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Aliases for OTX2 Gene

Aliases for OTX2 Gene

  • Orthodenticle Homeobox 2 2 3
  • Orthodenticle Homolog 2 3 4
  • MCOPS5 3 6
  • CPHD6 3 6
  • Orthodenticle Homolog 2 (Drosophila) 2
  • Homeobox Protein OTX2 3

External Ids for OTX2 Gene

Summaries for OTX2 Gene

Entrez Gene Summary for OTX2 Gene

  • 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]

GeneCards Summary for OTX2 Gene

OTX2 (Orthodenticle Homeobox 2) is a Protein Coding gene. Diseases associated with OTX2 include pituitary hormone deficiency, combined, 6 and otx2-related combined pituitary hormone deficiency. Among its related pathways are Wnt / Hedgehog / Notch and Neuroscience. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is PITX3.

UniProtKB/Swiss-Prot for OTX2 Gene

  • Probably plays a role in the development of the brain and the sense organs. Can bind to the BCD target sequence (BTS): 5-TCTAATCCC-3

Gene Wiki entry for OTX2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for OTX2 Gene

Genomics for OTX2 Gene

Genomic Location for OTX2 Gene

56,799,905 bp from pter
56,810,479 bp from pter
10,575 bases
Minus strand

Genomic View for OTX2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for OTX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for OTX2 Gene

Regulatory Elements for OTX2 Gene

Proteins for OTX2 Gene

  • Protein details for OTX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein OTX2
    Protein Accession:
    Secondary Accessions:
    • B2RAN5
    • Q6GTV3
    • Q9HAW3
    • Q9P2R1

    Protein attributes for OTX2 Gene

    289 amino acids
    Molecular mass:
    31636 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for OTX2 Gene


neXtProt entry for OTX2 Gene

Proteomics data for OTX2 Gene at MOPED

Post-translational modifications for OTX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for OTX2 Gene

Domains for OTX2 Gene

Gene Families for OTX2 Gene

  • PRD :Homeoboxes / PRD class


  • Contains 1 homeobox DNA-binding domain.:
    • P32243
  • Belongs to the paired homeobox family. Bicoid subfamily.:
    • P32243
genes like me logo Genes that share domains with OTX2: view

Function for OTX2 Gene

Molecular function for OTX2 Gene

GENATLAS Biochemistry: Drosophila orthodenticle (otd) homolog,paired-like homeo domain encoding gene 2,expressed in the developing brain of the anterior neural plate,in mouse embryo,playing a major role in gastrulation,essential for the early specification of neuroectoderm destined to become fore midbrain
UniProtKB/Swiss-Prot Function: Probably plays a role in the development of the brain and the sense organs. Can bind to the BCD target sequence (BTS): 5-TCTAATCCC-3

Gene Ontology (GO) - Molecular Function for OTX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 12559959
GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA 12559959
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity --
GO:0005515 protein binding IPI 20530484
genes like me logo Genes that share ontologies with OTX2: view
genes like me logo Genes that share phenotypes with OTX2: view

Animal Models for OTX2 Gene

MGI Knock Outs for OTX2:

miRNA for OTX2 Gene

miRTarBase miRNAs that target OTX2

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for OTX2 Gene

Localization for OTX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for OTX2 Gene

Subcellular locations from

Jensen Localization Image for OTX2 Gene COMPARTMENTS Subcellular localization image for OTX2 gene
Compartment Confidence
nucleus 4

Gene Ontology (GO) - Cellular Components for OTX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0030426 growth cone IDA 16267555
GO:0043234 protein complex IDA 20530484
genes like me logo Genes that share ontologies with OTX2: view

Pathways for OTX2 Gene

genes like me logo Genes that share pathways with OTX2: view

Pathways by source for OTX2 Gene

2 Cell Signaling Technology pathways for OTX2 Gene
1 BioSystems pathway for OTX2 Gene

Gene Ontology (GO) - Biological Process for OTX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001708 cell fate specification IEA --
GO:0006355 regulation of transcription, DNA-templated --
GO:0006357 regulation of transcription from RNA polymerase II promoter --
GO:0006461 protein complex assembly IDA 20530484
GO:0007275 multicellular organismal development --
genes like me logo Genes that share ontologies with OTX2: view

Compounds for OTX2 Gene

(1) Novoseek inferred chemical compound relationships for OTX2 Gene

Compound -log(P) Hits PubMed IDs
oligonucleotide 2.4 1
genes like me logo Genes that share compounds with OTX2: view

Transcripts for OTX2 Gene

Unigene Clusters for OTX2 Gene

Orthodenticle homeobox 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for OTX2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d · 5e
SP1: - - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - - -
SP5: - -
SP6: -
SP8: - - -

Relevant External Links for OTX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for OTX2 Gene

mRNA expression in normal human tissues for OTX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for OTX2 Gene

This gene is overexpressed in Brain - Cerebellum (21.2), Brain - Cerebellar Hemisphere (19.4), and Brain - Substantia nigra (4.7).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for OTX2 Gene

SOURCE GeneReport for Unigene cluster for OTX2 Gene Hs.288655

mRNA Expression by UniProt/SwissProt for OTX2 Gene

Tissue specificity: Expressed in brain
genes like me logo Genes that share expressions with OTX2: view

Orthologs for OTX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for OTX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia OTX2 36
  • 100 (n)
  • 100 (a)
OTX2 37
  • 100 (a)
(Bos Taurus)
Mammalia OTX2 36
  • 96.66 (n)
  • 98.96 (a)
OTX2 37
  • 99 (a)
(Canis familiaris)
Mammalia OTX2 36
  • 96.52 (n)
  • 99.33 (a)
OTX2 37
  • 99 (a)
(Mus musculus)
Mammalia Otx2 36
  • 94.84 (n)
  • 99.33 (a)
Otx2 16
Otx2 37
  • 99 (a)
(Monodelphis domestica)
Mammalia OTX2 37
  • 98 (a)
(Rattus norvegicus)
Mammalia LOC100911492 36
  • 94.39 (n)
  • 100 (a)
(Gallus gallus)
Aves OTX2 37
  • 99 (a)
(Anolis carolinensis)
Reptilia OTX2 37
  • 95 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11672 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10021 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6859 36
(Danio rerio)
Actinopterygii otx2 36
  • 79.47 (n)
  • 93.77 (a)
otx2 37
  • 94 (a)
fruit fly
(Drosophila melanogaster)
Insecta oc 37
  • 23 (a)
(Caenorhabditis elegans)
Secernentea ttx-1 37
  • 22 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3985 36
sea squirt
(Ciona savignyi)
Ascidiacea CS-OTX 37
  • 36 (a)
Species with no ortholog for OTX2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for OTX2 Gene

Gene Tree for OTX2 (if available)
Gene Tree for OTX2 (if available)

Paralogs for OTX2 Gene

Paralogs for OTX2 Gene

Selected SIMAP similar genes for OTX2 Gene using alignment to 6 proteins: Pseudogenes for OTX2 Gene

genes like me logo Genes that share paralogs with OTX2: view

Variants for OTX2 Gene

Sequence variations from dbSNP and Humsavar for OTX2 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs171978 -- 56,801,725(-) CTGTA(A/G)AACCT utr-variant-3-prime, nc-transcript-variant
rs198238 -- 56,800,680(-) ACACC(A/G)CTATT downstream-variant-500B
rs198239 -- 56,800,305(-) ATTTG(A/G)TTAAG downstream-variant-500B
rs198240 -- 56,800,210(-) TGATT(C/T)CTGAA downstream-variant-500B
rs698015 -- 56,803,107(-) AAGTG(A/G)TAAGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for OTX2 Gene

Variant ID Type Subtype PubMed ID
nsv901981 CNV Loss 21882294
dgv1941n71 CNV Loss 21882294

Relevant External Links for OTX2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

Disorders for OTX2 Gene

(2) OMIM Diseases for OTX2 Gene (600037)


  • Microphthalmia, syndromic, 5 (MCOPS5) [MIM:610125]: Patients manifest unilateral or bilateral microphthalmia/clinical anophthalmia and variable additional features including pituitary dysfunction, coloboma, microcornea, cataract, retinal dystrophy, hypoplasia or agenesis of the optic nerve, agenesis of the corpus callosum, developmental delay, joint laxity, hypotonia, and seizures. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269 PubMed:15846561, ECO:0000269 PubMed:20396904}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Pituitary hormone deficiency, combined, 6 (CPHD6) [MIM:613986]: Combined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD6 patients manifest neonatal hypoglycemia, and deficiencies of growth hormone, thyroid-stimulating hormone, luteinizing hormone, follicle stimulating hormone and adrenocorticotropic hormone. {ECO:0000269 PubMed:18728160}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) University of Copenhagen DISEASES for OTX2 Gene

(4) Novoseek inferred disease relationships for OTX2 Gene

Disease -log(P) Hits PubMed IDs
anophthalmia 85.4 5
microphthalmia 78 5
medulloblastoma 63.2 18
tumors 0 9

Relevant External Links for OTX2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with OTX2: view

Publications for OTX2 Gene

  1. Chromosome locations of human EMX and OTX genes. (PMID: 7959790) Kastury K. … Boncinelli E. (Genomics 1994) 2 3 23
  2. Polymorphisms in the homeobox gene OTX2 may be a risk factor for bipolar disorder. (PMID: 17541950) Sabunciyan S. … Weis S. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2007) 3 23 49
  3. Expression of the homeobox genes PAX6, OTX2, and OTX1 in the early human fetal retina. (PMID: 19414065) Larsen K.B. … ller M. (Int. J. Dev. Neurosci. 2009) 3 4 23
  4. A novel dominant negative mutation of OTX2 associated with combined pituitary hormone deficiency. (PMID: 18728160) Diaczok D. … Radovick S. (J. Clin. Endocrinol. Metab. 2008) 3 4 23
  5. A novel loss-of-function mutation in OTX2 in a patient with anophthalmia and isolated growth hormone deficiency. (PMID: 20396904) Ashkenazi-Hoffnung L. … Gat-Yablonski G. (Hum. Genet. 2010) 3 4 23

Products for OTX2 Gene

Sources for OTX2 Gene

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