Schema for xenoRefGene
  Database: calJac1    Primary Table: xenoRefGene    Row Count: 519,237   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001002980varchar(255) Name of gene (usually transcript_id from GTF)
chrom Contig1503varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 237242int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 264639int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 237242int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 264639int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned Number of exons
exonStarts 237242,258325,258343,260897...longblob Exon start positions (or end positions for minus strand item)
exonEnds 237290,258343,258427,260927...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 COL7A1varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 2,0,0,0,0,0,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.

To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.

Connected Tables and Joining Fields
        calJac1.all_est.qName (via xenoRefGene.name)
      calJac1.all_mrna.qName (via xenoRefGene.name)
      calJac1.refGene.name (via xenoRefGene.name)
      calJac1.refSeqAli.qName (via xenoRefGene.name)
      calJac1.xenoMrna.qName (via xenoRefGene.name)
      calJac1.xenoRefFlat.name (via xenoRefGene.name)
      calJac1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
73NM_001002980Contig1503+2372422646392372422646396237242,258325,258343,260897,262440,264600,237290,258343,258427,260927,262470,264639,0COL7A1incmplincmpl2,0,0,0,0,0,
586NM_001170562Contig1316+1319061338581319061323025131906,132252,133480,133644,133716,132248,132303,133626,133659,133858,0Peg12incmplcmpl0,1,-1,-1,-1,
585NM_001109900Contig9753+52386737075238673694952386,55207,56240,57367,59465,62871,67099,69169,73662,52464,55376,56356,57445,59588,62983,67252,69238,73707,0Akr1c15cmplcmpl0,2,1,0,0,0,0,0,1,
73NM_001109888Contig104-24453536503624516036481722244535,244970,245160,246676,248435,248777,250523,251910,253574,257901,260349,260688,267731,268546,268740,270453,270620,271272,27 ...244580,244985,245307,246802,248557,248900,250658,252044,253665,258051,260485,260854,267849,268644,268777,270530,270711,271382,27 ...0Ptprccmplincmpl-1,-1,0,0,0,0,0,1,0,0,2,1,0,1,0,1,0,1,0,2,0,-1,
586NM_001374692Contig775-1719221720151720151720151171922,172015,0POMT1unkunk-1,
585NM_001354018Contig2132-273241162792732439246827324,38958,39204,107597,113108,113491,115572,116049,27554,39086,39246,107848,113246,113545,115963,116279,0NETO1incmplincmpl0,1,1,-1,-1,-1,-1,-1,
585NM_001166466Contig4641+539247155453924682192753924,58142,61872,67395,68026,68366,68479,68532,68721,68761,69059,69139,69157,69196,69264,69354,69696,70212,70276,70365,70418,70 ...54039,58364,61935,67531,68356,68410,68521,68659,68749,68822,69070,69148,69170,69211,69295,69366,69710,70249,70333,70395,70457,70 ...0Spock1incmplcmpl0,1,1,1,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001271131Contig3659+70800711777080071169170800,71177,0Mrpl14incmplcmpl0,
587NM_001346628Contig1304-3532993537973532993537973353299,353488,353665,353383,353653,353797,0drn-1incmplincmpl0,0,0,
73NM_001313478Contig1306-3930128592239301285922339301,207097,285774,39346,207180,285922,0unc-75incmplincmpl0,1,0,

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

Other RefSeq (xenoRefGene) Track Description
 

Description

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

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 mouse genome using blat; those with an alignment of less than 15% were discarded. At least 40 bases must be aligned to DNA that is not repeat masked. 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 1.0% of the best and at least 35% 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