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OR1D4 Gene

pseudogene   GIFtS: 34
GCID: GC17P003144

Olfactory Receptor, Family 1, Subfamily D, Member 4 (Gene/Pseudogene)

(Previous names: olfactory receptor, family 1, subfamily D, member 4)
  See related disease
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
Olfactory Receptor, Family 1, Subfamily D, Member 4
(Gene/Pseudogene)1 2
OR17-302 3
Olfactory Receptor, Family 1, Subfamily D, Member 41
Olfactory Receptor 1D42
Olfactory Receptor 17-303

External Ids:    HGNC: 81851   Entrez Gene: 6531662   Ensembl: ENSG000002550957   UniProtKB: P478843   

Export aliases for OR1D4 gene to outside databases

Previous GC identifers: GC17P003458 GC17M003307 GC17M002916 GC17M003172 GC17P003350 GC17M002913 GC17P003090 GC17P003036


(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 OR1D4 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 2010)

GeneCards Summary for OR1D4 Gene:
OR1D4 (olfactory receptor, family 1, subfamily D, member 4 (gene/pseudogene)) is a pseudogene. Diseases associated with OR1D4 include neuronitis. GO annotations related to this gene include G-protein coupled receptor activity and olfactory receptor activity.

UniProtKB/Swiss-Prot: OR1D4_HUMAN, P47884
Function: Odorant receptor (Potential)




(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_010718.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the OR1D4 gene promoter:
         c-Fos   AML1a   AP-1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   C/EBPalpha   AREB6   c-Jun   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for OR1D4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat OR1D4


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

Entrez Gene cytogenetic band: 17p13.3   Ensembl cytogenetic band:  17p13.3   HGNC cytogenetic band: 17p13.3

OR1D4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OR1D4 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P003144:  view genomic region     (about GC identifiers)

Start:
3,143,970 bp from pter      End:
3,144,905 bp from pter
Size:
936 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: OR1D4_HUMAN, P47884 (See protein sequence)
Recommended Name: Olfactory receptor 1D4  
Size: 311 amino acids; 35227 Da
Secondary accessions: Q96RA5 Q9UM75

Explore the universe of human proteins at neXtProt for OR1D4: NX_P47884

Explore proteomics data for OR1D4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn5
  • HORDE protein sequence for OR1D4

    See OR1D4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    Reactome Protein details: P47884

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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:
    OR1: 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 P47884

    ProtoNet protein and cluster: P47884

    1 Blocks protein domain: IPB000725 Olfactory receptor signature

    UniProtKB/Swiss-Prot: OR1D4_HUMAN, P47884
    Similarity: Belongs to the G-protein coupled receptor 1 family


    OR1D4 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: OR1D4_HUMAN, P47884
    Function: Odorant receptor (Potential)

         Genatlas biochemistry entry for OR1D4:
    olfactory receptor,family 1,subfamily D,member 4,G protein coupled receptor superfamily

         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--
         
    OR1D4 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for OR1D4:
     Cell cycle / mitosis defect 

    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
    OR1D4_HUMAN, P47884: Cell membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral component of plasma membrane TAS8004088

    OR1D4 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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    Pathways by sourceSee SuperPaths
    Show all pathways


    1 Reactome Pathway for OR1D4
        Olfactory Signaling Pathway



    OR1D4 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for OR1D4
    Interactions:

        Search GeneGlobe Interaction Network for OR1D4

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007186G-protein coupled receptor signaling pathway TAS8004088
    GO:0007606sensory perception of chemical stimulus TAS8004088

    OR1D4 for ontologies           About GeneDecksing



    (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 OR1D4



    (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 OR1D4 gene: 
    NM_003552.2  

    Unigene Cluster for OR1D4:

    Olfactory receptor, family 1, subfamily D, member 4 (gene/pseudogene)
    Hs.653087
    Unigene Representative Sequence: BC118668
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000531680(uc002fvf.3) ENST00000525719
    miRNA
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    Additional mRNA sequence: 

    BC118668.1 BC122528.1 NR_033795.1 

    1 DOTS entry:

    DT.120948494 

    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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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    OR1D4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    OR1D4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.653087
        Custom PCR Arrays for OR1D4
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    In Situ
    Assay Products:
     

     
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    (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 OR1D4 (if available)
    TreeFam Gene Tree for OR1D4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for OR1D4 gene
    Selected SIMAP similar genes for OR1D4 using alignment to 1 protein entry:     OR1D4_HUMAN(see all similar genes):
    OR1D5    OR1D2    OR1F1    OR1E1    OR1F12    OR1L6
    OR1L8    OR1N2    OR7A2P    OR7D4    OR1F2P    OR1L1
    OR1M1    OR1N1    OR7C1    OR7A5    OR16-36    OR16-37

    OR1D4 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 OR1D4 (see all 35)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3698956241,2
    C--3142220(+) AAGAAC/TACCTT 1 -- us2k10--------
    rs2002261571,2
    --3142644(+) GAACT-/GTGGCT 1 -- us2k10--------
    rs2006750591,2
    --3142894(+) TCATC-/TTTTTT 1 -- us2k10--------
    rs26765711,2
    C,F,H--3142992(-) TTAAGA/GTATTA 1 -- us2k18Minor allele frequency- G:0.15NS EA NA CSA WA 542
    rs1430310591,2
    --3143255(+) GTTCGA/GGATCA 1 -- us2k10--------
    rs574251691,2
    C,F--3143324(+) CCCCCA/GAATCT 1 -- us2k12Minor allele frequency- G:0.50NA 8
    rs606721171,2
    C,F--3143371(+) CACAGG/AACGGT 1 -- us2k11Minor allele frequency- A:0.13WA 118
    rs2006864801,2
    C,F--3143983(+) AGATAA/GCCAGA 1 -- nc-transcript-variant1Minor allele frequency- G:0.27EU 565
    rs2018534111,2
    C--3144023(+) ATCTC-/AGAGAGT 1 -- nc-transcript-variant0--------
    rs1865247301,2
    --3144346(+) GGCCAC/TCTGCT 1 -- nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for OR1D4 ( 3143970 - 3144905 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for OR1D4 (see all 12):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2660206CNV Deletion23128226
    nsv507831CNV Insertion20534489
    nsv457637CNV Loss19166990
    nsv907555CNV Loss21882294
    nsv907553CNV Loss21882294
    nsv907554CNV Loss21882294
    nsv907557CNV Loss21882294
    nsv469609CNV Loss16826518
    nsv907556CNV Gain21882294
    nsv526486CNV Gain19592680

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    (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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    1 disease for OR1D4:    
    About MalaCards
    neuronitis


    OR1D4 for disorders           About GeneDecksing


    Export disorders for OR1D4 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 OR1D4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with OR1D4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sequence, structure, and evolution of a complete human olfactory receptor gene cluster. (PubMed id 10673334)1, 2, 3 Glusman G.... Lancet D. (Genomics 2000)
    2. Olfactory receptor gene cluster on human chromosome 17: possible duplication of an ancestral receptor repertoire. (PubMed id 8004088)1, 2, 3 Ben-Arie N.... North M.A. (Hum. Mol. Genet. 1994)
    3. DEFOG: a practical scheme for deciphering families of genes. (PubMed id 12213199)1, 2 Fuchs T.... Shamir R. (Genomics 2002)
    4. The human olfactory receptor gene family. (PubMed id 14983052)1 Malnic B.... Buck L.B. (Proc. Natl. Acad. Sci. U.S.A. 2004)
    5. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 653166 HGNC: 8185 Ensembl:ENSG00000255095 euGenes: HUgn653166 ECgene: OR1D4
    H-InvDB: OR1D4

    (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 OR1D4 Pharmacogenomics, SNPs, Pathways
    HORDE entry for OR1D4 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 OR1D4 gene:
    Search GeneIP for patents involving OR1D4

    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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