U.S. flag

An official website of the United States government

Links from GEO Profiles

    • Showing Current items.

    Pax6 paired box 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25509, updated on 4-Jan-2025

    Summary

    Official Symbol
    Pax6provided by RGD
    Official Full Name
    paired box 6provided by RGD
    Primary source
    RGD:3258
    See related
    EnsemblRapid:ENSRNOG00000004410 AllianceGenome:RGD:3258
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and minor groove of adenine-thymine-rich DNA binding activity. Involved in several processes, including enteroendocrine cell differentiation; nervous system development; and positive regulation of macromolecule biosynthetic process. Located in chromatin. Used to study autistic disorder. Biomarker of Smith-Lemli-Opitz syndrome and transient cerebral ischemia. Human ortholog(s) of this gene implicated in bilateral optic nerve hypoplasia; eye disease (multiple); glucose intolerance; and paranoid schizophrenia. Orthologous to human PAX6 (paired box 6). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Restricted expression toward (RPKM 32.2) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Pax6 in Genome Data Viewer
    Location:
    3q33
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (112590034..112611771)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (92128772..92157022)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (95700241..95728682)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene thioesterase superfamily member 7 Neighboring gene ribosomal protein L6, pseudogene 11 Neighboring gene reticulocalbin 1 Neighboring gene elongator acetyltransferase complex subunit 4 Neighboring gene ribosomal protein L35A like 6 Neighboring gene uncharacterized LOC120101618 Neighboring gene U2 spliceosomal RNA Neighboring gene inner mitochondrial membrane peptidase subunit 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Items 1 - 25 of 44
    Function Evidence Code Pubs
    enables DNA binding  
    enables DNA binding  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific  
    enables HMG box domain binding  
    enables HMG box domain binding  
    enables R-SMAD binding  
    enables R-SMAD binding  
    enables RNA binding  
    enables RNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II core promoter sequence-specific DNA binding  
    enables RNA polymerase II core promoter sequence-specific DNA binding  
    enables chromatin DNA binding  
    enables chromatin DNA binding  
    enables chromatin binding  
    enables co-SMAD binding  
    enables co-SMAD binding  
    enables double-stranded DNA binding PubMed 
    enables histone acetyltransferase binding  
    enables histone acetyltransferase binding  
    enables minor groove of adenine-thymine-rich DNA binding PubMed 
    enables protein kinase binding  
    enables protein kinase binding  
    enables sequence-specific DNA binding PubMed 
    enables sequence-specific DNA binding  
    enables sequence-specific double-stranded DNA binding  
    enables transcription cis-regulatory region binding  
    enables transcription cis-regulatory region binding  
    enables transcription coregulator binding  
    enables transcription coregulator binding  
    enables ubiquitin protein ligase binding  
    enables ubiquitin protein ligase binding  
    Items 1 - 25 of 44
    Items 1 - 25 of 170
    Process Evidence Code Pubs
    involved_in animal organ development  
    acts_upstream_of_or_within anterior/posterior pattern specification  
    involved_in astrocyte differentiation  
    involved_in astrocyte differentiation PubMed 
    acts_upstream_of_or_within astrocyte differentiation  
    involved_in astrocyte differentiation  
    involved_in axon guidance  
    acts_upstream_of_or_within axon guidance  
    acts_upstream_of_or_within axonogenesis  
    involved_in blood vessel development  
    involved_in blood vessel development  
    involved_in brain development  
    acts_upstream_of_or_within brain development  
    acts_upstream_of_or_within camera-type eye development  
    acts_upstream_of_or_within cell differentiation  
    acts_upstream_of_or_within cell fate commitment  
    involved_in cell fate determination  
    acts_upstream_of_or_within cell fate determination  
    acts_upstream_of cell population proliferation  
    involved_in cellular response to fibroblast growth factor stimulus PubMed 
    involved_in cellular response to glucose stimulus PubMed 
    involved_in cellular response to insulin stimulus PubMed 
    involved_in cellular response to leukemia inhibitory factor  
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor  
    involved_in cellular response to prostaglandin E stimulus PubMed 
    involved_in cellular response to xenobiotic stimulus PubMed 
    involved_in cerebellum development PubMed 
    involved_in cerebral cortex development  
    involved_in cerebral cortex regionalization  
    acts_upstream_of_or_within cerebral cortex regionalization  
    involved_in cerebral cortex regionalization  
    involved_in chromatin remodeling  
    involved_in chromatin remodeling  
    involved_in commitment of neuronal cell to specific neuron type in forebrain  
    acts_upstream_of_or_within commitment of neuronal cell to specific neuron type in forebrain  
    involved_in cornea development in camera-type eye  
    involved_in cornea development in camera-type eye  
    involved_in dorsal/ventral axis specification  
    acts_upstream_of_or_within dorsal/ventral axis specification  
    acts_upstream_of_or_within dorsal/ventral pattern formation  
    involved_in embryonic camera-type eye morphogenesis  
    acts_upstream_of_or_within embryonic camera-type eye morphogenesis  
    involved_in epithelial cell development PubMed 
    involved_in establishment of mitotic spindle orientation  
    acts_upstream_of_or_within establishment of mitotic spindle orientation  
    involved_in eye photoreceptor cell development  
    acts_upstream_of_or_within eye photoreceptor cell development  
    involved_in forebrain development  
    acts_upstream_of_or_within forebrain development  
    involved_in forebrain dorsal/ventral pattern formation  
    acts_upstream_of_or_within forebrain dorsal/ventral pattern formation  
    involved_in forebrain-midbrain boundary formation  
    acts_upstream_of_or_within forebrain-midbrain boundary formation  
    acts_upstream_of_or_within gene expression  
    involved_in gene expression  
    acts_upstream_of glandular epithelial cell differentiation  
    involved_in glucose homeostasis  
    involved_in glucose homeostasis  
    involved_in habenula development  
    acts_upstream_of_or_within habenula development  
    involved_in hindbrain development PubMed 
    involved_in hindbrain development PubMed 
    involved_in insulin metabolic process PubMed 
    involved_in interkinetic nuclear migration PubMed 
    involved_in iris morphogenesis  
    involved_in iris morphogenesis  
    involved_in keratinocyte differentiation  
    acts_upstream_of_or_within keratinocyte differentiation  
    involved_in lacrimal gland development  
    acts_upstream_of_or_within lacrimal gland development  
    involved_in learned vocalization behavior or vocal learning PubMed 
    involved_in lens development in camera-type eye  
    acts_upstream_of_or_within lens development in camera-type eye  
    involved_in negative regulation of epithelial cell proliferation  
    acts_upstream_of_or_within negative regulation of epithelial cell proliferation  
    acts_upstream_of_or_within negative regulation of neural precursor cell proliferation  
    involved_in negative regulation of neuroblast proliferation  
    acts_upstream_of_or_within negative regulation of neuroblast proliferation  
    involved_in negative regulation of neuron differentiation  
    acts_upstream_of_or_within negative regulation of neuron differentiation  
    acts_upstream_of_or_within negative regulation of protein phosphorylation  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in nervous system development  
    involved_in neural crest cell migration PubMed 
    involved_in neural precursor cell proliferation PubMed 
    acts_upstream_of neural precursor cell proliferation  
    involved_in neuroblast proliferation  
    acts_upstream_of neuroblast proliferation  
    acts_upstream_of neuron differentiation  
    involved_in neuron differentiation  
    involved_in neuron migration  
    involved_in neuron migration PubMed 
    acts_upstream_of_or_within neuron migration  
    involved_in neuron migration  
    involved_in olfactory bulb development PubMed 
    involved_in olfactory bulb mitral cell layer development PubMed 
    involved_in oligodendrocyte cell fate specification  
    acts_upstream_of_or_within oligodendrocyte cell fate specification  
    acts_upstream_of_or_within pallium development  
    involved_in pancreatic A cell development  
    involved_in pancreatic A cell development PubMed 
    involved_in pancreatic A cell development  
    involved_in pancreatic A cell differentiation PubMed 
    involved_in pituitary gland development  
    acts_upstream_of_or_within pituitary gland development  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of cell fate specification PubMed 
    involved_in positive regulation of epithelial cell differentiation  
    acts_upstream_of_or_within positive regulation of epithelial cell differentiation  
    involved_in positive regulation of gene expression  
    involved_in positive regulation of gene expression PubMed 
    involved_in positive regulation of gene expression  
    involved_in positive regulation of glutamatergic neuron differentiation PubMed 
    involved_in positive regulation of miRNA transcription  
    involved_in positive regulation of miRNA transcription  
    involved_in positive regulation of neuroblast proliferation  
    acts_upstream_of_or_within positive regulation of neuroblast proliferation  
    involved_in positive regulation of neuron migration PubMed 
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in protein localization to organelle  
    acts_upstream_of_or_within protein localization to organelle  
    acts_upstream_of protein phosphorylation  
    acts_upstream_of_or_within regionalization  
    involved_in regulation of asymmetric cell division  
    acts_upstream_of_or_within regulation of asymmetric cell division  
    involved_in regulation of cell migration  
    acts_upstream_of_or_within regulation of cell migration  
    acts_upstream_of_or_within regulation of gene expression  
    involved_in regulation of neurogenesis PubMed 
    acts_upstream_of_or_within regulation of neurogenesis  
    involved_in regulation of neuron differentiation PubMed 
    acts_upstream_of_or_within regulation of neuron differentiation  
    involved_in regulation of neuron projection development PubMed 
    involved_in regulation of timing of cell differentiation  
    acts_upstream_of_or_within regulation of timing of cell differentiation  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II  
    involved_in response to ethanol PubMed 
    involved_in response to wounding  
    involved_in response to wounding  
    involved_in retina development in camera-type eye  
    involved_in retina development in camera-type eye  
    involved_in retina development in camera-type eye PubMed 
    acts_upstream_of_or_within retina development in camera-type eye  
    involved_in rhombomere morphogenesis PubMed 
    involved_in salivary gland morphogenesis  
    acts_upstream_of_or_within salivary gland morphogenesis  
    involved_in sensory neuron migration PubMed 
    involved_in sensory organ development  
    involved_in signal transduction involved in regulation of gene expression  
    acts_upstream_of_or_within signal transduction involved in regulation of gene expression  
    involved_in smoothened signaling pathway  
    acts_upstream_of_or_within smoothened signaling pathway  
    involved_in spinal cord development PubMed 
    acts_upstream_of_or_within telencephalon regionalization  
    involved_in transcription by RNA polymerase II  
    acts_upstream_of transcription by RNA polymerase II  
    involved_in type B pancreatic cell differentiation  
    involved_in type B pancreatic cell differentiation  
    involved_in type B pancreatic cell differentiation PubMed 
    acts_upstream_of_or_within type B pancreatic cell differentiation  
    involved_in ventral spinal cord development  
    involved_in ventral spinal cord development  
    Items 1 - 25 of 170
    Component Evidence Code Pubs
    located_in chromatin PubMed 
    located_in chromatin  
    located_in chromatin  
    located_in cytoplasm  
    located_in cytosol  
    located_in cytosol  
    located_in nucleoplasm  
    located_in nucleoplasm  
    located_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    paired box protein Pax-6
    Names
    oculorhombin
    paired box gene 6
    paired box homeotic gene 6

    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.

    mRNA and Protein(s)

    1. NM_013001.2NP_037133.1  paired box protein Pax-6

      See identical proteins and their annotated locations for NP_037133.1

      Status: PROVISIONAL

      Source sequence(s)
      BC128741
      UniProtKB/Swiss-Prot
      A1A5N7, P63016, Q6QHS5, Q701Q8
      UniProtKB/TrEMBL
      E1AZB1
      Related
      ENSRNOP00000005882.3, ENSRNOT00000005882.7
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214266
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      112590034..112611771
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006234633.5XP_006234695.1  paired box protein Pax-6 isoform X1

      See identical proteins and their annotated locations for XP_006234695.1

      UniProtKB/TrEMBL
      E1AZB1
      Related
      ENSRNOP00000071013.2, ENSRNOT00000089525.3
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228281
      Homeobox; Homeobox domain
    2. XM_063283158.1XP_063139228.1  paired box protein Pax-6 isoform X2

      UniProtKB/Swiss-Prot
      A1A5N7, P63016, Q6QHS5, Q701Q8
      UniProtKB/TrEMBL
      E1AZB1
    3. XM_039104376.2XP_038960304.1  paired box protein Pax-6 isoform X1

      UniProtKB/TrEMBL
      E1AZB1
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228281
      Homeobox; Homeobox domain
    External link. Please review our privacy policy.