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    Otx2 orthodenticle homeobox 2 [ Mus musculus (house mouse) ]

    Gene ID: 18424, updated on 24-Sep-2024

    Summary

    Official Symbol
    Otx2provided by MGI
    Official Full Name
    orthodenticle homeobox 2provided by MGI
    Primary source
    MGI:MGI:97451
    See related
    Ensembl:ENSMUSG00000021848 AllianceGenome:MGI:97451
    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
    E130306E05Rik
    Summary
    This gene encodes a protein that belongs to the homeobox family of transcription factors. The encoded protein plays a role in the development and patterning of the head. This protein regulates development of the choroid plexuses in the brain affecting composition of cerebrospinal fluid in the developing brain and is thought to function in the development of sense organs in the embryo. In humans, mutations in this gene are associated with pituitary hormone deficiency. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2013]
    Expression
    Biased expression in CNS E11.5 (RPKM 12.6), whole brain E14.5 (RPKM 5.2) and 3 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Otx2 in Genome Data Viewer
    Location:
    14 C1; 14 25.36 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (48894238..48905101, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (48656781..48667644, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930572G02 gene Neighboring gene STARR-seq mESC enhancer starr_36609 Neighboring gene STARR-seq mESC enhancer starr_36610 Neighboring gene predicted gene, 35766 Neighboring gene STARR-seq mESC enhancer starr_36611 Neighboring gene orthodenticle homeobox 2 opposite strand 1 Neighboring gene STARR-seq mESC enhancer starr_36613 Neighboring gene predicted gene 48909 Neighboring gene predicted gene, 25380

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data 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

    Process Evidence Code Pubs
    acts_upstream_of_or_within anatomical structure development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within animal organ morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 
    involved_in axon guidance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within central nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within diencephalon morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within dopaminergic neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in dopaminergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within endoderm development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within eye photoreceptor cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within forebrain development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within forebrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inner ear morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of mesendoderm development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within metencephalon development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within midbrain development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within midbrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuroepithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron fate determination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within oligodendrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gastrulation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within 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 ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within primitive streak formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in primitive streak formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within somite rostral/caudal axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon regionalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in growth cone ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IC
    Inferred by Curator
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    homeobox protein OTX2
    Names
    orthodenticle homolog 2

    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_001286481.1NP_001273410.1  homeobox protein OTX2 isoform a

      See identical proteins and their annotated locations for NP_001273410.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 5 and 6 encode the same isoform (a).
      Source sequence(s)
      AC166574, AK053741, AV513527, BC029667, BQ959742
      Consensus CDS
      CCDS70575.1
      UniProtKB/TrEMBL
      Q8R0B5
      Related
      ENSMUSP00000112532.2, ENSMUST00000119070.8
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
    2. NM_001286482.1NP_001273411.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_001273411.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded protein (isoform b) is shorter than isoform a. Variants 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC166574, AK053741, AV513527, BC017609, BQ959742, CO424557
      Consensus CDS
      CCDS49473.1
      UniProtKB/TrEMBL
      Q8VD35
      Related
      ENSMUSP00000154066.2, ENSMUST00000227404.2
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    3. NM_001286483.1NP_001273412.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_001273412.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded protein (isoform b) is shorter than isoform a. Variants 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC166574, AK053741, AK081535, AV513527
      Consensus CDS
      CCDS49473.1
      UniProtKB/TrEMBL
      Q8VD35
      Related
      ENSMUSP00000113690.2, ENSMUST00000118578.9
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    4. NM_001360225.1NP_001347154.1  homeobox protein OTX2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 5 and 6 encode the same isoform (a).
      Source sequence(s)
      AC166574, AK053741, BC017609, CF725076, CK621536
      Consensus CDS
      CCDS70575.1
      UniProtKB/TrEMBL
      Q8R0B5
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
    5. NM_001360226.1NP_001347155.1  homeobox protein OTX2 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1, 5 and 6 encode the same isoform (a).
      Source sequence(s)
      AC166574, AK053741, BC017609, CF725076
      Consensus CDS
      CCDS70575.1
      UniProtKB/TrEMBL
      Q8R0B5
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
    6. NM_144841.5NP_659090.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_659090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded protein (isoform b) is shorter than isoform a. Variants 2, 3 and 4 encode the same protein.
      Source sequence(s)
      AC166574, AK053741, BC017609
      Consensus CDS
      CCDS49473.1
      UniProtKB/TrEMBL
      Q8VD35
      Related
      ENSMUSP00000113930.2, ENSMUST00000122009.8
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      48894238..48905101 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017315914.2XP_017171403.1  homeobox protein OTX2 isoform X1

      UniProtKB/TrEMBL
      Q8R0B5
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
    2. XM_011244988.3XP_011243290.1  homeobox protein OTX2 isoform X1

      See identical proteins and their annotated locations for XP_011243290.1

      UniProtKB/TrEMBL
      Q8R0B5
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
    3. XM_011244989.3XP_011243291.1  homeobox protein OTX2 isoform X2

      See identical proteins and their annotated locations for XP_011243291.1

      UniProtKB/TrEMBL
      Q8VD35
      Related
      ENSMUSP00000154264.2, ENSMUST00000226501.2
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    4. XM_030247685.1XP_030103545.1  homeobox protein OTX2 isoform X2

      UniProtKB/TrEMBL
      Q8VD35
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    5. XM_017315917.2XP_017171406.1  homeobox protein OTX2 isoform X2

      UniProtKB/TrEMBL
      Q8VD35
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor