Non-Mouse RefSeq Gene
 

Non-Mouse RefSeq Gene pax1a

RefSeq: NM_001172049.1   Status: Provisional
Description: Oryzias latipes paired box 1a (pax1a), mRNA.
Organism: Oryzias latipes
UCSC browser: NM_001172049 on Medaka (oryLat2)
Entrez Gene: 100335144
PubMed on Gene: pax1a
PubMed on Product: paired box protein Pax-1

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |   474   74.3%         12     ++  56743370  56743850          NM_001172049   264   738  1469
browser |   621   74.0%          2     ++ 147207652 147208272          NM_001172049   252   872  1469
Position: chr12:56743370-56743850
Genomic Size: 481
Strand: +
Gene Symbol: pax1a
CDS Start: not complete
CDS End: not complete

Position: chr2:147207652-147208272
Genomic Size: 621
Strand: +
Gene Symbol: pax1a
CDS Start: not complete
CDS End: not complete

Links to sequence:

Data schema/format description and download

Go to Other RefSeq track controls

Data last updated at UCSC: 2020-08-18

Description

The RefSeq mRNAs gene track for the mouse (Jun. 2020 (GRCm39/mm39)) genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.

Track statistics summary

Total genome size: 2,654,624,157 (not counting gaps)
Gene count: 22,442
Bases in genes: 838,462,469 (txStart to txEnd)
Genes percent genome coverage: % 31.585
Bases in exons: 53,564,706
Exons percent genome coverage: % 2.018

Search tips

Please note, the name searching system is not completely case insensitive. When in doubt, enter search names in all lower case to find gene names.

Methods

The mRNAs were aligned against the mouse (Jun. 2020 (GRCm39/mm39)) genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.

Specifically, the translated blat command is: 

blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl

where target.fa is one of the chromosome sequence of the genome assembly,
and the query.fa is the mRNAs from RefSeq
The resulting PSL outputs are filtered: 
pslCDnaFilter -minId=0.35 -minCover=0.25  -globalNearBest=0.0100 -minQSize=20 \
  -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap \
    all.results.psl mm39.xenoRefGene.psl
The filtered mm39.xenoRefGene.psl is converted to genePred data to display for this track.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518