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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

OTOP1 Gene

protein-coding   GIFtS: 44
GCID: GC04M004190

otopetrin 1
 Explore 3 diseases affiliated with
OTOP1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for OTOP1    

Aliases
for OTOP1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Otopetrin 11 2
Otopetrin-11

External Ids:    HGNC: 196561   Entrez Gene: 1330602   Ensembl: ENSG000001639827   OMIM: 6078065   UniProtKB: Q7RTM13   

Export aliases for OTOP1 gene to outside databases

Previous GC identifers: GC04M004183 GC04M004255 GC04M004308 GC04M004241 GC04M004126


Summaries
for OTOP1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: OTOP1_HUMAN, Q7RTM1
Function: Required for normal formation of otoconia in the inner ear. Inhibits P2Y purinoceptors. Modulates calcium
homeostasis and influx of calcium in response to extracellular ATP (By similarity)




Genomic Views
for OTOP1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_006051.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the OTOP1 gene promoter:
         AML1a   NCX/Ncx   Pax-2   Lmo2   Pax-2a   Evi-1   POU2F1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: OTOP1 promoter sequence
   Search SABiosciences Chromatin IP Primers for OTOP1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat OTOP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4p16.3   Ensembl cytogenetic band:  4p16.3   HGNC cytogenetic band: 4p16.2

OTOP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OTOP1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M004190:  view genomic region     (about GC identifiers)

Start:
 4,190,530 bp from pter      End:
 4,228,621 bp from pter
Size:
 38,092 bases      Orientation:
 minus strand

Proteins
for OTOP1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: OTOP1_HUMAN, Q7RTM1 (See protein sequence)
Recommended Name: Otopetrin-1  
Size: 612 amino acids; 67353 Da
Subcellular location: Membrane; Multi-pass membrane protein. Secreted, extracellular space. Note=Detected in the
gelatinous membrane overlying the inner ear macular epithelium (By similarity)
Miscellaneous: Otoconia are minute biomineral particles embedded in a gelatinous membrane that overlies the sensory
epithelium in the inner ear. Gravity and acceleration cause the octoconia to deflect the stereocilia of sensory hair
cells. Otoconia are required for normal processing of information regarding spatial orientation and acceleration
Secondary accessions: A1L476

Explore the universe of human proteins at neXtProt for OTOP1: NX_Q7RTM1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q7RTM1

    • OTOP1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_819056.1  
    ENSEMBL proteins: 
     ENSP00000296358  

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    Uscn Proteins for OTOP1

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--


    OTOP1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for OTOP1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    OTOP1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR004878 Otopetrin

    Graphical View of Domain Structure for InterPro Entry Q7RTM1

    ProtoNet protein and cluster: Q7RTM1

    UniProtKB/Swiss-Prot: OTOP1_HUMAN, Q7RTM1
    Similarity: Belongs to the otopetrin family


    Function
    for OTOP1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: OTOP1_HUMAN, Q7RTM1
    Function: Required for normal formation of otoconia in the inner ear. Inhibits P2Y purinoceptors. Modulates calcium
    homeostasis and influx of calcium in response to extracellular ATP (By similarity)

    miRNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Animal Models:
         3 MGI mutant phenotypes (inferred from 4 alleles) (MGI details for Otop1):
     behavior/neurological  hearing/vestibular/ear  nervous system 

    OTOP1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for OTOP1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for OTOP1

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009590detection of gravity IEA--
    GO:0031214biomineral tissue development IEA--
    GO:0042472inner ear morphogenesis IEA--


    OTOP1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for OTOP1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for OTOP1

    1 HMDB Compound for OTOP1    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about OTOP1 

    Transcripts
    for OTOP1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section
    REFSEQ mRNAs for OTOP1 gene: 
    NM_177998.1  

    Unigene Cluster for OTOP1:

    Otopetrin 1
    Hs.534544
    Unigene Representative Sequence: BC130432
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000296358(uc003ghp.1)

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    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for OTOP1 (see all 7)
    OriGene shRNA RFP: OTOP1
    OriGene siRNA: OTOP1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat OTOP1
    Clone
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    GenScript: all cDNA clones in your preferred vector: OTOP1 (NM_177998)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for OTOP1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat OTOP1 
    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat OTOP1

    Additional cDNA sequence: 

    BC130430.1 BC130432.1 

    1 DOTS entry:

    DT.100740998 

    2 AceView cDNA sequences:

    BK000653 NM_177998 

    GeneLoc Exon Structure


    Expression
    for OTOP1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    OTOP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCTTTTTCTA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    OTOP1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    AdiposeInterscapular Brown Adipose DepotAdipose
    AdiposeThoracic Perivascular AdiposeAdipose
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See OTOP1 Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.534544
        SABiosciences Custom PCR Arrays for OTOP1
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat OTOP1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTOP1

    Orthologs
    for OTOP1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for OTOP1 gene from 6/17 species (see all 17)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Otop11 , 5 otopetrin 11, 5 79.27(n)1
    80(a)1    		   5 (20.35 cM)5
    219061  NM_172709.31  NP_766297.21 
     382774045 
    chicken
    (Gallus gallus)    		 Aves OTOP11 otopetrin 1 68.56(n)
    67.73(a)    		   422844  XM_420790.3  XP_420790.3 
    lizard
    (Anolis carolinensis)    		 Reptilia OTOP16
    		 --
    		 64(a)
    		 1 ↔ 1
    		 GL343236.1(558509-591110)
    zebrafish
    (Danio rerio)    		 Actinopterygii otop12 otopetrin 1 75.6(n)   322893  AY170648.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG422656
    CG33326
    (see all 3)    		 --
    		 8(a)
    14(a)
    (see all 3)    		 many ↔ many
    many ↔ many
    (see all 3)    		 X(5544600-5556875)
    2L(3275794-3280533)
    worm
    (Caenorhabditis elegans)    		 Secernentea otpl-36
    otpl-26
    (see all 8)    		 OToPetrin-Like family member (otpl-2)
    (see all 8)    		 15(a)
    14(a)
    (see all 8)    		 many ↔ many
    many ↔ many
    (see all 8)    		 X(6921607-6924411)
    V(4073740-4077533)


    ENSEMBL Gene Tree for OTOP1 (if available)
    TreeFam Gene Tree for OTOP1 (if available) 

    Paralogs
    for OTOP1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for OTOP1 gene
    OTOP22  OTOP32  
    2 SIMAP similar genes for OTOP1 using alignment to 1 protein entry:     OTOP1_HUMAN:
    OTOP2    OTOP3

    OTOP1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for OTOP1
    PGOHUM00000240766


    Genomic Variants
    for OTOP1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for OTOP1
         3 CNVs: 51403 91892 3477
    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for OTOP1

    Disorders / Diseases
    for OTOP1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OTOP1 for disorders           About GeneDecksing

    OMIM gene information: 607806    OMIM disorders: --

    3 diseases for OTOP1:    About MalaCards
    benign paroxysmal positional nystagmus    nystagmus    usher syndrome

    2 diseases from the University of Copenhagen DISEASES database for OTOP1:
    Benign paroxysmal positional nystagmus     Usher syndrome

    Export disorders for OTOP1 gene to outside databases

    Publications
    for OTOP1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for OTOP1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with OTOP1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Non-syndromic vestibular disorder with otoconial agenesis in tilted/mergulhador mice caused by mutations in otopetrin 1. (PubMed id 12651873)1, 2, 3 Hurle B.... Ornitz D.M. (2003)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    4. Otopetrin 1 activation by purinergic nucleotides regulates intracellular calcium. (PubMed id 17606897)9 Hughes I....Ornitz D.M. (2007)

    External Searches for OTOP1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing OTOP1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 133060 HGNC: 19656 AceView: OTOP1 Ensembl:ENSG00000163982 euGenes: HUgn133060
    ECgene: OTOP1 H-InvDB: OTOP1

    Other Databases showing OTOP1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing OTOP1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for OTOP1 Pharmacogenomics, SNPs, Pathways
    Protein Spotlighthttp://web.expasy.org/spotlight/back_issues/sptlt089.shtml

    Intellectual Property
    for OTOP1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for OTOP1 gene:
    Search GeneIP for patents involving OTOP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for OTOP1 gene

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    Advanced Cell Diagnostics
    About This Section

     
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