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PAX6 paired box 6 [ Homo sapiens (human) ]

Gene ID: 5080, updated on 20-Jan-2019

Summary

Official Symbol
PAX6provided by HGNC
Official Full Name
paired box 6provided by HGNC
Primary source
HGNC:HGNC:8620
See related
Ensembl:ENSG00000007372 MIM:607108
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; ASGD5; 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]
Expression
Broad expression in brain (RPKM 3.5), stomach (RPKM 2.6) and 15 other tissues See more
Orthologs

Genomic context

See PAX6 in Genome Data Viewer
Location:
11p13
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 elongator acetyltransferase complex subunit 4 Neighboring gene E100 enhancer downstream of PAX6 Neighboring gene E60 enhancer downstream of PAX6 Neighboring gene enhancer region in intron 7 of PAX6 Neighboring gene regulatory region in intron 4 of PAX6 Neighboring gene PAX6 upstream regulatory region Neighboring gene PAX6 antisense RNA 1 Neighboring gene PAX6 upstream antisense RNA Neighboring gene VISTA enhancer hs1531

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Aniridia 1
MedGen: C0344542 OMIM: 106210 GeneReviews: PAX6-Related Aniridia
Compare labs
Anophthalmia-microphthalmia syndrome Compare labs
Coloboma of optic disc
MedGen: C0155299 OMIM: 120430 GeneReviews: Not available
Compare labs
Congenital ocular coloboma
MedGen: C0009363 OMIM: 120200 GeneReviews: Not available
Compare labs
Foveal hypoplasia and presenile cataract syndrome
MedGen: C3805604 OMIM: 136520 GeneReviews: Not available
Compare labs
Irido-corneo-trabecular dysgenesis
MedGen: C4310809 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: PAX6-Related 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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC17209

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
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 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
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 sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter 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 binding ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin protein ligase binding IEA
Inferred from Electronic Annotation
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
 
cellular response to leukemia inhibitory factor 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 by RNA polymerase II 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 core promoter binding IDA
Inferred from Direct Assay
more info
PubMed 
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 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 
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
 
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 by RNA polymerase II 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 
cytosol IDA
Inferred from Direct Assay
more info
 
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 

General protein information

Preferred Names
paired box protein Pax-6
Names
aniridia type II protein
oculorhombin
paired box homeotic gene-6

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_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
    ENSP00000495109.1, ENST00000643871.1
    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
    ENSP00000241001.8, ENST00000241001.13
    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
    ENSP00000494722.1, ENST00000645710.1
    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
    ENSP00000492476.1, ENST00000639409.1
    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
    ENSP00000491295.1, ENST00000640610.1
    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
    ENSP00000490963.1, ENST00000639916.1
    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
    Related
    ENSP00000491872.1, ENST00000640975.1
    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
    Consensus CDS
    CCDS86190.1
    UniProtKB/Swiss-Prot
    P26367
    UniProtKB/TrEMBL
    D1KF47
    Related
    ENSP00000491679.1, ENST00000639034.2
    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
    Consensus CDS
    CCDS86189.1
    UniProtKB/TrEMBL
    A0A1W2PRA8
    Related
    ENSP00000490971.1, ENST00000638629.1
    Conserved Domains (2) summary
    pfam00046
    Location:78130
    Homeobox; Homeobox domain
    pfam03999
    Location:63214
    MAP65_ASE1; Microtubule associated protein (MAP65/ASE1 family)
  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
    Consensus CDS
    CCDS86189.1
    UniProtKB/Swiss-Prot
    P26367
    UniProtKB/TrEMBL
    A0A1W2PRA8
    Related
    ENSP00000492205.1, ENST00000481563.6
    Conserved Domains (2) summary
    pfam00046
    Location:78130
    Homeobox; Homeobox domain
    pfam03999
    Location:63214
    MAP65_ASE1; Microtubule associated protein (MAP65/ASE1 family)
  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
    ENSP00000404100.1, ENST00000419022.6
    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 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

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