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PAX2 paired box 2 [ Homo sapiens (human) ]

Gene ID: 5076, updated on 3-Nov-2018

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

Genomic context

See PAX2 in Genome Data Viewer
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_000010.11Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit B8 Neighboring gene hypoxia inducible factor 1 subunit alpha inhibitor Neighboring gene VISTA enhancer hs229 Neighboring gene Sharpr-MPRA regulatory region 13917 Neighboring gene SMC5-SMC6 complex localization factor 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

Pathways from BioSystems

  • 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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

Preferred Names
paired box protein Pax-2
Names
paired box homeotic gene 2

NCBI Reference Sequences (RefSeq)

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_008680.2 RefSeqGene

    Range
    15003..99233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000278.4NP_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:16140
    PAX; Paired Box domain
    pfam12403
    Location:282392
    Pax2_C; Paired-box protein 2 C terminal
    cl00084
    Location:232255
    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.
  2. NM_001304569.1NP_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:47171
    PAX; Paired Box domain
    pfam12403
    Location:313423
    Pax2_C; Paired-box protein 2 C terminal
  3. NM_003987.4NP_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:16140
    PAX; Paired Box domain
    pfam12403
    Location:305415
    Pax2_C; Paired-box protein 2 C terminal
    cl00084
    Location:255278
    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.
  4. NM_003988.4NP_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:16140
    PAX; Paired Box domain
    pfam12403
    Location:282340
    Pax2_C; Paired-box protein 2 C terminal
    cl00084
    Location:232255
    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.
  5. NM_003989.4NP_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:16140
    PAX; Paired Box domain
    pfam12403
    Location:282367
    Pax2_C; Paired-box protein 2 C terminal
    cl00084
    Location:232255
    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.
  6. NM_003990.4NP_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:16140
    PAX; Paired Box domain
    pfam12403
    Location:305390
    Pax2_C; Paired-box protein 2 C terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    100735709..100829941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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