Schema for RefSeq Genes - RefSeq Genes
  Database: hg38    Primary Table: refGene    Row Count: 64,537   Data last updated: 2022-01-31
fieldexampleSQL type info
bin 585smallint(5) unsigned range
name NR_046018varchar(255) values
chrom chr1varchar(255) values
strand +char(1) values
txStart 11873int(10) unsigned range
txEnd 14409int(10) unsigned range
cdsStart 14409int(10) unsigned range
cdsEnd 14409int(10) unsigned range
exonCount 3int(10) unsigned range
exonStarts 11873,12612,13220,longblob  
exonEnds 12227,12721,14409,longblob  
score 0int(11) range
name2 DDX11L1varchar(255) values
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
exonFrames -1,-1,-1,longblob  

Connected Tables and Joining Fields
        hg38.ccdsInfo.mrnaAcc (via refGene.name)
      hg38.knownToRefSeq.value (via refGene.name)
      hg38.refFlat.name (via refGene.name)
      hg38.refSeqAli.qName (via refGene.name)
      hg38.wgEncodeGencodeRefSeqV25.rnaAcc (via refGene.name)
      hg38.wgEncodeGencodeRefSeqV28.rnaAcc (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NR_046018chr1+11873144091440914409311873,12612,13220,12227,12721,14409,0DDX11L1unkunk-1,-1,-1,
585NR_024540chr1-143612937029370293701114361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,0WASH7Punkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NR_106918chr1-17368174361743617436117368,17436,0MIR6859-1unkunk-1,
585NR_107062chr1-17368174361743617436117368,17436,0MIR6859-2unkunk-1,
585NR_107063chr1-17368174361743617436117368,17436,0MIR6859-3unkunk-1,
585NR_128720chr1-17368174361743617436117368,17436,0MIR6859-4unkunk-1,
585NR_036051chr1+30365305033050330503130365,30503,0MIR1302-2unkunk-1,
585NR_036266chr1+30365305033050330503130365,30503,0MIR1302-9unkunk-1,
585NR_036267chr1+30365305033050330503130365,30503,0MIR1302-10unkunk-1,
585NR_036268chr1+30365305033050330503130365,30503,0MIR1302-11unkunk-1,

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

RefSeq Genes (refGene) Track Description
 

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.

  • 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. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.
  • 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. PMID: 11932250; PMC: PMC187518

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. PMID: 15608248; PMC: PMC539979