PAX2 paired box 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PAX2provided by HGNC
Official Full Name: paired box 2provided by HGNC
Primary source: HGNC:HGNC:8616
See related: Ensembl:ENSG00000075891 MIM:167409; Vega:OTTHUMG00000018913
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: FSGS7; PAPRS
Summary: PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression: Restricted expression toward kidney (RPKM 4.2) See more
Orthologs: mouse all

Genomic context

Location:: 10q24.31

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	10	NC_000010.11 (100735709..100829941)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (102495316..102589698)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Our data suggested that high expression of PAX2 could be associated with better survival in estrogen receptor positive tamoxifen-treated breast carcinoma patients.
Title: PAX2 expression is correlated with better survival in tamoxifen-treated breast carcinoma patients.
During the ensuing weeks, the PAX2/FOXA1 boundary progressively extended cranially such that by 21 weeks the entire vaginal epithelium was FOXA1-reactive and PAX2-negative. This observation supports Bulmer's proposal that human vaginal epithelium derives solely from urogenital sinus epithelium
Title: New insights into human female reproductive tract development.
PAX2 is involved in the carcinogenesis of endometrial cancer by stimulating cell growth and promoting cell motility; the overexpression of PAX2 in endometrial cancer is regulated by promoter hypermethylation and the transcription factor MZF1
Title: DNA methylation promotes paired box 2 expression via myeloid zinc finger 1 in endometrial cancer.
This case unravels a previously unrecognized phenotype of camptodactyly due to a significant skeletal deformity of Papillorenal syndrome with a heterogeneous PAX2 mutation of hexanucleotide duplication.
Title: Rethinking genotype-phenotype correlations in papillorenal syndrome: a case report on an unusual congenital camptodactyly and skeletal deformity with a heterogeneous PAX2 mutation of hexanucleotide duplication.
Mutant p53 and PTEN loss negatively regulated PAX2 and PAX2 re-expression in high-grade serous ovarian cancer cells induced cell death.
Title: PAX2 function, regulation and targeting in fallopian tube-derived high-grade serous ovarian cancer.
The polymorphism rs12266644 of PAX2 might be a risk factor for mullerian duct anomalies in Chinese Han females
Title: Genetic association between PAX2 and mullerian duct anomalies in Han Chinese females.
PAX2, PAX8, CDX2 immunostains was preformed to the TMA slides.
Title: PAX2, PAX8 and CDX2 Expression in Metastatic Mucinous, Primary Ovarian Mucinous and Seromucinous Tumors and Review of the Literature.
we demonstrated that miR-497 is decreased in human ovarian cancer tissues and cells, and acts as a tumor suppressor. We also confirmed PAX2 is a target gene of miR-497
Title: Overexpression of microRNA-497 suppresses cell proliferation and induces apoptosis through targeting paired box 2 in human ovarian cancer.
Vimentin, Nestin and WT1. Sox2 was expressed by the stem/progenitor cells of the ventricular zone, whereas the postmitotic neurons of the cortical plate were immunostained by PAX2 and NSE.
Title: Immunohistochemical markers of neural progenitor cells in the early embryonic human cerebral cortex.
PAX2 and PAX5 are useful biomarker in the differential diagnosis of lung cancer
Title: Diagnostic utility of PAX2 and PAX5 in distinguishing non-small cell lung cancer from small cell lung cancer.

Submit: New GeneRIF Correction See all GeneRIFs (109)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Anophthalmia-microphthalmia syndrome MedGen: CN120488 GeneReviews: Microphthalmia/Anophthalmia/Coloboma Spectrum	Compare labs
Focal segmental glomerulosclerosis 7 MedGen: C4014925 OMIM: 616002 GeneReviews: Not available	Compare labs
Renal coloboma syndrome MedGen: C1852759 OMIM: 120330 GeneReviews: PAX2-Related Disorder	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated (2013-03-14) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated (2013-03-14) ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Genome-wide scan of copy number variation in late-onset Alzheimer's disease. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from BioSystems

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ID signaling pathway, organism-specific biosystem (from WikiPathways)
ID signaling pathway, organism-specific biosystemThe Inhibitor of DNA binding (ID) proteins belong to the class V HLH family of transcription factors. Four ID proteins (ID 1-4)are known in humans. Unlike the basic HLH (bHLH) transcription factors, ...
Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80285 (e-PCR)
- UniSTS:88437

D10S2478 (e-PCR)
- UniSTS:74159

D10S278 (e-PCR)
- UniSTS:147948

NoName (e-PCR)
- UniSTS:482033

Homology

Homologs of the PAX2 gene: The PAX2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and zebrafish.
Orthologs from Annotation Pipeline: 204 organisms have orthologs with human gene PAX2
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	IDA Inferred from Direct Assay more info	PubMed
DNA binding	ISS Inferred from Sequence or Structural Similarity more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	NAS Non-traceable Author Statement more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
proximal promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
superoxide-generating NADPH oxidase activity	ISS Inferred from Sequence or Structural Similarity more info
transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
transcription regulatory region DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
aging	IEA Inferred from Electronic Annotation more info
axonogenesis	TAS Traceable Author Statement more info	PubMed
brain morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
branching involved in ureteric bud morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
cell fate determination	ISS Inferred from Sequence or Structural Similarity more info
cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
cellular response to hydrogen peroxide	ISS Inferred from Sequence or Structural Similarity more info
cellular response to retinoic acid	ISS Inferred from Sequence or Structural Similarity more info
cochlea development	ISS Inferred from Sequence or Structural Similarity more info
cochlea morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
glial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
inner ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
mesenchymal to epithelial transition	ISS Inferred from Sequence or Structural Similarity more info
mesenchymal to epithelial transition involved in metanephros morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
mesodermal cell fate specification	ISS Inferred from Sequence or Structural Similarity more info
mesonephros development	ISS Inferred from Sequence or Structural Similarity more info
metanephric collecting duct development	ISS Inferred from Sequence or Structural Similarity more info
metanephric distal convoluted tubule development	ISS Inferred from Sequence or Structural Similarity more info
metanephric epithelium development	IEP Inferred from Expression Pattern more info	PubMed
metanephric mesenchymal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
metanephric mesenchyme development	ISS Inferred from Sequence or Structural Similarity more info
metanephric nephron tubule formation	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of apoptotic process involved in metanephric collecting duct development	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of apoptotic process involved in metanephric nephron tubule development	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	IDA Inferred from Direct Assay more info	PubMed
negative regulation of cytolysis	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of mesenchymal cell apoptotic process involved in metanephros development	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of programmed cell death	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of reactive oxygen species metabolic process	IDA Inferred from Direct Assay more info	PubMed
negative regulation of transcription, DNA-templated	IMP Inferred from Mutant Phenotype more info	PubMed
nephric duct formation	ISS Inferred from Sequence or Structural Similarity more info
neural tube closure	ISS Inferred from Sequence or Structural Similarity more info
optic chiasma development	ISS Inferred from Sequence or Structural Similarity more info
optic cup morphogenesis involved in camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
optic nerve development	ISS Inferred from Sequence or Structural Similarity more info
optic nerve morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
optic nerve structural organization	ISS Inferred from Sequence or Structural Similarity more info
oxidation-reduction process	IEA Inferred from Electronic Annotation more info
positive regulation of branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of epithelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of metanephric DCT cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of metanephric glomerulus development	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of optic nerve formation	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
pronephric field specification	ISS Inferred from Sequence or Structural Similarity more info
pronephros development	ISS Inferred from Sequence or Structural Similarity more info
protein kinase B signaling	ISS Inferred from Sequence or Structural Similarity more info
reactive oxygen species metabolic process	ISS Inferred from Sequence or Structural Similarity more info
regulation of metanephric nephron tubule epithelial cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
regulation of metanephros size	IMP Inferred from Mutant Phenotype more info	PubMed
response to nutrient levels	IEA Inferred from Electronic Annotation more info
retinal pigment epithelium development	ISS Inferred from Sequence or Structural Similarity more info
stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
transcription, DNA-templated	ISS Inferred from Sequence or Structural Similarity more info
ureter development	ISS Inferred from Sequence or Structural Similarity more info
ureter maturation	ISS Inferred from Sequence or Structural Similarity more info
urogenital system development	ISS Inferred from Sequence or Structural Similarity more info
vestibulocochlear nerve formation	ISS Inferred from Sequence or Structural Similarity more info
visual perception	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
Golgi apparatus	IDA Inferred from Direct Assay more info
centriolar satellite	IDA Inferred from Direct Assay more info	PubMed
lysosome	IEA Inferred from Electronic Annotation more info
microtubule organizing center	IDA Inferred from Direct Assay more info	PubMed
nucleolus	IDA Inferred from Direct Assay more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
protein-DNA complex	ISS Inferred from Sequence or Structural Similarity more info
protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: paired box protein Pax-2

Names: paired box homeotic gene 2

NCBI Reference Sequences (RefSeq)

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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

NG_008680.2 RefSeqGene

Range

15003..99233

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000278.4 → NP_000269.3 paired box protein Pax-2 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (b) lacks an alternate in-frame exon and uses an alternate splice site in the 3' coding region, compared to variant e. This results in a protein (isoform b) with a shorter, distinct C-terminus compared to isoform e.

Source sequence(s)

AL138762, AL589862, M89470

Consensus CDS

CCDS41561.1

UniProtKB/Swiss-Prot

Q02962

Related

ENSP00000347385.2, OTTHUMP00000020286, ENST00000355243.7, OTTHUMT00000049868

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 392

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_001304569.1 → NP_001291498.1 paired box protein Pax-2 isoform f

See identical proteins and their annotated locations for NP_001291498.1

Status: REVIEWED

Description

Transcript Variant: This variant (f) has multiple differences compared to variant e. These differences result in the use of an alternate start codon and a translational frameshift in the 3' coding region. The encoded isoform (f) has a longer and distinct N- and C-termini compared to isoform e.

Source sequence(s)

AL138762, AL589862, BJ989901, DB077633, M89470

UniProtKB/Swiss-Prot

Q02962

Conserved Domains (2) summary

smart00351
Location:47 → 171

PAX; Paired Box domain

pfam12403
Location:313 → 423

Pax2_C; Paired-box protein 2 C terminal
NM_003987.4 → NP_003978.3 paired box protein Pax-2 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (a) uses an alternate in-frame splice site in the 3' coding region, compared to variant e, resulting in a shorter protein (isoform a) that has a shorter, distinct C-terminus compared to isoform e.

Source sequence(s)

AL138762, AL589862, M89470

UniProtKB/Swiss-Prot

Q02962

Related

ENSP00000396259.1, ENST00000428433.5

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:305 → 415

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:255 → 278

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003988.4 → NP_003979.2 paired box protein Pax-2 isoform c

See identical proteins and their annotated locations for NP_003979.2

Status: REVIEWED

Description

Transcript Variant: This variant (c) has multiple differences in the coding region, compared to variant e, one of which results in a translational frameshift. The resulting protein (isoform c) has a distinct C-terminus and is shorter than isoform e.

Source sequence(s)

AL138762, AL589862, M89470

Consensus CDS

CCDS7499.1

UniProtKB/Swiss-Prot

Q02962

Related

ENSP00000359319.3, OTTHUMP00000020287, ENST00000370296.6, OTTHUMT00000049869

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 340

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003989.4 → NP_003980.3 paired box protein Pax-2 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (d) lacks an alternate in-frame exon compared to variant e. This results in an isoform (isoform d) that is shorter than isoform e.

Source sequence(s)

AL138762, AL589862, M89470

UniProtKB/Swiss-Prot

Q02962

Conserved Domains (3) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:282 → 367

Pax2_C; Paired-box protein 2 C terminal

cl00084
Location:232 → 255

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
NM_003990.4 → NP_003981.3 paired box protein Pax-2 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (e) encodes the longest isoform (e).

Source sequence(s)

AL138762, AL589862, M89470

UniProtKB/Swiss-Prot

Q02962

Conserved Domains (2) summary

smart00351
Location:16 → 140

PAX; Paired Box domain

pfam12403
Location:305 → 390

Pax2_C; Paired-box protein 2 C terminal