Schema for ncbiRefSeqCurated
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Database: saiBol1 Primary Table: ncbiRefSeqCurated Row Count: 28   Data last updated: 2020-03-30
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 960 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | NM_001291087.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | JH378107 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 49207164 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 49220327 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 49207442 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 49215509 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 2 | int(10) unsigned | range | Number of exons |
exonStarts | 49207164,49214305, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 49207447,49220327, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | PEG10 | 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 | 0,2, | 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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960 | NM_001291087.1 | JH378107 | + | 49207164 | 49220327 | 49207442 | 49215509 | 2 | 49207164,49214305, | 49207447,49220327, | 0 | PEG10 | cmpl | cmpl | 0,2, |
960 | NM_001291086.1 | JH378107 | + | 49207164 | 49220327 | 49207442 | 49216657 | 3 | 49207164,49214305,49215488, | 49207447,49215488,49220327, | 0 | PEG10 | cmpl | cmpl | 0,2,1, |
102 | NM_001279999.1 | JH378108 | - | 30516687 | 30539954 | 30516687 | 30539954 | 12 | 30516687,30518670,30519753,30520739,30521184,30521993,30523330,30526401,30526755,30532408,30534993,30539750, | 30516903,30518852,30519931,30520888,30521358,30522177,30523527,30526543,30526889,30532532,30535185,30539954, | 0 | PCSK9 | cmpl | cmpl | 0,1,0,1,1,0,1,0,1,0,0,0, |
14 | NM_001279973.1 | JH378108 | + | 47041119 | 47419849 | 47041119 | 47419849 | 17 | 47041119,47112830,47113627,47151078,47160460,47161408,47161976,47162614,47169495,47170994,47171831,47265561,47355870,47363366,47 ... | 47041367,47112905,47113699,47151147,47160618,47161551,47162118,47162911,47169519,47171059,47171934,47265750,47356001,47363539,47 ... | 0 | NTRK3 | cmpl | cmpl | 0,2,2,2,2,1,0,1,1,1,0,1,1,0,2,0,0, |
840 | NM_001280014.1 | JH378112 | - | 33447676 | 33514894 | 33447730 | 33514874 | 10 | 33447676,33449214,33451630,33460912,33464958,33471899,33492084,33493106,33509098,33514769, | 33447838,33449454,33451816,33460996,33465049,33472056,33492199,33493249,33509243,33514894, | 0 | FKBP5 | cmpl | cmpl | 0,0,0,0,2,1,0,1,0,0, |
696 | NM_001278540.1 | JH378115 | - | 14636588 | 14650439 | 14636835 | 14643579 | 9 | 14636588,14637206,14637546,14637927,14638875,14642506,14643089,14643439,14650319, | 14636947,14637262,14637681,14637979,14638943,14642608,14643267,14643617,14650439, | 0 | DHRS2 | cmpl | cmpl | 2,0,0,2,0,0,2,0,-1, |
10 | NM_001279987.1 | JH378131 | + | 15475910 | 15820369 | 15475910 | 15820364 | 8 | 15475910,15646508,15711757,15754855,15757219,15787907,15793816,15820208, | 15477664,15646648,15711874,15755203,15757364,15788038,15793974,15820369, | 0 | NR3C2 | cmpl | cmpl | 0,2,1,1,1,2,1,0, |
597 | NM_001280003.1 | JH378137 | - | 1629687 | 1634741 | 1629687 | 1634741 | 5 | 1629687,1630484,1631948,1632322,1634571, | 1630067,1630650,1632226,1632549,1634741, | 0 | LHX1 | cmpl | cmpl | 1,0,1,2,0, |
696 | NM_001281860.1 | JH378137 | - | 14592061 | 14616008 | 14593243 | 14615862 | 7 | 14592061,14594594,14599927,14601219,14607320,14608590,14615850, | 14593270,14594723,14600059,14601309,14607465,14608673,14616008, | 0 | TVP23B | cmpl | cmpl | 0,0,0,0,2,0,0, |
672 | NM_001279960.1 | JH378149 | + | 11488783 | 11498517 | 11488783 | 11498517 | 6 | 11488783,11489444,11494987,11497000,11497301,11498182, | 11488879,11489624,11495176,11497177,11497443,11498517, | 0 | AIPL1 | cmpl | cmpl | 0,0,0,0,0,1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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