Non-Mouse RefSeq Gene
 

Non-Mouse RefSeq Gene PAX9

RefSeq: NM_001372076.1   Status: Reviewed
Description: Homo sapiens paired box 9 (PAX9), transcript variant 1, mRNA.
Organism: Homo sapiens
UCSC browser: NM_001372076 on Human (hg38)
CDS: completeness unknown
OMIM: 167416
Entrez Gene: 5083
PubMed on Gene: PAX9
PubMed on Product: paired box protein Pax-9

Summary of PAX9

This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.

mRNA/Genomic Alignments

BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |  2419   86.9%         12     ++  56742419  56759601          NM_001372076     1  4166  4166
Position: chr12:56742419-56759601
Genomic Size: 17183
Strand: +
Gene Symbol: PAX9
CDS Start: 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