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Aliases for PAX1 Gene

Aliases for PAX1 Gene

  • Paired Box 1 2 3 5
  • Paired Box Gene 1 2 3
  • HUP48 3 4
  • Paired Domain Gene HuP48 3
  • OFC2 3

External Ids for PAX1 Gene

Previous GeneCards Identifiers for PAX1 Gene

  • GC20P021675
  • GC20P021682
  • GC20P021634

Summaries for PAX1 Gene

Entrez Gene Summary for PAX1 Gene

  • This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]

GeneCards Summary for PAX1 Gene

PAX1 (Paired Box 1) is a Protein Coding gene. Diseases associated with PAX1 include otofaciocervical syndrome 2 and otofaciocervical syndrome. An important paralog of this gene is PAX4.

UniProtKB/Swiss-Prot for PAX1 Gene

  • This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity).

Gene Wiki entry for PAX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PAX1 Gene

Genomics for PAX1 Gene

Regulatory Elements for PAX1 Gene

Genomic Location for PAX1 Gene

21,705,659 bp from pter
21,718,486 bp from pter
12,828 bases
Plus strand

Genomic View for PAX1 Gene

Genes around PAX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX1 Gene

Proteins for PAX1 Gene

  • Protein details for PAX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Paired box protein Pax-1
    Protein Accession:
    Secondary Accessions:
    • B4E0D6
    • Q642X9
    • Q6NTC0
    • Q9Y558

    Protein attributes for PAX1 Gene

    534 amino acids
    Molecular mass:
    55499 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH69134.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAU21037.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for PAX1 Gene


neXtProt entry for PAX1 Gene

Proteomics data for PAX1 Gene at MOPED

Post-translational modifications for PAX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PAX1 Gene

Antibody Products

No data available for DME Specific Peptides for PAX1 Gene

Domains & Families for PAX1 Gene

Gene Families for PAX1 Gene

Protein Domains for PAX1 Gene

Suggested Antigen Peptide Sequences for PAX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 paired domain.
  • Contains 1 paired domain.
genes like me logo Genes that share domains with PAX1: view

Function for PAX1 Gene

Molecular function for PAX1 Gene

GENATLAS Biochemistry:
paired box (DNA binding) containing protein 1,with homeo domain,expressed in the sclerotome,controlling chondrogenesis through SHH signaling,involved in the development of vertebral column,homologous to undulated
UniProtKB/Swiss-Prot Function:
This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column (By similarity).
genes like me logo Genes that share phenotypes with PAX1: view

Human Phenotype Ontology for PAX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PAX1 Gene

MGI Knock Outs for PAX1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for PAX1 Gene

Localization for PAX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX1 Gene

Subcellular locations from

Jensen Localization Image for PAX1 Gene COMPARTMENTS Subcellular localization image for PAX1 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for PAX1 Gene

Pathways & Interactions for PAX1 Gene

SuperPathways for PAX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PAX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9671740
GO:0001756 somitogenesis IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007389 pattern specification process IEA --
genes like me logo Genes that share ontologies with PAX1: view

No data available for Pathways by source and SIGNOR curated interactions for PAX1 Gene

Drugs & Compounds for PAX1 Gene

No Compound Related Data Available

Transcripts for PAX1 Gene

mRNA/cDNA for PAX1 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(5) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PAX1 Gene

Paired box 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PAX1 Gene

No ASD Table

Relevant External Links for PAX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PAX1 Gene

mRNA expression in normal human tissues for PAX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX1 Gene

This gene is overexpressed in Esophagus - Mucosa (x8.7), Muscle - Skeletal (x7.6), Thyroid (x7.2), Skin - Sun Exposed (Lower leg) (x5.6), and Minor Salivary Gland (x4.5).

Protein differential expression in normal tissues from HIPED for PAX1 Gene

This gene is overexpressed in Platelet (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PAX1 Gene

SOURCE GeneReport for Unigene cluster for PAX1 Gene Hs.122310

genes like me logo Genes that share expression patterns with PAX1: view

Protein tissue co-expression partners for PAX1 Gene

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for PAX1 Gene

Orthologs for PAX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PAX1 35
  • 88.54 (n)
  • 89.96 (a)
PAX1 36
  • 84 (a)
(Canis familiaris)
Mammalia PAX1 35
  • 89.96 (n)
  • 91.52 (a)
PAX1 36
  • 83 (a)
(Mus musculus)
Mammalia Pax1 35
  • 86.92 (n)
  • 91.7 (a)
Pax1 16
Pax1 36
  • 88 (a)
(Monodelphis domestica)
Mammalia PAX1 36
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia PAX1 36
  • 78 (a)
(Pan troglodytes)
Mammalia PAX1 36
  • 99 (a)
(Gallus gallus)
Aves PAX1 35
  • 79.39 (n)
  • 80.06 (a)
PAX1 36
  • 76 (a)
(Anolis carolinensis)
Reptilia PAX1 36
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pax1 35
  • 70.69 (n)
  • 75.56 (a)
(Danio rerio)
Actinopterygii pax1a 35
  • 68.56 (n)
  • 73.3 (a)
pax1a 36
  • 69 (a)
pax1b 36
  • 66 (a)
fruit fly
(Drosophila melanogaster)
Insecta Poxm 37
  • 88 (a)
Poxn 37
  • 66 (a)
sv 37
  • 69 (a)
Poxm 36
  • 41 (a)
(Caenorhabditis elegans)
Secernentea egl-38 37
  • 67 (a)
K06B9.5 37
  • 63 (a)
K07C11.1 37
  • 72 (a)
pax-1 36
  • 42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 41 (a)
Species with no ortholog for PAX1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PAX1 Gene

Gene Tree for PAX1 (if available)
Gene Tree for PAX1 (if available)

Paralogs for PAX1 Gene

Paralogs for PAX1 Gene

(8) SIMAP similar genes for PAX1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PAX1: view

Variants for PAX1 Gene

Sequence variations from dbSNP and Humsavar for PAX1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
VAR_003787 -
rs17861058 - 21,714,514(+) CCGGA(C/G)GCCCT reference, missense
rs17861059 - 21,714,556(+) TCGAC(C/T)TCCTA reference, synonymous-codon, missense
rs17861061 - 21,714,709(+) ACGCC(A/C/T)AGCCA reference, missense, utr-variant-3-prime
VAR_070922 Otofaciocervical syndrome 2 (OFC2)

Structural Variations from Database of Genomic Variants (DGV) for PAX1 Gene

Variant ID Type Subtype PubMed ID
nsv828703 CNV Gain 20364138

Variation tolerance for PAX1 Gene

Residual Variation Intolerance Score: 34.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.24; 52.58% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PAX1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX1 Gene

Disorders for PAX1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PAX1 Gene - From: OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
otofaciocervical syndrome 2
  • ofc2
otofaciocervical syndrome
  • fara chlupackova syndrome
spondylocostal dysostosis 1, autosomal recessive
  • jarcho-levin syndrome
klippel-feil syndrome
  • autosomal dominant klippel-feil syndrome
  • defect in vertebral ossification with nephrogenic rests
- elite association - COSMIC cancer census association via MalaCards
Search PAX1 in MalaCards View complete list of genes associated with diseases


  • Otofaciocervical syndrome 2 (OFC2) [MIM:615560]: A disorder characterized by facial dysmorphism, cup-shaped low-set ears, preauricular fistulas, hearing loss, branchial defects, skeletal anomalies including vertebral defects, low-set clavicles, winged scapulae, sloping shoulders, and mild intellectual disability. {ECO:0000269 PubMed:23851939}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PAX1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PAX1: view

No data available for Genatlas for PAX1 Gene

Publications for PAX1 Gene

  1. Pax1, a member of the paired box-containing class of developmental control genes, is mapped to human chromosome 20p11.2 by in situ hybridization (ISH and FISH). (PMID: 1358810) Schnittger S. … Hansmann I. (Genomics 1992) 2 3 23 67
  2. Aberrant Pax1 and Pax9 expression in Jarcho-Levin syndrome: report of two Caucasian siblings and literature review. (PMID: 12833407) Bannykh S.I. … Masliah E. (Am. J. Med. Genet. A 2003) 3 23
  3. A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females. (PMID: 25784220) Sharma S. … Wise C.A. (Nat Commun 2015) 3
  4. High Methylation Rate of LMX1A, NKX6-1, PAX1, PTPRR, SOX1, and ZNF582 Genes in Cervical Adenocarcinoma. (PMID: 24407576) Chang C.C. … Lai H.C. (Int. J. Gynecol. Cancer 2014) 3
  5. PAX1 methylation analysis by MS-HRM is useful in triage of high-grade squamous intraepithelial lesions. (PMID: 24568514) Wang Z.M. (Asian Pac. J. Cancer Prev. 2014) 3

Products for PAX1 Gene

Sources for PAX1 Gene

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