OTX1 Gene (Protein Coding)

Orthodenticle Homeobox 1

GC02P063050
GIFtS:
43
This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. A similar protein in mouse is required for proper brain and sensory organ development and can cause epilepsy. Alternative splicing results in multiple transcript varian... See more...

Aliases for OTX1 Gene

Aliases for OTX1 Gene

  • Orthodenticle Homeobox 1 2 3 5
  • Orthodenticle Homolog 1 3 4
  • Homeobox Protein OTX1 3 4
  • Orthodenticle (Drosophila) Homolog 1 2
  • Orthodenticle Homolog 1 (Drosophila) 2
  • OTX1 5

External Ids for OTX1 Gene

Previous GeneCards Identifiers for OTX1 Gene

  • GC02P063406
  • GC02P063234
  • GC02P063252
  • GC02P063189
  • GC02P063131
  • GC02P063016
  • GC02P063277

Summaries for OTX1 Gene

Entrez Gene Summary for OTX1 Gene

  • This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. A similar protein in mouse is required for proper brain and sensory organ development and can cause epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

GeneCards Summary for OTX1 Gene

OTX1 (Orthodenticle Homeobox 1) is a Protein Coding gene. Diseases associated with OTX1 include Agnathia-Otocephaly Complex and Epilepsy. Among its related pathways are Transcriptional Regulatory Network in Embryonic Stem Cell and Signaling pathways regulating pluripotency of stem cells. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific. An important paralog of this gene is OTX2.

UniProtKB/Swiss-Prot Summary for OTX1 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 OTX1 Gene

Additional gene information for OTX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for OTX1 Gene

Genomics for OTX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for OTX1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OTX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for OTX1

Top Transcription factor binding sites by QIAGEN in the OTX1 gene promoter:
  • AREB6
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HOXA5
  • POU2F1
  • SRY

Genomic Locations for OTX1 Gene

Latest Assembly
chr2:63,049,735-63,057,836
(GRCh38/hg38)
Size:
8,102 bases
Orientation:
Plus strand

Previous Assembly
chr2:63,276,870-63,284,966
(GRCh37/hg19 by Entrez Gene)
Size:
8,097 bases
Orientation:
Plus strand

chr2:63,277,192-63,284,971
(GRCh37/hg19 by Ensembl)
Size:
7,780 bases
Orientation:
Plus strand

Genomic View for OTX1 Gene

Genes around OTX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
OTX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for OTX1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for OTX1 Gene

Proteins for OTX1 Gene

Products:

  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for OTX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P32242-OTX1_HUMAN
    Recommended name:
    Homeobox protein OTX1
    Protein Accession:
    P32242
    Secondary Accessions:
    • A6NHA2
    • B3KTJ4
    • Q53TG6

    Protein attributes for OTX1 Gene

    Size:
    354 amino acids
    Molecular mass:
    37327 Da
    Quaternary structure:
    No Data Available

neXtProt entry for OTX1 Gene

Protein Expression for OTX1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for OTX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for OTX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for OTX1
  • Santa Cruz Biotechnology (SCBT) Antibodies for OTX1

No data available for DME Specific Peptides for OTX1 Gene

Domains & Families for OTX1 Gene

Gene Families for OTX1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for OTX1 Gene

InterPro:
Blocks:
  • Otx transcription factor signature
  • Otx1 transcription factor signature
ProtoNet:

Suggested Antigen Peptide Sequences for OTX1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ38361 fis, clone FEBRA2000532, highly similar to HOMEOBOX PROTEIN OTX1 (B3KTJ4_HUMAN)
  • Orthodenticle homolog 1 (Drosophila), isoform CRA_a (D6W5E5_HUMAN)
  • Orthodenticle homolog 1 (OTX1_HUMAN)
  • Homeobox protein OTX1 (Q9P2R2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P32242

UniProtKB/Swiss-Prot:

OTX1_HUMAN :
  • Belongs to the paired homeobox family. Bicoid subfamily.
Family:
  • Belongs to the paired homeobox family. Bicoid subfamily.
genes like me logo Genes that share domains with OTX1: view

Function for OTX1 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for OTX1 Gene

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'.
GENATLAS Biochemistry:
Drosophila orthodenticle (otd) homolog,paired-like homeo domain encoding gene 1,expressed in the developing brain of mouse embryo,required for corticogenesis and sense organ development

Phenotypes From GWAS Catalog for OTX1 Gene

Gene Ontology (GO) - Molecular Function for OTX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 18849347
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 18849347
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with OTX1: view
genes like me logo Genes that share phenotypes with OTX1: view

Animal Models for OTX1 Gene

MGI Knock Outs for OTX1:
  • Otx1 Otx1<tm1Asim>
  • Otx1 Otx1<tm1Sia>
  • Otx1 Otx1<tm2(otd)Asim>
  • Otx1 Otx1<tm3(OTX2)Asim>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for OTX1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for OTX1 Gene

Localization for OTX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for OTX1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for OTX1 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
cytosol 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nuclear speckles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for OTX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with OTX1: view

Pathways & Interactions for OTX1 Gene

PathCards logo

SuperPathways for OTX1 Gene

SuperPathway Contained pathways
1 Signaling pathways regulating pluripotency of stem cells
Signaling pathways regulating pluripotency of stem cells
-
2 Transcriptional Regulatory Network in Embryonic Stem Cell
Transcriptional Regulatory Network in Embryonic Stem Cell
-
3 DAG and IP3 signaling
Development Role of Activin A in cell differentiation and proliferation
.32
genes like me logo Genes that share pathways with OTX1: view

Pathways by source for OTX1 Gene

1 GeneGo (Thomson Reuters) pathway for OTX1 Gene
  • Development Role of Activin A in cell differentiation and proliferation
1 Qiagen pathway for OTX1 Gene
  • Transcriptional Regulatory Network in Embryonic Stem Cell

SIGNOR curated interactions for OTX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for OTX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0009952 anterior/posterior pattern specification IEA --
GO:0022037 metencephalon development IEA --
genes like me logo Genes that share ontologies with OTX1: view

Drugs & Compounds for OTX1 Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for OTX1 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for OTX1 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for OTX1

Alternative Splicing Database (ASD) splice patterns (SP) for OTX1 Gene

No ASD Table

Relevant External Links for OTX1 Gene

GeneLoc Exon Structure for
OTX1

Expression for OTX1 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for OTX1 Gene

mRNA expression in normal human tissues for OTX1 Gene
mRNA expression by GTEx for OTX1 GenemRNA expression by BioGPS for OTX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for OTX1 Gene

This gene is overexpressed in Minor Salivary Gland (x14.7), Skin - Sun Exposed (Lower leg) (x8.7), and Skin - Not Sun Exposed (Suprapubic) (x6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for OTX1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for OTX1

SOURCE GeneReport for Unigene cluster for OTX1 Gene:

Hs.734360

mRNA Expression by UniProt/SwissProt for OTX1 Gene:

P32242-OTX1_HUMAN
Tissue specificity: Expressed in brain. Detected in the anterior part of the neural fetal retina (at protein level).

Evidence on tissue expression from TISSUES for OTX1 Gene

  • Nervous system(4.7)
  • Eye(4.4)
genes like me logo Genes that share expression patterns with OTX1: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for OTX1 Gene

Orthologs for OTX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for OTX1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia OTX1 30 31
  • 98.78 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia OTX1 31
  • 92 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia OTX1 30 31
  • 90.4 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia OTX1 30 31
  • 89.74 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Otx1 30 17 31
  • 88.79 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Otx1 30
  • 88.7 (n)
Chicken
(Gallus gallus)
 Aves OTX1 31
  • 68 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia OTX1 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia otx1 30
  • 75.08 (n)
MGC75643 30
African clawed frog
(Xenopus laevis)
 Amphibia otx1-A 30
Zebrafish
(Danio rerio)
 Actinopterygii otx1b 30 31
  • 74.92 (n)
 OneToMany
otx1a 31
  • 69 (a)
 OneToMany
-- 30
Fruit Fly
(Drosophila melanogaster)
 Insecta oc 31
  • 25 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CS-OTX 31
  • 39 (a)
 OneToMany
Species where no ortholog for OTX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for OTX1 Gene

ENSEMBL:
Gene Tree for OTX1 (if available)
TreeFam:
Gene Tree for OTX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for OTX1: view image

Paralogs for OTX1 Gene

Paralogs for OTX1 Gene

(9) SIMAP similar genes for OTX1 Gene using alignment to 4 proteins:

  • OTX1_HUMAN
  • B5MC54_HUMAN
  • D6W5E5_HUMAN
  • Q9P2R2_HUMAN
genes like me logo Genes that share paralogs with OTX1: view

Variants for OTX1 Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for OTX1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs147660988 Benign: not provided 63,053,017(+) A/T
NM_014562.4(OTX1):c.27A>T (p.Pro9=) 		NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs61742369 Benign: not provided 63,055,927(+) G/A
NM_014562.4(OTX1):c.676G>A (p.Gly226Ser) 		MISSENSE_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for OTX1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for OTX1 Gene

Variant ID Type Subtype PubMed ID
nsv1004678 CNV loss 25217958
nsv7313 OTHER inversion 18451855

Variation tolerance for OTX1 Gene

Residual Variation Intolerance Score: 14.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.56; 30.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for OTX1 Gene

Human Gene Mutation Database (HGMD)
OTX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
OTX1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for OTX1 Gene

Disorders for OTX1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for OTX1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
agnathia-otocephaly complex
  • agotc
epilepsy
  • epilepsy syndrome
dyslexia
medulloblastoma
  • mdb
cone-rod dystrophy 2
  • cord2
- elite association - COSMIC cancer census association via MalaCards
Search OTX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for OTX1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with OTX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for OTX1 Gene

Publications for OTX1 Gene

  1. Expression of the homeobox genes PAX6, OTX2, and OTX1 in the early human fetal retina. (PMID: 19414065) Larsen KB … Møller M (International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience 2009) 3 4
  2. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. (PMID: 19767753) Eeles RA … Easton DF (Nature genetics 2009) 3 41
  3. Polymorphisms of coding trinucleotide repeats of homeogenes in neurodevelopmental psychiatric disorders. (PMID: 19018235) Laroche F … Robel L (Psychiatric genetics 2008) 3 41
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

ExternalLinks

View latest publications for OTX1 gene in Mastermind

Products for OTX1 Gene

  • Addgene plasmids for OTX1

Sources for OTX1 Gene