Schema for Other RefSeq - Non-Human RefSeq Genes

Database: hg19 Primary Table: xenoRefGene Row Count: 128,312
Format description: A gene prediction with some additional info.

field	example	SQL type	info	description
`bin`	108	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`name`	NM_001107618	`varchar(255)`	values	Name of gene (usually transcript_id from GTF)
`chrom`	chr6	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	37604881	`int(10) unsigned`	range	Transcription start position
`txEnd`	37664946	`int(10) unsigned`	range	Transcription end position
`cdsStart`	37605143	`int(10) unsigned`	range	Coding region start
`cdsEnd`	37664587	`int(10) unsigned`	range	Coding region end
`exonCount`	18	`int(10) unsigned`	range	Number of exons
`exonStarts`	37604881,37604971,37605980,...	`longblob`		Exon start positions
`exonEnds`	37604947,37605235,37606089,...	`longblob`		Exon end positions
`score`	0	`int(11)`	range
`name2`	Mdga1	`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`	-1,1,0,1,1,0,0,1,2,1,1,1,0,...	`longblob`		Exon frame {0,1,2}, or -1 if no frame for exon

      hg19.all_est.qName (via xenoRefGene.name)
      hg19.all_mrna.qName (via xenoRefGene.name)
      hg19.gbCdnaInfo.acc (via xenoRefGene.name)
      hg19.gbMiscDiff.acc (via xenoRefGene.name)
      hg19.gbSeq.acc (via xenoRefGene.name)
      hg19.gbStatus.acc (via xenoRefGene.name)
      hg19.gbWarn.acc (via xenoRefGene.name)
      hg19.imageClone.acc (via xenoRefGene.name)
      hg19.refGene.name (via xenoRefGene.name)
      hg19.refSeqAli.qName (via xenoRefGene.name)
      hg19.seq.acc (via xenoRefGene.name)
      hg19.xenoMrna.qName (via xenoRefGene.name)
      hg19.xenoRefFlat.name (via xenoRefGene.name)
      hg19.xenoRefSeqAli.qName (via xenoRefGene.name)

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
108	NM_001107618	chr6	-	37604881	37664946	37605143	37664587	18	37604881,37604971,37605980,37606312,37611623,37612278,37613972,37614948,37616757,37617887,37619786,37622049,37622575,37623475,37 ...	37604947,37605235,37606089,37606443,37611725,37612426,37614151,37615100,37617040,37618181,37620116,37622319,37622708,37623672,37 ...	Mdga1	cmpl	cmpl	-1,1,0,1,1,0,0,1,2,1,1,1,0,1,0,1,0,-1,
2264	NM_001033286	chr1	-	220083950	220101786	220088924	220101782	8	220083950,220084297,220087701,220088130,220088924,220091596,220100369,220101337,	220084046,220084333,220087852,220088175,220089290,220091836,220100466,220101786,	Slc30a10	cmpl	incmpl	-1,-1,-1,-1,1,1,0,0,
140	NM_001095939	chr11	-	70317243	70563832	70318973	70563832	22	70317243,70318973,70319261,70319387,70331426,70331672,70332119,70332407,70332542,70332635,70332710,70333058,70333613,70335443,70 ...	70317305,70319249,70319312,70319528,70331636,70332026,70332275,70332515,70332602,70332680,70332803,70333601,70333832,70335453,70 ...	shank2	cmpl	cmpl	-1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,1,2,1,0,
1692	NM_001095210	chr8	+	145133631	145135501	145133631	145135501	3	145133631,145134845,145135144,	145133802,145135052,145135501,	exosc4	cmpl	incmpl	0,0,0,
612	NM_001020571	chr17	+	3558518	3563639	3558518	3563639	7	3558518,3558721,3559780,3559966,3561400,3563151,3563529,	3558641,3558726,3559877,3560089,3561469,3563269,3563639,	ctns	incmpl	incmpl	0,0,2,0,0,0,1,
593	NM_001113702	chr6_apd_hap1	+	1150243	1153133	1150243	1153119	8	1150243,1150421,1150930,1151787,1152169,1152720,1152894,1153112,	1150291,1150689,1151202,1152062,1152220,1152752,1152935,1153133,	SLA-2	incmpl	cmpl	0,0,1,0,1,2,1,2,
90	NM_001109755	chr7	-	17833669	17980126	17833669	17937071	26	17833669,17836449,17838312,17838630,17843038,17854456,17855804,17861131,17865644,17869632,17873674,17874383,17879429,17885217,17 ...	17833916,17836562,17838380,17838777,17843203,17854567,17855912,17861271,17865714,17869670,17873807,17874488,17879623,17885317,17 ...	SNX13	incmpl	incmpl	1,2,0,0,0,0,0,1,0,1,0,0,1,0,1,0,0,1,0,0,0,1,0,2,1,-1,
585	NM_001034099	chr1	-	34921	36077	34921	35736	2	34921,35719,	35174,36077,	F379	cmpl	incmpl	2,0,
1291	NM_001007574	chr1	+	92634447	92650065	92634518	92648169	20	92634447,92636953,92642385,92642619,92642781,92643045,92643388,92643866,92645821,92646475,92646876,92647245,92647938,92648728,92 ...	92634549,92637017,92642550,92642645,92642955,92643084,92643412,92644008,92646075,92646598,92647218,92647776,92648172,92648857,92 ...	A830010M20Rik	cmpl	cmpl	0,2,0,0,0,0,1,0,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1,
620	NM_001000542	chr11	+	4673768	4674705	4673768	4674705	1	4673768,	4674705,	Olr63	incmpl	incmpl	0,

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

Description

This track shows known protein-coding and non-protein-coding genes for organisms other than human, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated daily.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page.

Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely.
Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature.
Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box.

Methods

The RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept.

Credits

This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project.

References

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.