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PAX9 paired box 9 [ Homo sapiens (human) ]

Gene ID: 5083, updated on 3-May-2025
Official Symbol
PAX9provided by HGNC
Official Full Name
paired box 9provided by HGNC
Primary source
HGNC:HGNC:8623
See related
Ensembl:ENSG00000198807 MIM:167416; AllianceGenome:HGNC:8623
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
STHAG3
Summary
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]
Expression
Biased expression in esophagus (RPKM 29.7), salivary gland (RPKM 11.4) and 1 other tissue See more
Orthologs
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See PAX9 in Genome Data Viewer
Location:
14q13.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (36657568..36679362)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (30846888..30868704)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (37126773..37148567)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37049589-37050399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37050400-37051210 Neighboring gene RN7SK pseudogene 257 Neighboring gene NK2 homeobox 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37116557-37117386 Neighboring gene uncharacterized LOC105370455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37123150-37123888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:37125365-37126102 Neighboring gene PAX9 promoter region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37131533-37132044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37132045-37132554 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:37132555-37133065 Neighboring gene NANOG hESC enhancer GRCh37_chr14:37153788-37154289 Neighboring gene solute carrier family 25 member 21 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:37271122-37272321 Neighboring gene NANOG hESC enhancer GRCh37_chr14:37274394-37274895 Neighboring gene uncharacterized LOC107984668 Neighboring gene microRNA 4503

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associated conditions

Description Tests
Tooth agenesis, selective, 3
MedGen: C1970291 OMIM: 604625 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-07-08)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-08)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
paired box protein Pax-9
Names
paired domain gene 9

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013357.1 RefSeqGene

    Range
    9293..26795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001372076.1NP_001359005.1  paired box protein Pax-9

    Status: REVIEWED

    Source sequence(s)
    AL079303
    Consensus CDS
    CCDS9662.1
    UniProtKB/Swiss-Prot
    P55771, Q99582, Q9UQR4
    UniProtKB/TrEMBL
    B2R940, Q2L4T1
    Related
    ENSP00000355245.6, ENST00000361487.7
    Conserved Domains (1) summary
    cd00131
    Location:6131
    PAX; Paired Box domain
  2. NM_006194.4NP_006185.1  paired box protein Pax-9

    See identical proteins and their annotated locations for NP_006185.1

    Status: REVIEWED

    Source sequence(s)
    AB248958, AL079303, BC001159, DB196800, DB233208
    Consensus CDS
    CCDS9662.1
    UniProtKB/Swiss-Prot
    P55771, Q99582, Q9UQR4
    UniProtKB/TrEMBL
    B2R940, Q2L4T1
    Related
    ENSP00000384817.2, ENST00000402703.6
    Conserved Domains (1) summary
    cd00131
    Location:6131
    PAX; Paired Box domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    36657568..36679362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    30846888..30868704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)