | 843061 | 855954 | 843550 | 855951 | 16 | 843061,843898,844374,845031,845260,846995,847354,850025,850937,851349,852112,852719,852941,854860,855031,855840, | 843657,844003,844510,845145,845404,847097,847468,850137,851077,851538,852226,852830,853020,854951,855152,855954, | 0 | NOC2L | cmpl | cmpl | 1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0, |
591 | XM_008961355.1 | chr1 | - | 843061 | 855954 | 843550 | 855951 | 15 | 843061,843898,844374,845031,846995,847354,850025,850937,851349,852112,852719,852941,854860,855031,855840, | 843657,844003,844510,845145,847097,847468,850137,851077,851538,852226,852830,853020,854951,855152,855954, | 0 | NOC2L | cmpl | cmpl | 1,1,0,0,0,0,2,0,0,0,0,2,1,0,0, |
591 | XM_014342495.2 | chr1 | + | 859735 | 863859 | 859735 | 863730 | 10 | 859735,860022,860244,860768,861117,861522,861750,862333,862525,863718, | 859946,860144,860466,860885,861331,861667,861918,862422,862599,863859, | 0 | KLHL17 | cmpl | cmpl | 0,1,0,0,0,1,2,2,1,0, |
591 | XM_008961362.1 | chr1 | + | 859735 | 864476 | 859735 | 863947 | 11 | 859735,860022,860244,860768,861117,861522,861750,862333,862525,862767,863718, | 859946,860144,860466,860885,861331,861667,861918,862422,862599,862949,864476, | 0 | KLHL17 | cmpl | cmpl | 0,1,0,0,0,1,2,2,1,0,2, |
591 | XR_001337708.1 | chr1 | + | 859735 | 864471 | 864471 | 864471 | 11 | 859735,860022,860244,860768,861117,861522,861750,862333,862525,862767,863718, | 859946,860144,860466,860885,861331,861667,861918,862422,862586,862949,864471, | 0 | KLHL17 | none | none | -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, |
591 | XM_008961383.3 | chr1 | + | 864965 | 874854 | 864965 | 873575 | 17 | 864965,865461,868860,869104,869269,869462,869660,869907,870657,870870,871848,872173,872487,872820,873018,873315,873441, | 865372,865561,869007,869185,869342,869590,869792,869988,870733,871007,871998,872314,872628,873016,873050,873364,874854, | 0 | PLEKHN1 | cmpl | cmpl | 0,2,0,0,0,1,0,0,0,1,0,0,0,0,1,0,1, |
591 | XM_008961378.1 | chr1 | - | 874194 | 880993 | 875160 | 880993 | 5 | 874194,875487,877639,880012,880940, | 875258,875613,879533,880049,880993, | 0 | PERM1 | cmpl | cmpl | 1,1,0,2,0, |
591 | XM_008961370.1 | chr1 | - | 874194 | 881000 | 875160 | 879905 | 4 | 874194,875487,877639,880940, | 875258,875613,880049,881000, | 0 | PERM1 | cmpl | cmpl | 1,1,0,-1, |
592 | XM_003805983.3 | chr1 | + | 927416 | 928491 | 927524 | 928429 | 2 | 927416,927934, | 927527,928491, | 0 | ISG15 | cmpl | cmpl | 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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