Database: hg19    Primary Table: geneid    Row Count: 33,428
Format description: A gene prediction with some additional info.

field	example	SQL type	info	description
bin	585	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	14695	int(10) unsigned	range	Transcription start position
txEnd	35736	int(10) unsigned	range	Transcription end position
cdsStart	14695	int(10) unsigned	range	Coding region start
cdsEnd	35736	int(10) unsigned	range	Coding region end
exonCount	10	int(10) unsigned	range	Number of exons
exonStarts	14695,14969,15795,16853,172...	longblob		Exon start positions
exonEnds	14829,15038,15891,17055,172...	longblob		Exon end positions
score	0	int(11)	range
name2	chr1_1	varchar(255)	values	Alternate name (e.g. gene_id from GTF)
cdsStartStat	cmpl	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
cdsEndStat	cmpl	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
exonFrames	1,1,1,0,2,0,0,2,1,0,	longblob		Exon frame {0,1,2}, or -1 if no frame for exon

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	chr1_1.1	chr1	-	14695	35736	14695	35736	10	14695,14969,15795,16853,17232,17605,17914,18267,24737,35720,	14829,15038,15891,17055,17257,17742,18061,18379,24891,35736,	0	chr1_1	cmpl	cmpl	1,1,1,0,2,0,0,2,1,0,
586	chr1_2.1	chr1	-	228291	228654	228291	228654	1	228291,	228654,	0	chr1_2	cmpl	cmpl	0,
586	chr1_3.1	chr1	+	234205	234559	234205	234559	1	234205,	234559,	0	chr1_3	cmpl	cmpl	0,
587	chr1_4.1	chr1	-	321689	331663	321689	331663	2	321689,331504,	321818,331663,	0	chr1_4	cmpl	cmpl	0,0,
587	chr1_5.1	chr1	+	334155	368597	334155	368597	2	334155,367620,	334297,368597,	0	chr1_5	cmpl	cmpl	0,1,
589	chr1_6.1	chr1	+	558653	569756	558653	569756	3	558653,567505,569499,	558763,567819,569756,	0	chr1_6	cmpl	cmpl	0,2,1,
73	chr1_7.1	chr1	-	621095	805472	621095	805472	9	621095,655411,671766,675182,714118,741178,770817,787588,805150,	622072,655629,671982,675415,714673,741271,770978,787786,805472,	0	chr1_7	cmpl	cmpl	1,2,2,0,0,0,1,1,0,
591	chr1_8.1	chr1	+	808832	809729	808832	809729	1	808832,	809729,	0	chr1_8	cmpl	cmpl	0,
591	chr1_9.1	chr1	+	857387	879533	857387	879533	13	857387,858952,860071,865553,866418,871151,874419,874651,877789,877938,878551,879077,879287,	857398,859156,860328,865716,866469,871276,874509,874792,877868,878438,878757,879188,879533,	0	chr1_9	cmpl	cmpl	0,2,2,1,2,2,1,1,1,2,1,0,0,
591	chr1_10.1	chr1	-	880073	894620	880073	894620	17	880073,880897,881552,881781,883510,883869,886506,887379,887791,889161,889383,891302,891474,892273,892478,894308,894594,	880180,881033,881666,881925,883612,883983,886618,887519,887980,889272,889462,891393,891595,892423,892653,894461,894620,	0	chr1_10	cmpl	cmpl	1,0,0,0,0,0,2,0,0,0,2,1,0,0,2,2,0,

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

Description

This track shows gene predictions from the geneid program developed at the Genome Bionformatics Laboratory (GBL), which is part of the Grup de Recerca en Informàtica Biomèdica (GRIB) at the Institut Municipal d'Investigació Mèdica (IMIM) / Centre de Regulació Genòmica (CRG) in Barcelona."

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 GBL for providing these data.