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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

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Otopetrin 11 2
otopetrin-12

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


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for OTOP1 Gene: 
OTOP1 (otopetrin 1) is a protein-coding gene. Diseases associated with OTOP1 include benign paroxysmal positional nystagmus, and usher syndrome. An important paralog of this gene is OTOP2.

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)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.2  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 plasmidOTOP1 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

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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

Explore proteomics data for OTOP1 at MOPED 

Post-translational modifications:

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

  • OTOP1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    OTOP1 Protein Expression
    REFSEQ proteins: NP_819056.1  
    ENSEMBL proteins: 
     ENSP00000296358  

    Human Recombinant Protein Products for OTOP1: 
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    Cloud-Clone Corp. 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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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     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


    OTOP1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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)

    Phenotypes:
         3 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Otop1):

     behavior/neurological  hearing/vestibular/ear  nervous system 

    OTOP1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for OTOP1 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for OTOP1 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 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



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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
    Browse drugs & compounds from Enzo Life Sciences

    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

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    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)
    miRNA
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    OriGene ORF clones in mouse, rat for OTOP1
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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
    Sirion Biotech Customized lentivirus for stable overexpression of OTOP1 
                         Customized lentivirus expression plasmids for stable overexpression of OTOP1 
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for OTOP1
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat OTOP1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat OTOP1

    Additional mRNA sequence: 

    BC130430.1 BC130432.1 

    1 DOTS entry:

    DT.100740998 

    2 AceView cDNA sequences:

    BK000653 NM_177998 

    GeneLoc Exon Structure


    (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)      OTOP1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTTTTTCTA
    OTOP1 Expression
    About this image


    OTOP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/2 selected tissues (see all 2) fully expand
     
     Adipose (Muscoskeletal System)    fully expand to see all 3 entries
             Thoracic Perivascular Adipose
             white adipose tissue   
     
     Breast (Uncategorized)
             mammary gland   

    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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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTOP1

    (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 chordates.

    Orthologs for OTOP1 gene from 4/11 species (see all 11)    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
    --
    Uncharacterized protein
    65(a)
    32(a)
    1 ↔ 1
    possible ortholog
    GL343236.1(557675-591110)
    GL343239.1(174377-182945)
    zebrafish
    (Danio rerio)
    Actinopterygii otop12 otopetrin 1 75.6(n)   322893  AY170648.1 


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

    (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


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/1421 SNPs in OTOP1 are shown (see all 1421)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs20285841,2
    C,F,O,H--4190182(+) GTCACG/ATGATA 1 -- ds500116Minor allele frequency- A:0.37MN NS EA NA WA CSA 1874
    rs1838638891,2
    --4190304(+) ATTAGC/TATTTA 1 -- ds50010--------
    rs1136336041,2
    C--4190338(+) CACCTC/TATGGA 1 -- ds50011Minor allele frequency- T:0.50NA 2
    rs3772555031,2
    C--4190517(+) GTCTCC/TTGTGG 1 -- ds50010--------
    rs2011952091,2
    F--4190525(+) TGGACC/TCAGAC 1 -- ds50011Minor allele frequency- T:0.00EU 697
    rs1998471331,2
    F--4190526(+) GGACCC/TAGACT 1 -- ds50011Minor allele frequency- T:0.00EU 697
    rs1888050401,2
    --4190536(+) TATATA/CTTACA 2 K N mis10--------
    rs1997424511,2
    C--4190576(+) GCATTC/GGATAG 2 P R mis10--------
    rs2003684051,2
    C--4190577(+) CATTCC/G/TATAGA 3 R G syn1 mis10--------
    rs1491886711,2
    --4190586(+) GAAAAG/TAGAAA 2 I L mis10--------

    HapMap Linkage Disequilibrium report for OTOP1 (4190530 - 4228621 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for OTOP1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2726966CNV Deletion23290073
    nsv10436CNV Loss18304495
    nsv508270CNV Loss20534489
    nsv822448CNV Gain20364138
    nsv517008CNV Gain+Loss19592680
    dgv1566e1CNV Complex17122850
    nsv469857CNV Complex16826518

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 607806    OMIM disorders: --

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

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

    OTOP1 for disorders           About GeneDecksing


    Export disorders for OTOP1 gene to outside databases

    (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)

    (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)

    (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

    (According to HUGE)
    About This Section
      --

    (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

    (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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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