Schema for Geneid Genes - Geneid Gene Predictions
  Database: hg38    Primary Table: geneid    Row Count: 35,910   Data last updated: 2015-07-31
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name chr1_1.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 16857int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 35736int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 16857int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 35736int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 16857,17232,17605,17914,182...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 17055,17257,17742,18061,183...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 chr1_1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,2,0,0,2,1,0,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585chr1_1.1chr1-16857357361685735736716857,17232,17605,17914,18267,24737,35720,17055,17257,17742,18061,18379,24891,35736,0chr1_1incmplcmpl0,2,0,0,2,1,0,
73chr1_2.1chr1-1208161954381208161954389120816,129054,164765,185490,187375,187754,188129,188790,195262,120932,129223,164791,185559,187577,187779,188266,188902,195438,0chr1_2cmplcmpl1,0,1,1,0,2,0,2,0,
586chr1_3.1chr1-2585402589032585402589031258540,258903,0chr1_3cmplcmpl0,
73chr1_4.1chr1+3538493936663538493936663353849,368835,393552,354030,370016,393666,0chr1_4cmplcmpl0,1,0,
588chr1_5.1chr1-4507394851814507394851812450739,485039,451716,485181,0chr1_5cmplcmpl1,0,
588chr1_6.1chr1+4876734976474876734976472487673,497518,487832,497647,0chr1_6cmplcmpl0,0,
589chr1_7.1chr1+6232736305846232736305843623273,629685,630393,623383,630089,630584,0chr1_7cmplcmpl0,2,1,
590chr1_8.1chr1-6857157814826857157814826685715,720031,736386,739802,778738,781470,686692,720249,736602,740035,779293,781482,0chr1_8cmplcmpl1,2,2,0,0,0,
591chr1_9.1chr1+7888187889747888187889741788818,788974,0chr1_9cmplcmpl0,
591chr1_10.1chr1+7896687903887896687903881789668,790388,0chr1_10cmplcmpl0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Geneid Genes (geneid) Track Description
 

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