Format

Send to:

Choose Destination

Links from PubMed

    • Showing Current items.

    PAX6 paired box 6 [ Homo sapiens (human) ]

    Gene ID: 5080, updated on 6-Dec-2016
    Official Symbol
    PAX6provided by HGNC
    Official Full Name
    paired box 6provided by HGNC
    Primary source
    HGNC:HGNC:8620
    See related
    Ensembl:ENSG00000007372 MIM:607108; Vega:OTTHUMG00000041447
    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
    AN; AN2; FVH1; MGDA; WAGR; D11S812E
    Summary
    This gene encodes a homeobox and paired domain-containing protein that binds DNA and functions as a regulator of transcription. Activity of this protein is key in the development of neural tissues, particularly the eye. This gene is regulated by multiple enhancers located up to hundreds of kilobases distant from this locus. Mutations in this gene or in the enhancer regions can cause ocular disorders such as aniridia and Peter's anomaly. Use of alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2015]
    Orthologs
    Location:
    11p13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (31784792..31817961, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (31806340..31839509, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C24 Neighboring gene inner mitochondrial membrane peptidase subunit 1 Neighboring gene elongator acetyltransferase complex subunit 4 Neighboring gene uncharacterized LOC440034 Neighboring gene PAX6 upstream antisense RNA Neighboring gene uncharacterized LOC107984420

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Aniridia, cerebellar ataxia, and mental retardation
    MedGen: C0431401 OMIM: 206700 GeneReviews: Not available
    Compare labs
    Anophthalmia/Microphthalmia Compare labs
    Coloboma of optic disc
    MedGen: C0155299 OMIM: 120430 GeneReviews: Not available
    Compare labs
    Foveal hypoplasia and presenile cataract syndrome
    MedGen: C1850992 OMIM: 136520 GeneReviews: Not available
    Compare labs
    Irido-corneo-trabecular dysgenesis
    MedGen: C0344559 OMIM: 604229 GeneReviews: Not available
    Compare labs
    Keratitis, hereditary
    MedGen: C1835698 OMIM: 148190 GeneReviews: Not available
    Compare labs
    Optic nerve hypoplasia, bilateral
    MedGen: C1833797 OMIM: 165550 GeneReviews: Not available
    Compare labs
    Wilms tumor, aniridia, genitourinary anomalies, and mental retardation syndrome
    MedGen: C0206115 OMIM: 194072 GeneReviews: Aniridia
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2015-11-05)

    ClinGen Genome Curation Page
    Triplosensitivity

    Little evidence for dosage pathogenicity (Last evaluated (2015-11-05)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Meta-analysis identifies common variants associated with body mass index in east Asians.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC17209

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    HMG box domain binding IEA
    Inferred from Electronic Annotation
    more info
     
    R-SMAD binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    co-SMAD binding IEA
    Inferred from Electronic Annotation
    more info
     
    histone acetyltransferase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription factor activity, sequence-specific DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    ubiquitin protein ligase binding IEA
    Inferred from Electronic Annotation
    more info
     
    ubiquitin-protein transferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    astrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    blood vessel development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell fate determination IEA
    Inferred from Electronic Annotation
    more info
     
    central nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    cerebral cortex regionalization IEA
    Inferred from Electronic Annotation
    more info
     
    commitment of neuronal cell to specific neuron type in forebrain IEA
    Inferred from Electronic Annotation
    more info
     
    cornea development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    dorsal/ventral axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    embryonic camera-type eye morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    establishment of mitotic spindle orientation IEA
    Inferred from Electronic Annotation
    more info
     
    eye development TAS
    Traceable Author Statement
    more info
    PubMed 
    eye photoreceptor cell development IEA
    Inferred from Electronic Annotation
    more info
     
    forebrain dorsal/ventral pattern formation IEA
    Inferred from Electronic Annotation
    more info
     
    forebrain-midbrain boundary formation IEA
    Inferred from Electronic Annotation
    more info
     
    glucose homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    habenula development IEA
    Inferred from Electronic Annotation
    more info
     
    iris morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    keratinocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    lacrimal gland development IEA
    Inferred from Electronic Annotation
    more info
     
    lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of neurogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of protein phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    neuron fate commitment NAS
    Non-traceable Author Statement
    more info
    PubMed 
    neuron migration IEA
    Inferred from Electronic Annotation
    more info
     
    oligodendrocyte cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    pancreatic A cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    pituitary gland development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein localization to organelle IEA
    Inferred from Electronic Annotation
    more info
     
    protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of asymmetric cell division IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of timing of cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription from RNA polymerase II promoter involved in somatic motor neuron fate commitment IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification IEA
    Inferred from Electronic Annotation
    more info
     
    response to wounding IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    salivary gland morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    signal transduction involved in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    type B pancreatic cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    visual perception TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    paired box protein Pax-6
    Names
    aniridia type II protein
    oculorhombin
    paired box homeotic gene-6

    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_008679.1 RefSeqGene

      Range
      5001..38170
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_720

    mRNA and Protein(s)

    1. NM_000280.4NP_000271.1  paired box protein Pax-6 isoform a

      See identical proteins and their annotated locations for NP_000271.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) initiates from the B (P1) promoter and encodes isoform a. Variants 1, 3, 6 and 7 encode the same isoform (a).
      Source sequence(s)
      BP394576, DA078958, M93650, Z83307
      Consensus CDS
      CCDS31451.1
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      Q66SS1
      Related
      ENSP00000368418, OTTHUMP00000038835, ENST00000379123, OTTHUMT00000099288
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain
    2. NM_001127612.1NP_001121084.1  paired box protein Pax-6 isoform a

      See identical proteins and their annotated locations for NP_001121084.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. It initiates from the A (P0) promoter. Variants 1, 3, 6 and 7 encode the same isoform (a).
      Source sequence(s)
      AK314470, BE221553, BM557761, BM725029, BP394398, BP394576, BU072567, BX089704, BX114225, CA397536, DA183294, Z83307
      Consensus CDS
      CCDS31451.1
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      Q66SS1
      Related
      ENSP00000368427, OTTHUMP00000038838, ENST00000379132, OTTHUMT00000099293
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain
    3. NM_001258462.1NP_001245391.1  paired box protein Pax-6 isoform b

      See identical proteins and their annotated locations for NP_001245391.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and includes an alternate in-frame exon in the 5' coding region, compared to variant 1. It initiates from the A (P0) promoter. The encoded isoform (b, also known as 5a) is longer than isoform a. Variants 2, 4, 5 and 8 encode the same isoform (b).
      Source sequence(s)
      AB593092, BP394576, DA183294, Z83307
      Consensus CDS
      CCDS31452.1
      UniProtKB/TrEMBL
      F1T0F8
      Related
      ENSP00000404100, ENST00000419022
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228280
      Homeobox; Homeobox domain
    4. NM_001258463.1NP_001245392.1  paired box protein Pax-6 isoform b

      See identical proteins and their annotated locations for NP_001245392.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and includes an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (b, also known as 5a) is longer than isoform a. Variants 2, 4, 5 and 8 encode the same isoform (b).
      Source sequence(s)
      AB593093, BP394576, Z83307
      Consensus CDS
      CCDS31452.1
      UniProtKB/TrEMBL
      F1T0F8
      Related
      ENSP00000480026, ENST00000606377
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228280
      Homeobox; Homeobox domain
    5. NM_001258464.1NP_001245393.1  paired box protein Pax-6 isoform a

      See identical proteins and their annotated locations for NP_001245393.1

      Status: REVIEWED

      Description
      Transcript Variant:This variant (6) uses an alternate splice site in the 5' UTR compared to variant 1. It initiates from the P1 promoter. Variants 1, 3, 6 and 7 encode the same isoform (a).
      Source sequence(s)
      BC011953, BP394576, DA078958, Z83307
      Consensus CDS
      CCDS31451.1
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      Q66SS1
      Related
      ENSP00000241001, OTTHUMP00000038834, ENST00000241001, OTTHUMT00000099287
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain
    6. NM_001258465.1NP_001245394.1  paired box protein Pax-6 isoform a

      See identical proteins and their annotated locations for NP_001245394.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. It initiates from the B (P1) promoter. Variants 1, 3, 6 and 7 encode the same isoform (a).
      Source sequence(s)
      AY707088, BP394576, DA079367, M77844, Z83307
      Consensus CDS
      CCDS31451.1
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      Q66SS1
      Related
      ENSP00000368406, OTTHUMP00000038837, ENST00000379111, OTTHUMT00000099290
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain
    7. NM_001310158.1NP_001297087.1  paired box protein Pax-6 isoform b

      See identical proteins and their annotated locations for NP_001297087.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and includes an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (b, also known as 5a) is longer than isoform a. Variants 2, 4, 5 and 8 encode the same isoform (b).
      Source sequence(s)
      AB593094, BP394576, Z83307, Z95332
      Consensus CDS
      CCDS31452.1
      UniProtKB/TrEMBL
      F1T0F8
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228280
      Homeobox; Homeobox domain
    8. NM_001310159.1NP_001297088.1  paired box protein Pax-6 isoform c

      See identical proteins and their annotated locations for NP_001297088.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) has a shorter 5' UTR and lacks multiple 3' coding exons compared to variant 1. Its transcription extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR. The encoded isoform (c, also known as S) has a distinct, shorter C-terminus than isoform a.
      Source sequence(s)
      BM666662, GQ141695, M77844
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      D1KF47
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain
    9. NM_001310160.1NP_001297089.1  paired box protein Pax-6 isoform d

      See identical proteins and their annotated locations for NP_001297089.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) initiates from the P alpha promoter and contains multiple differences in the 5' region, compared to variant 1. The encoded isoform (d) has a shorter N-terminus and lacks the paired domain, compared to isoform a. Variants 10 and 11 encode the same isoform (d).
      Source sequence(s)
      AK094249, BP394576, CA397106, DA056636, DA089215, Z83307
      Conserved Domains (1) summary
      pfam00046
      Location:78130
      Homeobox; Homeobox domain
    10. NM_001310161.1NP_001297090.1  paired box protein Pax-6 isoform d

      See identical proteins and their annotated locations for NP_001297090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) initiates from the P alpha promoter and contains multiple differences in the 5' region, compared to variant 1. The encoded isoform (d) has a shorter N-terminus and lacks the paired domain, compared to isoform a. Variants 10 and 11 encode the same isoform (d).
      Source sequence(s)
      BP394576, CA397106, DA089215, DA571138, M93650, Z83307
      UniProtKB/Swiss-Prot
      P26367
      Conserved Domains (1) summary
      pfam00046
      Location:78130
      Homeobox; Homeobox domain
    11. NM_001604.5NP_001595.2  paired box protein Pax-6 isoform b

      See identical proteins and their annotated locations for NP_001595.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, and includes an alternate in-frame exon in the 5' coding region, compared to variant 1. It initiates from the B (P1) promoter. The encoded isoform (b, also known as 5a) is longer than isoform a. Variants 2, 4, 5 and 8 encode the same isoform (b).
      Source sequence(s)
      BP394576, BX640762, CV569250, DA078958, DA141443, Z83307
      Consensus CDS
      CCDS31452.1
      UniProtKB/Swiss-Prot
      P26367
      UniProtKB/TrEMBL
      F1T0F8
      Related
      ENSP00000368410, OTTHUMP00000038833, ENST00000379115, OTTHUMT00000099286
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228280
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      31784792..31817961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      31805847..31839030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center