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    PAX2 paired box 2 [ Homo sapiens (human) ]

    Gene ID: 5076, updated on 4-Jan-2025

    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
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    Genomic context

    See PAX2 in Genome Data Viewer
    Location:
    10q24.31
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100735396..100829944)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101618753..101713301)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102495153..102589701)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3893 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:102289335-102289917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3896 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 ATAC-STARR-seq lymphoblastoid silent region 2708 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 ATAC-STARR-seq lymphoblastoid active region 3899 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 ReSE screen-validated silencer GRCh37_chr10:102551431-102551607 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 ATAC-STARR-seq lymphoblastoid silent region 2709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102633779-102634445 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102649745-102650944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3901 Neighboring gene SMC5-SMC6 complex localization factor 2 Neighboring gene Sharpr-MPRA regulatory region 3697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2711 Neighboring gene semaphorin 4G Neighboring gene microRNA 608

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (16 hits/1277 screens)

    Associated conditions

    Description Tests
    Anophthalmia-microphthalmia syndrome
    MedGen: C5680330 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

    General gene information

    Gene Ontology Provided by GOA

    Items 1 - 25 of 65
    Process Evidence Code Pubs
    involved_in axonogenesis PubMed 
    involved_in brain morphogenesis  
    involved_in branching involved in ureteric bud morphogenesis PubMed 
    involved_in branching involved in ureteric bud morphogenesis  
    involved_in camera-type eye development  
    involved_in cell fate determination  
    involved_in cellular response to epidermal growth factor stimulus  
    involved_in cellular response to glucose stimulus  
    involved_in cellular response to retinoic acid  
    involved_in cochlea development  
    involved_in cochlea morphogenesis  
    involved_in glial cell differentiation  
    involved_in inner ear morphogenesis  
    involved_in mesenchymal to epithelial transition  
    involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis  
    involved_in mesodermal cell fate specification  
    involved_in mesonephros development  
    involved_in metanephric collecting duct development  
    involved_in metanephric distal convoluted tubule development  
    involved_in metanephric epithelium development PubMed 
    involved_in metanephric mesenchymal cell differentiation  
    involved_in metanephric mesenchyme development  
    involved_in metanephric nephron tubule formation  
    involved_in negative regulation of DNA-templated transcription PubMed 
    involved_in negative regulation of apoptotic process PubMed 
    involved_in negative regulation of apoptotic process PubMed 
    involved_in negative regulation of apoptotic process involved in metanephric collecting duct development  
    involved_in negative regulation of apoptotic process involved in metanephric nephron tubule development  
    involved_in negative regulation of cysteine-type endopeptidase activity PubMed 
    involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis  
    involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephros development  
    involved_in negative regulation of programmed cell death  
    involved_in negative regulation of reactive oxygen species metabolic process PubMed 
    involved_in nephric duct formation  
    involved_in nervous system development  
    involved_in neural tube closure  
    involved_in optic chiasma development  
    involved_in optic cup morphogenesis involved in camera-type eye development  
    involved_in optic nerve development  
    involved_in optic nerve morphogenesis  
    involved_in optic nerve structural organization  
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of epithelial cell proliferation PubMed 
    involved_in positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  
    involved_in positive regulation of metanephric DCT cell differentiation  
    involved_in positive regulation of metanephric glomerulus development  
    involved_in positive regulation of optic nerve formation  
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in pronephric field specification  
    involved_in pronephros development  
    involved_in regulation of metanephric nephron tubule epithelial cell differentiation  
    involved_in regulation of metanephros size PubMed 
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to nutrient levels  
    involved_in retinal pigment epithelium development  
    involved_in sensory organ development  
    involved_in stem cell differentiation  
    involved_in ureter development  
    involved_in ureter maturation  
    involved_in urogenital system development  
    involved_in vestibulocochlear nerve formation  
    involved_in visual perception PubMed 
    Items 1 - 25 of 65
    Component Evidence Code Pubs
    located_in centriolar satellite PubMed 
    located_in chromatin  
    located_in microtubule organizing center PubMed 
    located_in nucleoplasm  
    located_in nucleus PubMed 
    part_of protein-DNA complex  
    part_of protein-containing complex  

    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_000278.5 → NP_000269.3  paired box protein Pax-2 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      Consensus CDS
      CCDS41561.1
      UniProtKB/TrEMBL
      A0A7P0TAC9
      Related
      ENSP00000347385.3, ENST00000355243.8
      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.
    2. NM_001304569.2 → NP_001291498.1  paired box protein Pax-2 isoform f precursor

      See identical proteins and their annotated locations for NP_001291498.1

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, BJ989901, DB077633, M89470
      UniProtKB/TrEMBL
      A0A7P0TAC9, A0A9L9PYK3
      Related
      ENSP00000516729.1, ENST00000707078.1
      Conserved Domains (3) summary
      smart00351
      Location:47 → 171
      PAX; Paired Box domain
      pfam12403
      Location:313 → 423
      Pax2_C; Paired-box protein 2 C terminal
      cl00084
      Location:263 → 286
      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_001374303.1 → NP_001361232.1  paired box protein Pax-2 isoform g

      Status: REVIEWED

      Source sequence(s)
      AL589862
    4. NM_003987.5 → NP_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: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.
    5. NM_003988.5 → NP_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/TrEMBL
      A0A7P0TAC9
      Related
      ENSP00000359319.3, ENST00000370296.6
      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.
    6. NM_003989.5 → NP_003980.3  paired box protein Pax-2 isoform d

      Status: REVIEWED

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

      Status: REVIEWED

      Source sequence(s)
      AL138762, AL589862, M89470
      UniProtKB/TrEMBL
      A0A7P0TAC9, A0A9L9PXU6
      Related
      ENSP00000516730.1, ENST00000707079.1
      Conserved Domains (3) summary
      smart00351
      Location:16 → 140
      PAX; Paired Box domain
      pfam12403
      Location:305 → 390
      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.

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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)
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