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OTOP2 Gene

protein-coding   GIFtS: 44
GCID: GC17P072922

Otopetrin 2

  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)
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Aliases
Otopetrin 21 2
otopetrin-22

External Ids:    HGNC: 196571   Entrez Gene: 927362   Ensembl: ENSG000001830347   OMIM: 6078275   UniProtKB: Q7RTS63   

Export aliases for OTOP2 gene to outside databases

Previous GC identifers: GC17P073384 GC17P073517 GC17P070431 GC17P068330


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for OTOP2 Gene:
OTOP2 (otopetrin 2) is a protein-coding gene. Diseases associated with OTOP2 include vestibular disease, and usher syndrome. An important paralog of this gene is OTOP1.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000017.11  NC_018928.2  NT_010783.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the OTOP2 gene promoter:
         Nkx5-1   C/EBPalpha   CHOP-10   CREB   deltaCREB   FOXO1a   ZID   Pax-4a   FOXO1   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidOTOP2 promoter sequence
   Search Chromatin IP Primers for OTOP2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat OTOP2


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

Entrez Gene cytogenetic band: 17q25.1   Ensembl cytogenetic band:  17q25.1   HGNC cytogenetic band: 17q25.3

OTOP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OTOP2 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P072922:  view genomic region     (about GC identifiers)

Start:
72,920,370 bp from pter      End:
72,930,007 bp from pter
Size:
9,638 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: OTOP2_HUMAN, Q7RTS6 (See protein sequence)
Recommended Name: Otopetrin-2  
Size: 562 amino acids; 62236 Da

Explore the universe of human proteins at neXtProt for OTOP2: NX_Q7RTS6

Explore proteomics data for OTOP2 at MOPED


See OTOP2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_835454.1  
ENSEMBL proteins: 
 ENSP00000463837   ENSP00000332528  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR004878 Otopetrin

Graphical View of Domain Structure for InterPro Entry Q7RTS6

ProtoNet protein and cluster: Q7RTS6

UniProtKB/Swiss-Prot: OTOP2_HUMAN, Q7RTS6
Similarity: Belongs to the otopetrin family


OTOP2 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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for OTOP2
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
OTOP2_HUMAN, Q7RTS6: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
cytoskeleton1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

OTOP2 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for OTOP2
Interactions:

    Search GeneGlobe Interaction Network for OTOP2

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

Selected Interacting proteins for OTOP2 (Q7RTS62 ENSP000003325284) via UniProtKB, MINT, STRING, and/or I2D (see all 44)
InteractantInteraction Details
GeneCardExternal ID(s)
AGO2Q9UKV82, ENSP000002205924MINT-6489217 STRING: ENSP00000220592
AGO3Q9H9G72MINT-6489217
ATP1A3P136372MINT-6489217
C1QBPQ070212MINT-6489217
CLNS1AP541052MINT-6489217
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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for OTOP2



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for OTOP2 gene: 
NM_178160.2  

Unigene Cluster for OTOP2:

Otopetrin 2
Hs.352515  [show with all ESTs]
Unigene Representative Sequence: NM_178160
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000584711(uc002jmf.1) ENST00000580223 ENST00000331427(uc010wrp.2)

miRNA
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hsa-miR-875-3p hsa-miR-3148 hsa-miR-3647-3p
Browse SwitchGear 3'UTR luciferase reporter plasmids
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat OTOP2

Additional mRNA sequence: AK000063.1 

2 DOTS entries:

DT.97823595  DT.120908063 

7 AceView cDNA sequences:

BK000567 NM_178160 AW155641 BI828712 BM466860 AK000063 BQ326836 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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OTOP2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CACGCTGTGT
OTOP2 Expression
About this image

OTOP2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

OTOP2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.352515
    Custom PCR Arrays for OTOP2
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTOP2

(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)
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This gene was present in the common ancestor of animals.

Orthologs for OTOP2 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Otop21 , 5 otopetrin 21, 5 83.63(n)1
85.23(a)1
  11 (80.84 cM)5
2379871  NM_172801.21  NP_766389.21 
 1153071635 
chicken
(Gallus gallus)
Aves OTOP21 otopetrin 2 66.24(n)
62.43(a)
  422111  XM_003642368.2  XP_003642416.1 
lizard
(Anolis carolinensis)
Reptilia OTOP26
otopetrin 2
54(a)
1 ↔ 1
2(115115014-115127038)
tropical clawed frog
(Xenopus tropicalis)
Amphibia LOC1004961741 otopetrin-2-like 59.61(n)
54.25(a)
  100496174  XM_002939569.2  XP_002939615.2 
zebrafish
(Danio rerio)
Actinopterygii otop21 otopetrin 2 57.18(n)
47.76(a)
  494472  XM_001338043.4  XP_001338079.4 
fruit fly
(Drosophila melanogaster)
Insecta CG422651 CG42265 46.77(n)
30.49(a)
  7354434  NM_001144688.2  NP_001138160.2 


ENSEMBL Gene Tree for OTOP2 (if available)
TreeFam Gene Tree for OTOP2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for OTOP2 gene
OTOP12  OTOP32  
2 SIMAP similar genes for OTOP2 using alignment to 1 protein entry:     OTOP2_HUMAN:
OTOP3    OTOP1

OTOP2 for paralogs           About GeneDecksing



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for OTOP2 (see all 297)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0377604
A colorectal cancer sample4--see VAR_0377602 A V mis40--------
rs1928845641,2
--72925511(+) TGTTTG/TTTTGT 1 -- int10--------
rs1123217361,2
C--72926094(+) CCAACG/ATGGCG 1 -- int11Minor allele frequency- A:0.50CSA 2
rs1135654261,2
C,F--74002375(+) CCACCA/GTTGCT 1 -- us2k13Minor allele frequency- G:0.12CSA WA 122
rs1127956051,2
C,F--74002450(+) TTTGGA/C/TGCCCT 1 -- us2k12CSA WA 120
rs1896856161,2
--74002505(+) CGCTGG/TGTGAC 1 -- us2k10--------
rs1445296451,2
C--74002525(+) CCGGAG/TAACGT 1 -- us2k10--------
rs1927494231,2
--74002618(+) CCCCTC/TGAGAC 1 -- us2k10--------
rs1851447321,2
C--74002848(+) ACAAAC/TGCCAG 1 -- us2k10--------
rs1118014141,2
F--74002873(+) CCTGTC/GTGCAG 1 -- us2k12Minor allele frequency- G:0.07CSA WA 120

HapMap Linkage Disequilibrium report for OTOP2 (72920370 - 72930007 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for OTOP2:    About this table    
Variant IDTypeSubtypePubMed ID
nsv470601CNV Loss18288195
nsv518292CNV Loss19592680
dgv3255n71CNV Loss21882294
nsv833540CNV Loss17160897
nsv908744CNV Loss21882294
dgv3254n71CNV Loss21882294
nsv457909CNV Gain19166990

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for OTOP2

(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.)
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OMIM gene information: 607827    OMIM disorders: --

4 diseases for OTOP2:    
About MalaCards
vestibular disease    usher syndrome    breast and colorectal cancer    colorectal cancer

1 disease from the University of Copenhagen DISEASES database for OTOP2:
Usher syndrome

OTOP2 for disorders           About GeneDecksing


Export disorders for OTOP2 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)
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PubMed articles for OTOP2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with OTOP2)
    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. (Hum. Mol. Genet. 2003)
  2. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
  3. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 92736 HGNC: 19657 AceView: OTOP2 Ensembl:ENSG00000183034 euGenes: HUgn92736
ECgene: OTOP2 H-InvDB: OTOP2

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for OTOP2 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for OTOP2 gene:
Search GeneIP for patents involving OTOP2

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for OTOP2
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for OTOP2
 LSBio Antibodies in human, mouse, rat for OTOP2
Customized transgenic rodents for:
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 Tissue-specific gene expresssion
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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