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Database: hg17 Primary Table: mgcGenes Row Count: 30,831   Data last updated: 2020-01-27
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 588 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | BC137547 | 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 | 407502 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 408497 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 407521 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 408460 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 407502, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 408497, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | | 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, | 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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588 | BC137547 | chr1 | + | 407502 | 408497 | 407521 | 408460 | 1 | 407502, | 408497, | 0 | | cmpl | cmpl | 0, |
588 | BC137568 | chr1 | + | 407502 | 408497 | 407521 | 408460 | 1 | 407502, | 408497, | 0 | | cmpl | cmpl | 0, |
590 | BC137547 | chr1 | - | 660921 | 661916 | 660958 | 661897 | 1 | 660921, | 661916, | 0 | | cmpl | cmpl | 0, |
590 | BC137568 | chr1 | - | 660921 | 661916 | 660958 | 661897 | 1 | 660921, | 661916, | 0 | | cmpl | cmpl | 0, |
73 | BC024295 | chr1 | + | 911288 | 920097 | 914832 | 919676 | 10 | 911288,914562,914797,916666,917658,917932,918081,918775,919220,919430, | 911419,914652,914935,916829,917774,918011,918581,918900,919331,920097, | 0 | | cmpl | cmpl | -1,-1,0,1,2,1,2,1,0,0, |
73 | BC033213 | chr1 | + | 914832 | 920104 | 914832 | 919676 | 8 | 914832,916666,917658,917932,918081,918775,919220,919430, | 914983,916829,917774,918011,918581,918900,919331,920104, | 0 | | cmpl | cmpl | 0,1,2,1,2,1,0,0, |
592 | BC003555 | chr1 | - | 919738 | 934795 | 920216 | 934763 | 19 | 919738,920579,921040,921695,921924,923653,924012,926649,927522,927934,928697,929304,929526,931445,931617,932416,932621,934451,93 ... | 920323,920669,921176,921809,922068,923755,924126,926761,927662,928123,928811,929415,929605,931536,931738,932548,932796,934604,93 ... | 0 | | cmpl | cmpl | 1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0, |
592 | BC166618 | chr1 | + | 936216 | 940636 | 936216 | 940636 | 12 | 936216,936815,937151,937348,937877,938226,938631,938859,939442,939629,939871,940409, | 936323,937075,937273,937570,937994,938440,938776,939027,939531,939703,940053,940636, | 0 | | cmpl | incmpl | 0,2,1,0,0,0,1,2,2,1,0,2, |
592 | BC101386 | chr1 | + | 941948 | 950455 | 941978 | 950022 | 15 | 941948,942150,945723,945967,946132,946325,946523,946770,947521,947734,948307,948946,949279,949762,949888, | 942061,942250,945870,946048,946205,946453,946655,946851,947597,947871,948457,949087,949498,949811,950455, | 0 | | cmpl | cmpl | 0,2,0,0,0,1,0,0,0,1,0,0,0,0,1, |
592 | BC101387 | chr1 | + | 941948 | 950455 | 941978 | 950022 | 15 | 941948,942150,945723,945967,946132,946523,946770,947521,947734,948307,948632,948946,949279,949762,949888, | 942061,942250,945870,946048,946453,946655,946851,947597,947871,948457,948773,949087,949498,949811,950455, | 0 | | cmpl | cmpl | 0,2,0,0,0,0,0,0,1,0,0,0,0,0,1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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