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

Gene ID: 25509, updated on 26-Jan-2021

Summary

Official Symbol
Pax6provided by RGD
Official Full Name
paired box 6provided by RGD
Primary source
RGD:3258
See related
Ensembl:ENSRNOG00000004410
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
homeodomain (HD)-containing transcription factor; may play a role in the differentiation of the hindbrain somatic (SM) motoneurones and V1 interneurones in the hindbrain and/or spinal cord [RGD, Feb 2006]
Expression
Restricted expression toward (RPKM 32.2) See more
Orthologs
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Genomic context

See Pax6 in Genome Data Viewer
Location:
3q33
Exon count:
17
Annotation release Status Assembly Chr Location
108 current 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_051338.1Genomic Context describing neighboring genes Neighboring gene hypothetical protein LOC691083 Neighboring gene reticulocalbin 1 Neighboring gene elongator acetyltransferase complex subunit 4 Neighboring gene 60S ribosomal protein L35a pseudogene Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC120101618 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

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

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
    P63016
    Related
    ENSRNOP00000005882.3, ENSRNOT00000005882.5
    Conserved Domains (2) summary
    smart00351
    Location:4128
    PAX; Paired Box domain
    pfam00046
    Location:214266
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Rattus norvegicus 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 mRatBN7.2 Primary Assembly

Genomic

  1. NC_051338.1 Reference mRatBN7.2 Primary Assembly

    Range
    92128772..92157022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006234636.4XP_006234698.1  paired box protein Pax-6 isoform X1

    See identical proteins and their annotated locations for XP_006234698.1

    UniProtKB/Swiss-Prot
    P63016
    Conserved Domains (2) summary
    smart00351
    Location:4142
    PAX; Paired Box domain
    pfam00046
    Location:228280
    Homeobox; Homeobox domain
  2. XM_006234634.4XP_006234696.1  paired box protein Pax-6 isoform X1

    See identical proteins and their annotated locations for XP_006234696.1

    UniProtKB/Swiss-Prot
    P63016
    Conserved Domains (2) summary
    smart00351
    Location:4142
    PAX; Paired Box domain
    pfam00046
    Location:228280
    Homeobox; Homeobox domain
  3. XM_039104377.1XP_038960305.1  paired box protein Pax-6 isoform X2

  4. XM_006234633.4XP_006234695.1  paired box protein Pax-6 isoform X1

    See identical proteins and their annotated locations for XP_006234695.1

    UniProtKB/Swiss-Prot
    P63016
    Conserved Domains (2) summary
    smart00351
    Location:4142
    PAX; Paired Box domain
    pfam00046
    Location:228280
    Homeobox; Homeobox domain
  5. XM_006234635.4XP_006234697.1  paired box protein Pax-6 isoform X1

    See identical proteins and their annotated locations for XP_006234697.1

    UniProtKB/Swiss-Prot
    P63016
    Conserved Domains (2) summary
    smart00351
    Location:4142
    PAX; Paired Box domain
    pfam00046
    Location:228280
    Homeobox; Homeobox domain
  6. XM_039104376.1XP_038960304.1  paired box protein Pax-6 isoform X1

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