Database: hg19    Primary Table: vegaPseudoGene    Row Count: 11,590
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	OTTHUMT00000362751	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	11868	int(10) unsigned	range	Transcription start position
txEnd	14409	int(10) unsigned	range	Transcription end position
cdsStart	14409	int(10) unsigned	range	Coding region start
cdsEnd	14409	int(10) unsigned	range	Coding region end
exonCount	3	int(10) unsigned	range	Number of exons
exonStarts	11868,12612,13220,	longblob		Exon start positions
exonEnds	12227,12721,14409,	longblob		Exon end positions
score	0	int(11)	range
name2	RP11-34P13.1	varchar(255)	values	Alternate name (e.g. gene_id from GTF)
cdsStartStat	none	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
cdsEndStat	none	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
exonFrames	-1,-1,-1,	longblob		Exon frame {0,1,2}, or -1 if no frame for exon

      hg19.vegaGene.name (via vegaPseudoGene.name)
      hg19.vegaGtp.transcript (via vegaPseudoGene.name)
      hg19.vegaPep.name (via vegaPseudoGene.name)

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
585	OTTHUMT00000362751	chr1	+	11868	14409	14409	14409	3	11868,12612,13220,	12227,12721,14409,	0	RP11-34P13.1	none	none	-1,-1,-1,
585	OTTHUMT00000002844	chr1	+	12009	13670	13670	13670	6	12009,12178,12612,12974,13220,13452,	12057,12227,12697,13052,13374,13670,	0	RP11-34P13.1	none	none	-1,-1,-1,-1,-1,-1,
585	OTTHUMT00000002839	chr1	-	14403	29570	29570	29570	11	14403,15004,15795,16606,16857,17232,17605,17914,18267,24737,29533,	14501,15038,15947,16765,17055,17368,17742,18061,18366,24891,29570,	0	RP11-34P13.2	none	none	-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585	OTTHUMT00000003224	chr1	+	62947	63887	63887	63887	1	62947,	63887,	0	OR4G11P	none	none	-1,
586	OTTHUMT00000003691	chr1	+	131103	133923	133923	133923	1	131103,	133923,	0	RP11-34P13.10	none	none	-1,
586	OTTHUMT00000007034	chr1	-	135246	138039	138039	138039	2	135246,137568,	136006,138039,	0	RP11-34P13.11	none	none	-1,-1,
586	OTTHUMT00000007241	chr1	-	228318	228775	228775	228775	1	228318,	228775,	0	AP006222.1	none	none	-1,
587	OTTHUMT00000008000	chr1	+	326095	328112	328112	328112	2	326095,327347,	326569,328112,	0	RP4-669L17.8	none	none	-1,-1,
587	OTTHUMT00000127609	chr1	-	329425	332243	332243	332243	1	329425,	332243,	0	RP4-669L17.9	none	none	-1,
587	OTTHUMT00000007996	chr1	+	329783	334271	334271	334271	2	329783,334128,	329976,334271,	0	RP4-669L17.4	none	none	-1,-1,

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

Description and Methods

This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Human Genome Annotation project:

• Vega Protein Coding Annotations
• Vega Annotated Pseudogenes and Immunoglobulin Segments

The following information is an excerpt from the Vertebrate Genome Annotation home page:

"The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only."

"In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery."

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here.

Credits

Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here.