Schema for wgEncodeGencodeCompV49

Database: hg38 Primary Table: wgEncodeGencodeCompV49 Row Count: 516,441 Data last updated: 2025-09-08
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`name`	ENST00000832824.1	`varchar(255)`	Name of gene (usually transcript_id from GTF)
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	+ or - for strand
`txStart`	11120	`int(10) unsigned`	Transcription start position (or end position for minus strand item)
`txEnd`	14413	`int(10) unsigned`	Transcription end position (or start position for minus strand item)
`cdsStart`	11120	`int(10) unsigned`	Coding region start (or end position for minus strand item)
`cdsEnd`	11120	`int(10) unsigned`	Coding region end (or start position for minus strand item)
`exonCount`	4	`int(10) unsigned`	Number of exons
`exonStarts`	11120,12009,12612,13452,	`longblob`	Exon start positions (or end positions for minus strand item)
`exonEnds`	11211,12227,12721,14413,	`longblob`	Exon end positions (or start positions for minus strand item)
`score`	0	`int(11)`	score
`name2`	DDX11L16	`varchar(255)`	Alternate name (e.g. gene_id from GTF)
`cdsStartStat`	none	`enum('none', 'unk', 'incmpl', 'cmpl')`	Status of CDS start annotation (none, unknown, incomplete, or complete)
`cdsEndStat`	none	`enum('none', 'unk', 'incmpl', 'cmpl')`	Status of CDS end annotation (none, unknown, incomplete, or complete)
`exonFrames`	-1,-1,-1,-1,	`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.

Connected Tables and Joining Fields


	hg38.wgEncodeGencodeAttrsV49.transcriptId (via wgEncodeGencodeCompV49.name)

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	ENST00000832824.1	chr1	+	11120	14413	11120	11120	4	11120,12009,12612,13452,	11211,12227,12721,14413,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832825.1	chr1	+	11124	14405	11124	11124	4	11124,12009,12612,13402,	11211,12227,12721,14405,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832826.1	chr1	+	11409	14413	11409	11409	4	11409,12009,12594,13482,	11671,12227,12721,14413,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832827.1	chr1	+	11410	14413	11410	11410	4	11410,12009,12612,13482,	11671,12227,12721,14413,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832828.1	chr1	+	11425	14409	11425	11425	4	11425,12009,12612,13220,	11671,12227,12721,14409,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832829.1	chr1	+	11769	14416	11769	11769	4	11769,12009,12612,13482,	11844,12227,12721,14416,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832830.1	chr1	+	11818	14413	11818	11818	4	11818,12009,12612,13482,	11844,12227,12697,14413,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832837.1	chr1	+	11822	14406	11822	11822	4	11822,12009,12594,13220,	11844,12227,12721,14406,	DDX11L16	none	none	-1,-1,-1,-1,
585	ENST00000832836.1	chr1	+	11823	14409	11823	11823	3	11823,12009,13482,	11844,12697,14409,	DDX11L16	none	none	-1,-1,-1,
585	ENST00000832832.1	chr1	+	11823	14413	11823	11823	4	11823,12009,12612,13486,	11844,12227,12721,14413,	DDX11L16	none	none	-1,-1,-1,-1,

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