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    OTX2 orthodenticle homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 5015, updated on 17-Jun-2019

    Summary

    Official Symbol
    OTX2provided by HGNC
    Official Full Name
    orthodenticle homeobox 2provided by HGNC
    Primary source
    HGNC:HGNC:8522
    See related
    Ensembl:ENSG00000165588 MIM:600037
    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
    CPHD6; MCOPS5
    Summary
    This gene encodes a member of the bicoid subfamily of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and plays a role in brain, craniofacial, and sensory organ development. The encoded protein also influences the proliferation and differentiation of dopaminergic neuronal progenitor cells during mitosis. Mutations in this gene cause syndromic microphthalmia 5 (MCOPS5) and combined pituitary hormone deficiency 6 (CPHD6). This gene is also suspected of having an oncogenic role in medulloblastoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Pseudogenes of this gene are known to exist on chromosomes two and nine. [provided by RefSeq, Jul 2012]
    Expression
    Low expression observed in reference dataset See more
    Orthologs

    Genomic context

    See OTX2 in Genome Data Viewer
    Location:
    14q22.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (56799905..56810479, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (57267425..57277194, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene transmembrane protein 260 Neighboring gene uncharacterized LOC105370515 Neighboring gene ribosomal protein L36a pseudogene 1 Neighboring gene OTX2 antisense RNA 1 (head to head) Neighboring gene RNA, U6 small nuclear 1204, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 461, pseudogene

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-03-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-03-08)

    ClinGen Genome Curation PagePubMed

    Pathways from BioSystems

    • Dopaminergic Neurogenesis, organism-specific biosystem (from WikiPathways)
      Dopaminergic Neurogenesis, organism-specific biosystemConverted to human from mouse: http://www.wikipathways.org/index.php/Pathway:WP1498
    • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
      Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
    • TP53 Network, organism-specific biosystem (from WikiPathways)
      TP53 Network, organism-specific biosystemP53 is not a lonely genome guardian, it operates with the assistance of p73 and p63 within a complex network including distinct but complementary pathways. This protein family presents a high le...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC45000

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dopaminergic neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    dopaminergic neuron differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    forebrain development TAS
    Traceable Author Statement
    more info
    PubMed 
    midbrain development TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of gastrulation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    primitive streak formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of fibroblast growth factor receptor signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of smoothened signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    growth cone IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein-containing 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)

    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_008204.1 RefSeqGene

      Range
      9840..14760
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001270523.2NP_001257452.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_001257452.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment of the coding region, compared to variant 1, and, compared to isoform a, encodes a shorter isoform (b). Variants 2-4 encode the same protein (isoform b).
      Source sequence(s)
      AB593058, AL161757, BC032579, CV812961
      Consensus CDS
      CCDS41960.1
      UniProtKB/Swiss-Prot
      P32243
      UniProtKB/TrEMBL
      F1T0D1
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    2. NM_001270524.2NP_001257453.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_001257453.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an in-frame segment of the coding region, compared to variant 1, and, compared to isoform a, encodes a shorter isoform (b). Variants 2-4 encode the same protein (isoform b).
      Source sequence(s)
      AB593058, AK314271, AL161757, BC032579
      Consensus CDS
      CCDS41960.1
      UniProtKB/Swiss-Prot
      P32243
      UniProtKB/TrEMBL
      F1T0D1
      Related
      ENSP00000452336.1, ENST00000555006.5
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor
    3. NM_001270525.2NP_001257454.1  homeobox protein OTX2 isoform a

      See identical proteins and their annotated locations for NP_001257454.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1, and encodes the longer isoform (a). Variants 1 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AB593056, AL161757, BC032579, BU176852
      Consensus CDS
      CCDS9728.1
      UniProtKB/Swiss-Prot
      P32243
      UniProtKB/TrEMBL
      F1T0C9, F1T0D1
      Related
      ENSP00000451357.1, ENST00000554845.1
      Conserved Domains (2) summary
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
    4. NM_021728.4NP_068374.1  homeobox protein OTX2 isoform a

      See identical proteins and their annotated locations for NP_068374.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AB593058, AL161757, BC032579
      Consensus CDS
      CCDS9728.1
      UniProtKB/Swiss-Prot
      P32243
      UniProtKB/TrEMBL
      F1T0D1
      Related
      ENSP00000343819.4, ENST00000339475.9
      Conserved Domains (2) summary
      pfam03529
      Location:161242
      TF_Otx; Otx1 transcription factor
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
    5. NM_172337.3NP_758840.1  homeobox protein OTX2 isoform b

      See identical proteins and their annotated locations for NP_758840.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame segment of the coding region, compared to variant 1, and, compared to isoform a, encodes a shorter isoform (b). Variants 2-4 encode the same protein (isoform b).
      Source sequence(s)
      AB593056, AB593057, AL161757, BC032579
      Consensus CDS
      CCDS41960.1
      UniProtKB/Swiss-Prot
      P32243
      UniProtKB/TrEMBL
      F1T0C9, F1T0D0
      Related
      ENSP00000386185.3, ENST00000408990.7
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:153234
      TF_Otx; Otx1 transcription factor

    RNA

    1. NR_073034.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an exon in the coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated.
      Source sequence(s)
      AL161757, BC032579, DB294481
    2. NR_073036.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and lacks an exon in the coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated.
      Source sequence(s)
      AB593056, AL161757, BC032579

    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.p13 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

      Range
      56799905..56810479 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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