Non-Mouse RefSeq Gene
 

Non-Mouse RefSeq Gene pax9

RefSeq: NM_131298.1   Status: Provisional
Description: Danio rerio paired box 9 (pax9), mRNA.
Organism: Danio rerio
UCSC browser: NM_131298 on Zebrafish (danRer11)
Entrez Gene: 30558
PubMed on Gene: pax9
PubMed on Product: paired box protein Pax-9

mRNA/Genomic Alignments

BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |   879   70.9%         12     ++  56743358  56756692             NM_131298   148  1176  1939
Position: chr12:56743358-56756692
Genomic Size: 13335
Strand: +
Gene Symbol: pax9
CDS Start: not complete
CDS End: 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