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OR5D13 Gene

protein-coding   GIFtS: 47
GCID: GC11P055540

Olfactory Receptor, Family 5, Subfamily D, Member 13

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(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
Olfactory Receptor, Family 5, Subfamily D, Member 131 2
Olfactory Receptor OR11-1422 3
Olfactory Receptor OR11-1482 3
Olfactory Receptor 5D132

External Ids:    HGNC: 152801   Entrez Gene: 3901422   Ensembl: ENSG000001988777   UniProtKB: Q8NGL43   

Export aliases for OR5D13 gene to outside databases

Previous GC identifers: GC11U990434 GC11P055298


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for OR5D13 Gene:
Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the
perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled
receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain
structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G
protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the
genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent
of other organisms. (provided by RefSeq, Jul 2008)

GeneCards Summary for OR5D13 Gene:
OR5D13 (olfactory receptor, family 5, subfamily D, member 13) is a protein-coding gene. GO annotations related to this gene include G-protein coupled receptor activity and olfactory receptor activity. An important paralog of this gene is OR5D14.

UniProtKB/Swiss-Prot: OR5DD_HUMAN, Q8NGL4
Function: Odorant receptor (Potential)

Gene Wiki entry for OR5D13 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_167190.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the OR5D13 gene promoter:
         Nkx3-1   Nkx3-1 v4   AML1a   Nkx3-1 v1   AREB6   Nkx3-1 v2   POU2F1   POU2F1a   Nkx3-1 v3   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidOR5D13 promoter sequence
   Search Chromatin IP Primers for OR5D13

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat OR5D13


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

Entrez Gene cytogenetic band: 11q11   Ensembl cytogenetic band:  11q11   HGNC cytogenetic band: 11q11

OR5D13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OR5D13 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P055540:  view genomic region     (about GC identifiers)

Start:
55,540,914 bp from pter      End:
55,541,855 bp from pter
Size:
942 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: OR5DD_HUMAN, Q8NGL4 (See protein sequence)
Recommended Name: Olfactory receptor 5D13  
Size: 314 amino acids; 35447 Da
Sequence caution: Sequence=BAC05998.1; Type=Erroneous initiation;
Secondary accessions: Q6IF68 Q6IFC9

Explore the universe of human proteins at neXtProt for OR5D13: NX_Q8NGL4

Explore proteomics data for OR5D13 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn7
  • Modification sites at PhosphoSitePlus
  • HORDE protein sequence for OR5D13

    See OR5D13 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001001967.1  
    ENSEMBL proteins: 
     ENSP00000354800  
    Reactome Protein details: Q8NGL4

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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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    HGNC Gene Families:
    OR5: GPCR / Class A : Olfactory receptors

    3 InterPro protein domains:
     IPR017452 GPCR_Rhodpsn_7TM
     IPR000725 Olfact_rcpt
     IPR000276 GPCR_Rhodpsn

    Graphical View of Domain Structure for InterPro Entry Q8NGL4

    ProtoNet protein and cluster: Q8NGL4

    1 Blocks protein domain: IPB000725 Olfactory receptor signature

    UniProtKB/Swiss-Prot: OR5DD_HUMAN, Q8NGL4
    Similarity: Belongs to the G-protein coupled receptor 1 family


    Find genes that share domains with OR5D13           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: OR5DD_HUMAN, Q8NGL4
    Function: Odorant receptor (Potential)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004930G-protein coupled receptor activity IEA--
    GO:0004984olfactory receptor activity IEA--
         
    Find genes that share ontologies with OR5D13           About GenesLikeMe


    Animal Models:
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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
    OR5DD_HUMAN, Q8NGL4: Cell membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with OR5D13           About GenesLikeMe


    (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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    SuperPaths for OR5D13 About    
    See pathways by source

    SuperPathContained pathways About
    1Olfactory Signaling Pathway
    Olfactory Signaling Pathway0.82
    Olfactory transduction0.82
    2Signaling by GPCR
    Signaling by GPCR0.90
    Signal Transduction0.58
    GPCR downstream signaling0.90


    Find genes that share SuperPaths with OR5D13           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for OR5D13
        Olfactory Signaling Pathway


    1 Kegg Pathway  (Kegg details for OR5D13):
        Olfactory transduction

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for OR5D13
    Interactions:

        Search GeneGlobe Interaction Network for OR5D13

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for OR5D13 (ENSP000003548004) via UniProtKB, MINT, STRING, and/or I2D (see all 273)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    OR52E6ENSP000003288784STRING: ENSP00000369279 STRING: ENSP00000328878
    GNALENSP000003340514STRING: ENSP00000334051
    GNGT1ENSP000002485724STRING: ENSP00000248572
    OR10A3ENSP000003539884STRING: ENSP00000353988
    OR10A4ENSP000003691574STRING: ENSP00000369157
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007186G-protein coupled receptor signaling pathway ----

    Find genes that share ontologies with OR5D13           About GenesLikeMe



    (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 OR5D13 (OR5DD)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for OR5D13 gene: 
    NM_001001967.1  

    Unigene Cluster for OR5D13:

    Olfactory receptor, family 5, subfamily D, member 13
    Hs.553743
    Unigene Representative Sequence: NM_001001967
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000361760(uc010ril.2)
    miRNA
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    1 AceView cDNA sequence:

    NM_001001967 

    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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    OR5D13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTGAAAAAT
    OR5D13 Expression
    About this image

    OR5D13 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    OR5D13 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.553743
        Custom PCR Arrays for OR5D13
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OR5D13

    (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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    ENSEMBL Gene Tree for OR5D13 (if available)
    TreeFam Gene Tree for OR5D13 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for OR5D13 gene
    OR5D142  OR5D162  OR5D182  OR5L22  OR5L12  
    Selected SIMAP similar genes for OR5D13 using alignment to 1 protein entry:     OR5DD_HUMAN(see all similar genes):
    OR5D3    OR5D18    OR5D14    OR5D16    OR5L2    OR5L1
    OR5B2    OR8I2    OR8U1    OR8U8    OR8U9    OR5A2
    OR5AR1    OR5AS1    OR5B12    OR5B17    OR5R1    OR8D1

    Find genes that share paralogs with OR5D13           About GenesLikeMe


    4 Pseudogenes.org Pseudogenes for OR5D13
    PGOHUM00000242717 PGOHUM00000257884 PGOHUM00000257885 PGOHUM00000242718


    (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 OR5D13 (see all 92)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1397717061,2
    C--55538981(+) TTATGA/TGATAT 1 -- us2k10--------
    rs1431421771,2
    --55538982(+) TATGAA/GATATT 1 -- us2k10--------
    rs354109381,2
    C,F--55539192(+) TTGAAG/AGGCAA 1 -- us2k15Minor allele frequency- A:0.11NA WA EA 362
    rs1461929181,2
    --55539224(+) AATGAC/TAATGA 1 -- us2k10--------
    rs133775651,2
    C,H--55539302(+) TGTTGA/GGGGTT 1 -- us2k14Minor allele frequency- G:0.00NS EA 414
    rs1390889871,2
    --55539349(+) GCTTGA/GCACTC 1 -- us2k10--------
    rs786422691,2
    F--55539357(+) CTCATT/CTCAGG 1 -- us2k11Minor allele frequency- C:0.09WA 118
    rs112309651,2
    C,H--55539361(+) TTTCAG/AGGAAA 1 -- us2k14Minor allele frequency- A:0.00NS EA 420
    rs1499170081,2
    C--55539785(+) AGTGCA/GTGTTG 1 -- us2k10--------
    rs1505793491,2
    --55539832(+) TAGCCA/CACTGA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for OR5D13 ( 55540914 - 55541855 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for OR5D13 (see all 20):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv212e199CNV Deletion23128226
    nsv821668CNV Loss15273396
    nsv469885CNV Loss16826518
    nsv469958CNV Loss18288195
    dgv150n27CNV Loss19166990
    dgv51e55CNV Loss17911159
    dgv13n68CNV Loss17160897
    nsv437717CNV Loss16327808
    nsv468566CNV Loss19166990
    essv101806CNV Loss18971310

    Human Gene Mutation Database (HGMD): OR5D13
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing OR5D13
    DNA2.0 Custom Variant and Variant Library Synthesis for OR5D13

    (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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    Find genes that share disorders with OR5D13           About GenesLikeMe


    Export disorders for OR5D13 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 OR5D13 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with OR5D13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human olfactory receptor gene family. (PubMed id 14983052)1, 2 Malnic B.... Buck L.B. (Proc. Natl. Acad. Sci. U.S.A. 2004)
    2. (PubMed id )2 

    (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: 390142 HGNC: 15280 AceView: OR5D13 Ensembl:ENSG00000198877 euGenes: HUgn390142
    ECgene: OR5D13 Kegg: 390142 H-InvDB: OR5D13

    (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 OR5D13 Pharmacogenomics, SNPs, Pathways
    HORDE entry for OR5D13 The Human Olfactory Receptor Data Explorer at the Weizmann Institute of Science

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for OR5D13 gene:
    Search GeneIP for patents involving OR5D13

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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     Search Addgene for plasmids for OR5D13
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      eBioscience FlowRNA Probe Sets
           
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