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    PAX2 paired box 2 [ Homo sapiens (human) ]

    Gene ID: 5076, updated on 20-Sep-2023

    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; AllianceGenome:HGNC:8616
    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; PAX-2
    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]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Restricted expression toward kidney (RPKM 4.2) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PAX2 in Genome Data Viewer
    Location:
    10q24.31
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100735396..100829944)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101618753..101713301)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102495153..102589701)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:102289335-102289917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102321666-102322304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102322305-102322942 Neighboring gene NADH:ubiquinone oxidoreductase subunit B8 Neighboring gene hypoxia inducible factor 1 subunit alpha inhibitor Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:102401951-102402580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102421749-102422248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102440375-102440986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102443611-102444112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102447267-102447771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102473509-102474318 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102496683-102497428 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102497429-102498172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102505530-102506071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102509961-102510895 Neighboring gene VISTA enhancer hs229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102550131-102551044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102562802-102563302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102567263-102567763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102576822-102577322 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102606788-102607987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102633779-102634445 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102649745-102650944 Neighboring gene SMC5-SMC6 complex localization factor 2 Neighboring gene Sharpr-MPRA regulatory region 3697 Neighboring gene semaphorin 4G Neighboring gene microRNA 608

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Anophthalmia-microphthalmia syndrome
    MedGen: CN120488 GeneReviews: Not available
    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 2020-02-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-02-26)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide scan of copy number variation in late-onset Alzheimer's disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anatomical structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in axonogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in brain morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in branching involved in ureteric bud morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in camera-type eye development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell fate determination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to epidermal growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to glucose stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to hydrogen peroxide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to retinoic acid ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cochlea development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cochlea morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glial cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal to epithelial transition ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesodermal cell fate specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesonephros development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric collecting duct development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric distal convoluted tubule development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric epithelium development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in metanephric mesenchymal cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric mesenchyme development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric nephron tubule formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process involved in metanephric collecting duct development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of apoptotic process involved in metanephric nephron tubule development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephros development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of programmed cell death ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of reactive oxygen species metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nephric duct formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neural tube closure ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic chiasma development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic cup morphogenesis involved in camera-type eye development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic nerve development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic nerve morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in optic nerve structural organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of branching involved in ureteric bud morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of epithelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of metanephric DCT cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of metanephric glomerulus development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of optic nerve formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pronephric field specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pronephros development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in reactive oxygen species metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of metanephric nephron tubule epithelial cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of metanephros size IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in response to nutrient levels IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retinal pigment epithelium development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ureter development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ureter maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in urogenital system development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in vestibulocochlear nerve formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in microtubule organizing center IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-DNA complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of 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)

    NEW Try the new Transcript table

    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
      14874..99236
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000278.5NP_000269.3  paired box protein Pax-2 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      Consensus CDS
      CCDS41561.1
      UniProtKB/Swiss-Prot
      Q02962
      UniProtKB/TrEMBL
      A0A7P0TAC9
      Related
      ENSP00000347385.3, ENST00000355243.8
      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_001304569.2NP_001291498.1  paired box protein Pax-2 isoform f

      See identical proteins and their annotated locations for NP_001291498.1

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, BJ989901, DB077633, M89470
      UniProtKB/Swiss-Prot
      Q02962
      UniProtKB/TrEMBL
      A0A7P0TAC9, A0A9L9PYK3
      Related
      ENSP00000516729.1, ENST00000707078.1
      Conserved Domains (3) summary
      smart00351
      Location:47171
      PAX; Paired Box domain
      pfam12403
      Location:313423
      Pax2_C; Paired-box protein 2 C terminal
      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_001374303.1NP_001361232.1  paired box protein Pax-2 isoform g

      Status: REVIEWED

      Source sequence(s)
      AL589862
    4. NM_003987.5NP_003978.3  paired box protein Pax-2 isoform a

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862
      Consensus CDS
      CCDS53569.1
      UniProtKB/Swiss-Prot
      Q02962, Q15105, Q15110, Q15837, Q5SZP2, Q5SZP3
      UniProtKB/TrEMBL
      A0A7P0TAC9
      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.
    5. NM_003988.5NP_003979.2  paired box protein Pax-2 isoform c

      See identical proteins and their annotated locations for NP_003979.2

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      Consensus CDS
      CCDS7499.1
      UniProtKB/Swiss-Prot
      Q02962
      UniProtKB/TrEMBL
      A0A7P0TAC9
      Related
      ENSP00000359319.3, ENST00000370296.6
      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.
    6. NM_003989.5NP_003980.3  paired box protein Pax-2 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      Consensus CDS
      CCDS91319.1
      UniProtKB/Swiss-Prot
      Q02962
      UniProtKB/TrEMBL
      A0A7P0TAC9, Q5SZP1
      Related
      ENSP00000398652.2, ENST00000427256.6
      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.
    7. NM_003990.5NP_003981.3  paired box protein Pax-2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      UniProtKB/Swiss-Prot
      Q02962
      UniProtKB/TrEMBL
      A0A7P0TAC9, A0A9L9PXU6
      Related
      ENSP00000516730.1, ENST00000707079.1
      Conserved Domains (3) summary
      smart00351
      Location:16140
      PAX; Paired Box domain
      pfam12403
      Location:305390
      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.

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      100735396..100829944
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      101618753..101713301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)