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    PAX2 paired box 2 [ Homo sapiens (human) ]

    Gene ID: 5076, updated on 8-Aug-2016
    Official Symbol
    PAX2provided by HGNC
    Official Full Name
    paired box 2provided by HGNC
    Primary source
    HGNC:HGNC:8616
    See related
    Ensembl:ENSG00000075891 HPRD:01330; 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]
    Orthologs
    Location:
    10q24
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (100732940..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 alpha subunit inhibitor Neighboring gene SMC5-SMC6 complex localization factor 2 Neighboring gene semaphorin 4G Neighboring gene microRNA 608

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Anophthalmia/Microphthalmia Compare labs
    Focal segmental glomerulosclerosis 7
    MedGen: CN219277 OMIM: 616002 GeneReviews: Not available
    Compare labs
    Renal adysplasia
    MedGen: C1619700 OMIM: 191830 GeneReviews: Not available
    Compare labs
    Renal coloboma syndrome
    MedGen: C1852759 OMIM: 120330 GeneReviews: Renal Coloboma Syndrome
    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
    • Id Signaling Pathway, organism-specific biosystem (from WikiPathways)
      Id Signaling Pathway, organism-specific biosystemInhibitor of DNA binding (ID) proteins are members of the helix-loop-helix (HLH) family of proteins which lack a DNA binding domain themselves but bind to other family members inhibiting their DNA bi...
    • Wnt Signaling Pathway NetPath, organism-specific biosystem (from WikiPathways)
      Wnt Signaling Pathway NetPath, organism-specific biosystemWnt family of proteins are a large family of cysteine-rich secreted glycoproteins that regulate cell-cell interactions. They bind to members of the Frizzled family of 7 transmembrane receptors. Bindi...
    Products Interactant Other Gene Complex Source Pubs Description

    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
     
    core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    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 from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter 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 from RNA polymerase II promoter 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 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein-DNA complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Preferred Names
    paired box protein Pax-2
    Names
    paired box homeotic gene 2

    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, OTTHUMP00000020286, ENST00000355243, OTTHUMT00000049868
    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 (4) summary
      cd00131
      Location:47173
      PAX; Paired Box domain
      pfam12403
      Location:312424
      Pax2_C; Paired-box protein 2 C terminal
      pfam13551
      Location:69171
      HTH_29; Winged helix-turn helix
      cl00084
      Location:263286
      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.
    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, ENST00000428433
      Conserved Domains (4) summary
      cd00131
      Location:16142
      PAX; Paired Box domain
      pfam12403
      Location:304416
      Pax2_C; Paired-box protein 2 C terminal
      pfam13551
      Location:38140
      HTH_29; Winged helix-turn helix
      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, OTTHUMP00000020287, ENST00000370296, OTTHUMT00000049869
      Conserved Domains (4) summary
      cd00131
      Location:16142
      PAX; Paired Box domain
      pfam12403
      Location:281340
      Pax2_C; Paired-box protein 2 C terminal
      pfam13551
      Location:38140
      HTH_29; Winged helix-turn helix
      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 (4) summary
      cd00131
      Location:16142
      PAX; Paired Box domain
      pfam12403
      Location:281367
      Pax2_C; Paired-box protein 2 C terminal
      pfam13551
      Location:38140
      HTH_29; Winged helix-turn helix
      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 (4) summary
      cd00131
      Location:16142
      PAX; Paired Box domain
      pfam12403
      Location:304390
      Pax2_C; Paired-box protein 2 C terminal
      pfam13551
      Location:38140
      HTH_29; Winged helix-turn helix
      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.

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

      Range
      100732940..100829941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017016281.1XP_016871770.1  

    2. XM_017016285.1XP_016871774.1  

    3. XM_017016284.1XP_016871773.1  

    4. XM_017016286.1XP_016871775.1  

    5. XM_017016288.1XP_016871777.1  

    6. XM_017016283.1XP_016871772.1  

    7. XM_017016282.1XP_016871771.1  

    8. XM_017016287.1XP_016871776.1  

    9. XM_017016289.1XP_016871778.1  

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      102779745..102873990
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)