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    OTX2 orthodenticle homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 5015, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:8522
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See OTX2 in Genome Data Viewer
    Location:
    14q22.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (56799905..56810479, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (51005697..51016270, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (57266623..57277197, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903433 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:57199769-57200270 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:57200271-57200770 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:57228911-57229123 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:57260608-57261532 Neighboring gene uncharacterized LOC124903322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:57263762-57264356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:57270522-57271360 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:57272200-57273038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:57278577-57279469 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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Anophthalmia-microphthalmia syndrome
    MedGen: C5680330 GeneReviews: Not available
    Compare labs
    Pituitary hormone deficiency, combined, 6
    MedGen: C3151440 OMIM: 613986 GeneReviews: Not available
    Compare labs
    Syndromic microphthalmia type 5
    MedGen: C1864690 OMIM: 610125 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-09-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-08)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC45000

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of 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)

    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.

    Genomic

    1. NG_008204.2 RefSeqGene

      Range
      11215..21789
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_718

    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
      B2RAN5, P32243, Q6GTV3, Q9HAW3, Q9P2R1
      UniProtKB/TrEMBL
      F1T0D0
      Related
      ENSP00000343819.5, ENST00000339475.10
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:155234
      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
      B2RAN5, P32243, Q6GTV3, Q9HAW3, Q9P2R1
      UniProtKB/TrEMBL
      F1T0D0
      Related
      ENSP00000452336.1, ENST00000555006.5
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:155234
      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/TrEMBL
      F1T0D0, F1T0D1
      Related
      ENSP00000451357.2, ENST00000554845.2
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:163242
      TF_Otx; Otx1 transcription factor
    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/TrEMBL
      F1T0D0, F1T0D1
      Related
      ENSP00000500115.1, ENST00000672264.2
      Conserved Domains (2) summary
      pfam00046
      Location:50102
      Homeobox; Homeobox domain
      pfam03529
      Location:163242
      TF_Otx; Otx1 transcription factor
    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
      B2RAN5, P32243, Q6GTV3, Q9HAW3, Q9P2R1
      UniProtKB/TrEMBL
      F1T0D0
      Related
      ENSP00000386185.3, ENST00000408990.8
      Conserved Domains (2) summary
      pfam00046
      Location:4294
      Homeobox; Homeobox domain
      pfam03529
      Location:155234
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      51005697..51016270 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)