Database: hg19    Primary Table: refGene    Row Count: 36,002
Format description: A gene prediction with some additional info.

field	example	SQL type	info	description
bin	971	smallint(5) unsigned	range	Indexing field to speed chromosome range queries.
name	NR_024227	varchar(255)	values	Name of gene (usually transcript_id from GTF)
chrom	chr19	varchar(255)	values	Reference sequence chromosome or scaffold
strand	-	char(1)	values	+ or - for strand
txStart	50595745	int(10) unsigned	range	Transcription start position
txEnd	50595866	int(10) unsigned	range	Transcription end position
cdsStart	50595866	int(10) unsigned	range	Coding region start
cdsEnd	50595866	int(10) unsigned	range	Coding region end
exonCount	1	int(10) unsigned	range	Number of exons
exonStarts	50595745,	longblob		Exon start positions
exonEnds	50595866,	longblob		Exon end positions
score	0	int(11)	range
name2	SNAR-A6	varchar(255)	values	Alternate name (e.g. gene_id from GTF)
cdsStartStat	unk	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
cdsEndStat	unk	enum('none','unk','incmpl','cmpl')	values	enum('none','unk','incmpl','cmpl')
exonFrames	-1,	longblob		Exon frame {0,1,2}, or -1 if no frame for exon

      hg19.all_est.qName (via refGene.name)
      hg19.all_mrna.qName (via refGene.name)
      hg19.ccdsInfo.mrnaAcc (via refGene.name)
      hg19.gbCdnaInfo.acc (via refGene.name)
      hg19.gbMiscDiff.acc (via refGene.name)
      hg19.gbSeq.acc (via refGene.name)
      hg19.gbStatus.acc (via refGene.name)
      hg19.gbWarn.acc (via refGene.name)
      hg19.imageClone.acc (via refGene.name)
      hg19.kgXref.refseq (via refGene.name)
      hg19.knownToRefSeq.value (via refGene.name)
      hg19.mrnaOrientInfo.name (via refGene.name)
      hg19.refFlat.name (via refGene.name)
      hg19.refLink.mrnaAcc (via refGene.name)
      hg19.refSeqAli.qName (via refGene.name)
      hg19.refSeqStatus.mrnaAcc (via refGene.name)
      hg19.refSeqSummary.mrnaAcc (via refGene.name)
      hg19.seq.acc (via refGene.name)
      hg19.xenoMrna.qName (via refGene.name)
      hg19.xenoRefGene.name (via refGene.name)
      hg19.xenoRefSeqAli.qName (via refGene.name)

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	score	name2	cdsStartStat	cdsEndStat	exonFrames
971	NR_024227	chr19	-	50595745	50595866	50595866	50595866	1	50595745,	50595866,	0	SNAR-A6	unk	unk	-1,
971	NR_024227	chr19	-	50601082	50601203	50601203	50601203	1	50601082,	50601203,	0	SNAR-A6	unk	unk	-1,
1	NM_001033605	chr7	+	33169151	33645680	33185864	33644838	22	33169151,33185853,33192312,33195249,33217089,33296847,33303901,33312623,33313438,33376052,33380508,33384192,33388679,33390830,33 ...	33169653,33185976,33192463,33195314,33217203,33297022,33303986,33312807,33313568,33376234,33380585,33384246,33388782,33390935,33 ...	0	BBS9	cmpl	cmpl	-1,0,1,2,1,1,2,0,1,2,1,0,0,1,1,1,1,0,0,0,1,1,
1026	NM_001167609	chr12	+	57853933	57866045	57857474	57865844	11	57853933,57857447,57858485,57858893,57859389,57859570,57860022,57861115,57861776,57863213,57864099,	57853984,57857574,57858651,57859038,57859479,57859708,57860172,57861280,57862007,57863481,57866045,	0	GLI1	cmpl	cmpl	-1,0,1,2,0,0,0,0,0,0,1,
705	NM_024329	chr1	+	15736390	15756839	15736467	15755220	4	15736390,15752366,15753645,15755088,	15736775,15752514,15753780,15756839,	0	EFHD2	cmpl	cmpl	0,2,0,0,
768	NM_024328	chr14	+	24025197	24028786	24025966	24028049	2	24025197,24027903,	24026513,24028786,	0	THTPA	cmpl	cmpl	0,1,
1379	NM_024326	chr10	+	104179570	104182893	104180886	104182750	4	104179570,104181110,104181543,104182560,	104180939,104181264,104182049,104182893,	0	FBXL15	cmpl	cmpl	0,2,0,2,
826	NM_138275	chr6	+	31691160	31692850	31691160	31692850	4	31691160,31691415,31692541,31692746,	31691221,31691763,31692621,31692850,	0	C6orf25	cmpl	incmpl	0,1,1,0,
609	NM_138275	chr6_cox_hap2	+	3200777	3202467	3200777	3202467	4	3200777,3201032,3202158,3202363,	3200838,3201380,3202238,3202467,	0	C6orf25	cmpl	incmpl	0,1,1,0,
607	NM_138275	chr6_dbb_hap3	+	2976730	2978420	2976730	2978420	4	2976730,2976985,2978111,2978316,	2976791,2977333,2978191,2978420,	0	C6orf25	cmpl	incmpl	0,1,1,0,

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

Description

The RefSeq Genes track shows known human protein-coding and non-protein-coding genes 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. This page is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu.

• 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

RefSeq 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 0.1% of the best and at least 96% 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.

Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.