Schema for Geneid Genes - Geneid Gene Predictions |
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Database: mm10 Primary Table: geneid Row Count: 36,771 Data last updated: 2015-06-26
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 609 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | chr1_1.1 | 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 | 3216021 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3226700 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 3216021 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 3226700 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 2 | int(10) unsigned | range | Number of exons |
| exonStarts | 3216021,3226633, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3216968,3226700, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | chr1_1 | 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, | 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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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 | chr1_1.1 | chr1 | - | 3216021 | 3226700 | 3216021 | 3226700 | 2 | 3216021,3226633, | 3216968,3226700, | 0 | chr1_1 | cmpl | cmpl | 1,0, |
| 76 | chr1_2.1 | chr1 | - | 3366315 | 3431648 | 3366315 | 3431648 | 4 | 3366315,3401410,3421701,3431490, | 3366478,3401438,3421901,3431648, | 0 | chr1_2 | cmpl | cmpl | 2,1,2,0, |
| 76 | chr1_3.1 | chr1 | + | 3531794 | 3582227 | 3531794 | 3582227 | 5 | 3531794,3531922,3532304,3553600,3582101, | 3531902,3532277,3532716,3553745,3582227, | 0 | chr1_3 | cmpl | cmpl | 0,0,1,2,0, |
| 76 | chr1_4.1 | chr1 | - | 3637517 | 3729879 | 3637517 | 3729879 | 5 | 3637517,3670551,3674518,3706173,3729866, | 3637764,3671049,3674537,3706200,3729879, | 0 | chr1_4 | cmpl | cmpl | 2,2,1,1,0, |
| 9 | chr1_5.1 | chr1 | - | 3999556 | 4284883 | 3999556 | 4284883 | 22 | 3999556,4007655,4019069,4024735,4041887,4056161,4092616,4120014,4142611,4143170,4147811,4148653,4170204,4197533,4206659,4226610, ... | 3999617,4007737,4019148,4024890,4042107,4056278,4092780,4120073,4142905,4143238,4147963,4148744,4170404,4197641,4206837,4226934, ... | 0 | chr1_5 | cmpl | cmpl | 2,1,0,1,0,0,1,2,2,0,1,0,1,1,0,0,0,1,0,0,1,0, |
| 618 | chr1_6.1 | chr1 | - | 4344599 | 4377998 | 4344599 | 4377998 | 4 | 4344599,4351909,4352201,4377860, | 4350013,4352081,4352837,4377998, | 0 | chr1_6 | cmpl | cmpl | 1,0,0,0, |
| 619 | chr1_7.1 | chr1 | - | 4491715 | 4493406 | 4491715 | 4493406 | 2 | 4491715,4493099, | 4492668,4493406, | 0 | chr1_7 | cmpl | cmpl | 1,0, |
| 619 | chr1_8.1 | chr1 | + | 4497119 | 4536211 | 4497119 | 4536211 | 5 | 4497119,4522787,4524677,4525859,4536077, | 4497206,4523132,4525329,4526024,4536211, | 0 | chr1_8 | cmpl | cmpl | 0,0,0,1,1, |
| 620 | chr1_9.1 | chr1 | + | 4603383 | 4610830 | 4603383 | 4610830 | 2 | 4603383,4610506, | 4603464,4610830, | 0 | chr1_9 | cmpl | cmpl | 0,0, |
| 620 | chr1_10.1 | chr1 | - | 4687975 | 4689404 | 4687975 | 4689404 | 3 | 4687975,4688473,4689296, | 4688283,4689026,4689404, | 0 | chr1_10 | cmpl | cmpl | 1,0,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Geneid Genes (geneid) Track Description
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Description
This track shows gene predictions from the
geneid program developed by
Roderic Guigó's Computational Biology of RNA Processing
group which is part of the
Centre de Regulació Genòmica
(CRG) in Barcelona, Catalunya, Spain.
Methods
Geneid is a program to predict genes in anonymous genomic sequences designed
with a hierarchical structure. In the first step, splice sites, start and stop
codons are predicted and scored along the sequence using Position Weight Arrays
(PWAs). Next, exons are built from the sites. Exons are scored as the sum of the
scores of the defining sites, plus the the log-likelihood ratio of a
Markov Model for coding DNA. Finally, from the set of predicted exons, the gene
structure is assembled, maximizing the sum of the scores of the assembled exons.
Credits
Thanks to Computational Biology of RNA Processing
for providing these data.
References
Blanco E, Parra G, Guigó R.
Using geneid to identify genes.
Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3.
PMID: 18428791
Parra G, Blanco E, Guigó R.
GeneID in Drosophila.
Genome Res. 2000 Apr;10(4):511-5.
PMID: 10779490; PMC: PMC310871
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