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    Pax6 paired box 6 [ Mus musculus (house mouse) ]

    Gene ID: 18508, updated on 27-Nov-2024

    Summary

    Official Symbol
    Pax6provided by MGI
    Official Full Name
    paired box 6provided by MGI
    Primary source
    MGI:MGI:97490
    See related
    Ensembl:ENSMUSG00000027168 AllianceGenome:MGI:97490
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Dey; Sey; AEY11; Pax-6; Gsfaey11; 1500038E17Rik
    Summary
    This gene encodes a homeobox-containing protein that functions as a regulator of transcription. It plays a key role in the development of neural tissues, particularly the eye. Activity of this protein is also required for expression of glucagon in the pancreas. This gene is regulated by multiple enhancers located up to tens or hundreds of kilobases upstream and downstream of the transcription start sites. Mutations in this gene or deletion of these regulatory elements results in severe defects in eye development. Alternative splicing and the use of alternative promoters results in multiple transcript variants, some of which encode proteins that lack the N-terminal paired domain. [provided by RefSeq, Jul 2015]
    Expression
    Biased expression in cerebellum adult (RPKM 9.1), whole brain E14.5 (RPKM 7.7) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Pax6 in Genome Data Viewer
    Location:
    2 E3; 2 55.31 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (105499241..105528755)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (105668896..105698410)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene paired box 6 opposite strand 1 Neighboring gene STARR-seq mESC enhancer starr_05312 Neighboring gene Pax6 upstream regulatory region Neighboring gene predicted gene, 35946 Neighboring gene STARR-seq mESC enhancer starr_05314 Neighboring gene enhancer in intron 4 of Pax6 Neighboring gene enhancer region in intron 7 of Pax6 Neighboring gene Pax6 upstream antisense RNA Neighboring gene STARR-seq mESC enhancer starr_05317 Neighboring gene elongator acetyltransferase complex subunit 4 Neighboring gene RB enhancer downstream of Pax6 Neighboring gene Pax6 downstream regulatory region Neighboring gene STARR-seq mESC enhancer starr_05318 Neighboring gene STARR-seq mESC enhancer starr_05319 Neighboring gene STARR-positive B cell enhancer ABC_E639 Neighboring gene IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:105843384-105843567 Neighboring gene DnaJ heat shock protein family (Hsp40) member C24 Neighboring gene doublecortin domain containing 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables HMG box domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables R-SMAD binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables R-SMAD binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables co-SMAD binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone acetyltransferase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables minor groove of adenine-thymine-rich DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables minor groove of adenine-thymine-rich DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coregulator binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior pattern specification IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within anterior/posterior pattern specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within astrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in astrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in astrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in blood vessel development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within camera-type eye development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell fate commitment IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell fate determination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to fibroblast growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to insulin stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cellular response to prostaglandin E stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebellum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebral cortex development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cerebral cortex regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within commitment of neuronal cell to specific neuron type in forebrain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cornea development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cornea development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dorsal/ventral axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within embryonic camera-type eye morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in epithelial cell development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within establishment of mitotic spindle orientation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within eye photoreceptor cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in forebrain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within forebrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forebrain dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forebrain-midbrain boundary formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of glandular epithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glucose homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within habenula development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hindbrain development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in insulin metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in insulin metabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in interkinetic nuclear migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in interkinetic nuclear migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in iris morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in iris morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within keratinocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lacrimal gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in learned vocalization behavior or vocal learning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in learned vocalization behavior or vocal learning ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within lens development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of neural precursor cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neural crest cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural crest cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of neural precursor cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory bulb development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory bulb mitral cell layer development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in olfactory bulb mitral cell layer development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within oligodendrocyte cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within pallium development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pancreatic A cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pancreatic A cell development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in pancreatic A cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within pituitary gland development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell fate specification ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of core promoter binding ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of core promoter binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of epithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of glutamatergic neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of glutamatergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of miRNA transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of miRNA transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within protein localization to organelle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within regulation of asymmetric cell division IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of neurogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of neurogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within regulation of timing of cell differentiation 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
     
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to ethanol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to wounding IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina development in camera-type eye IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within retina development in camera-type eye IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in rhombomere morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in rhombomere morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within salivary gland morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory neuron migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sensory organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within signal transduction involved in regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within smoothened signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in type B pancreatic cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within type B pancreatic cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in type B pancreatic cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ventral spinal cord development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular anatomical structure IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    paired box protein Pax-6
    Names
    Dickie's small eye
    oculorhombin
    paired box 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_001244198.2NP_001231127.1  paired box protein Pax-6 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). It initiates from the P0 promoter. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK032616, AK139054, AL512589, CF724474, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000106715.3, ENSMUST00000111086.11
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228281
      Homeobox; Homeobox domain
    2. NM_001244200.2NP_001231129.1  paired box protein Pax-6 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. It initiates from the P1 promoter. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK139054, AL512589, AY064175, CN538503, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      UniProtKB/TrEMBL
      Q8VBX9
      Related
      ENSMUSP00000129344.3, ENSMUST00000167211.9
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228281
      Homeobox; Homeobox domain
    3. NM_001244201.2NP_001231130.1  paired box protein Pax-6 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 1. It initiates from the P0 promoter. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK032616, AK139054, AL512589, CA751997, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P32117, P63015, P70601, Q3UTV5, Q62222, Q64037, Q8CEI5, Q8VDB5, Q921Q8
      Related
      ENSMUSP00000106716.3, ENSMUST00000111087.10
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214267
      Homeobox; Homeobox domain
    4. NM_001244202.2NP_001231131.1  paired box protein Pax-6 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK045805, AK139054, AL512589, BF466986, CA751997, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P32117, P63015, P70601, Q3UTV5, Q62222, Q64037, Q8CEI5, Q8VDB5, Q921Q8
      Related
      ENSMUSP00000106711.2, ENSMUST00000111082.8
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214267
      Homeobox; Homeobox domain
    5. NM_001310144.1NP_001297073.1  paired box protein Pax-6 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an in-frame exon in the 5' coding region compared to variant 1. It initiates from the P1 promoter. The encoded isoform (2) is shorter than isoform 1. Variants 4, 5, and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AK139054, AL512589, AY064175, CD805985, CN539431, CN539723, CX565124
      Consensus CDS
      CCDS57181.1
      UniProtKB/Swiss-Prot
      P32117, P63015, P70601, Q3UTV5, Q62222, Q64037, Q8CEI5, Q8VDB5, Q921Q8
      Related
      ENSMUSP00000087878.7, ENSMUST00000090397.13
      Conserved Domains (2) summary
      smart00351
      Location:4128
      PAX; Paired Box domain
      pfam00046
      Location:214267
      Homeobox; Homeobox domain
    6. NM_001310145.1NP_001297074.1  paired box protein Pax-6 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It initiates from the P alpha promoter. The encoded isoform (3) has a shorter N-terminus and lacks the paired domain, compared to isoform 1. Variants 7 and 8 encode the same protein (isoform 3, also known as DeltaPD).
      Source sequence(s)
      AK139054, AL512589, CK617741, CN539723, CX565124
      UniProtKB/Swiss-Prot
      P63015
      Conserved Domains (1) summary
      pfam00046
      Location:78131
      Homeobox; Homeobox domain
    7. NM_001310146.1NP_001297075.1  paired box protein Pax-6 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and lacks a portion of the 5' coding region compared to variant 1. It initiates from the P alpha promoter. The encoded isoform (3) has a shorter N-terminus and lacks the paired domain, compared to isoform 1. Variants 7 and 8 encode the same protein (isoform 3, also known as DeltaPD).
      Source sequence(s)
      AK139054, AL512589, CN539723, CV784112, CX565124
      UniProtKB/Swiss-Prot
      P63015
      Conserved Domains (1) summary
      pfam00046
      Location:78131
      Homeobox; Homeobox domain
    8. NM_013627.6NP_038655.1  paired box protein Pax-6 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein (isoform 1, also known as 5a).
      Source sequence(s)
      AK045805, AK139054, AL512589, BF466986, CF724474, CN539723, CX565124
      Consensus CDS
      CCDS16499.1
      UniProtKB/Swiss-Prot
      P63015
      Related
      ENSMUSP00000087870.6, ENSMUST00000090391.13
      Conserved Domains (2) summary
      smart00351
      Location:4142
      PAX; Paired Box domain
      pfam00046
      Location:228281
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      105499241..105528755
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)