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LYPD4 Gene

protein-coding   GIFtS: 50
GCID: GC19M042341

LY6/PLAUR Domain Containing 4

  Search for LYPD4
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
LY6/PLAUR Domain Containing 41 2
SMR2
Ly6/PLAUR Domain-Containing Protein 42
Sperm Membrane Receptor2

External Ids:    HGNC: 286591   Entrez Gene: 1477192   Ensembl: ENSG000001831037   UniProtKB: Q6UWN03   

Export aliases for LYPD4 gene to outside databases

Previous GC identifers: GC19M047033 GC19M038774


(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 LYPD4 Gene:
LYPD4 (LY6/PLAUR domain containing 4) is a protein-coding gene. An important paralog of this gene is CD177.


(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_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LYPD4 gene promoter:
         PPAR-alpha   GR   p53   GR-beta   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLYPD4 promoter sequence
   Search Chromatin IP Primers for LYPD4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LYPD4


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

Entrez Gene cytogenetic band: 19q13.2   Ensembl cytogenetic band:  19q13.2   HGNC cytogenetic band: 19q13.2

LYPD4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYPD4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M042341:  view genomic region     (about GC identifiers)

Start:
42,341,148 bp from pter      End:
42,348,760 bp from pter
Size:
7,613 bases      Orientation:
minus 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: LYPD4_HUMAN, Q6UWN0 (See protein sequence)
Recommended Name: Ly6/PLAUR domain-containing protein 4 precursor  
Size: 246 amino acids; 26763 Da
Secondary accessions: Q8IYW0
Alternative splicing: 2 isoforms:  Q6UWN0-1   Q6UWN0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LYPD4: NX_Q6UWN0

Explore proteomics data for LYPD4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn117

  • See LYPD4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_775777.3  
    ENSEMBL proteins: 
     ENSP00000328737   ENSP00000472570   ENSP00000339568  

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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:
     IPR001526 LY6_UPAR

    Graphical View of Domain Structure for InterPro Entry Q6UWN0

    ProtoNet protein and cluster: Q6UWN0

    1 Blocks protein domain: IPB001526 CD59 antigen

    UniProtKB/Swiss-Prot: LYPD4_HUMAN, Q6UWN0
    Similarity: Contains 1 UPAR/Ly6 domain


    Find genes that share domains with LYPD4           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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    Phenotypes:
         2 GenomeRNAi human phenotypes for LYPD4:
     Decreased Tat-dependent transc  Decreased p24 protein expressi 

         1 MGI phenotypic allele for Lypd4 (no phenotypes)

    Find genes that share phenotypes with LYPD4           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Lypd4tm1Lex for LYPD4

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LYPD4
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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
    LYPD4_HUMAN, Q6UWN0: Cell membrane; Lipid-anchor, GPI-anchor (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular3
    lysosome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0031225anchored component of membrane IEA--

    Find genes that share ontologies with LYPD4           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LYPD4
    Interactions:

        Search GeneGlobe Interaction Network for LYPD4

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

    1 Interacting protein for LYPD4 (ENSP000003287374) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SHBGENSP000003698164STRING: ENSP00000369816
    About this table

    (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 LYPD4



    (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 LYPD4 gene: 
    NM_173506.5  

    Unigene Cluster for LYPD4:

    LY6/PLAUR domain containing 4
    Hs.98660  [show with all ESTs]
    Unigene Representative Sequence: AK292305
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000330743(uc002orp.1 uc002orq.1) ENST00000601246 ENST00000343055

    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat LYPD4

    Additional mRNA sequence: 

    AK292305.1 AY358726.1 AY771680.1 BC034629.2 

    3 DOTS entries:

    DT.110445  DT.97812100  DT.121491242 

    23 AceView cDNA sequences:

    AA430173 BC034629 AA759304 AA431328 AA813342 NM_173506 AI688054 AA725624 
    AI335754 BX283069 AA431616 AY358726 BX280836 BI831626 BG211938 AA923430 
    AI656828 AI014589 BU852651 AA912641 BG722930 AW340541 BQ376364 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for LYPD4    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6
    SP1:              -           -                     
    SP2:                                -               


    ECgene alternative splicing isoforms for LYPD4

    (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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    LYPD4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGTGTGCTC
    LYPD4 Expression
    About this image


    LYPD4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Testis (Reproductive System)
             Mature Sertoli Cells Seminiferous Tubules
    LYPD4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LYPD4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.98660
        Custom PCR Arrays for LYPD4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYPD4

    (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 human and mouse.

    Orthologs for LYPD4 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lypd41 , 5 Ly6/Plaur domain containing 41, 5 77.64(n)1
    69.96(a)1
      7 (13.30 cM)5
    2329731  NM_182785.31  NP_877586.11 
     248646205 


    ENSEMBL Gene Tree for LYPD4 (if available)
    TreeFam Gene Tree for LYPD4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LYPD4 gene
    CD1772  TEX1012  
    1 SIMAP similar gene for LYPD4 using alignment to 2 protein entries:     LYPD4_HUMAN (see all proteins):
    CD177

    Find genes that share paralogs with LYPD4           About GenesLikeMe



    (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 LYPD4 (see all 182)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs129765711,2
    C,F,A,H--42340769(+) ATTCGA/GGACCA 1 -- ds500115Minor allele frequency- G:0.36NS EA NA WA CSA 792
    rs81049581,2
    C,F,A,H--42340805(+) CCCCAT/CGTCAA 1 -- ds500122Minor allele frequency- C:0.37NS EA NA WA CSA 2347
    rs1389732751,2
    --42340945(+) GACCCG/TGATTA 1 -- ds50010--------
    rs1421057261,2
    --42341141(+) CAGGAC/TAATGC 1 -- ds50010--------
    rs1504311991,2
    --42341153(+) GAAAGA/GGAACT 1 -- ut310--------
    rs2006944581,2
    --42341203(+) GTCGGA/GTGCAG 1 -- ut310--------
    rs1381825321,2
    C--42341205(+) CGGGTA/GCAGCT 1 -- ut310--------
    rs1431310741,2
    C--42341219(+) TGGTCA/GGTCCC 2 R * stop-lost1Minor allele frequency- G:0.00NA 4552
    rs1482568981,2
    C--42341250(+) AAGACG/AACACC 2 /V syn11Minor allele frequency- A:0.00NA 4552
    rs1860475311,2
    C--42341287(+) CTGCAC/TCAACA 2 D G mis10--------

    HapMap Linkage Disequilibrium report for LYPD4 (42341148 - 42348760 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for LYPD4:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv3882n71CNV Loss21882294
    nsv522854CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
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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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    Find genes that share disorders with LYPD4           About GenesLikeMe

    Genetic Association Database (GAD): LYPD4
    Human Genome Epidemiology (HuGE) Navigator: LYPD4 (1 document)

    Export disorders for LYPD4 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 LYPD4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with LYPD4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. (PubMed id 21083371)4 Chinn L.W....O'Brien S.J. (J. Infect. Dis. 2010)
    4. Identification of host proteins required for HIV infection through a functional genomic screen. (PubMed id 18187620)1 Brass A.L....Elledge S.J. (Science 2008)
    5. A germline-specific class of small RNAs binds mammalian Piwi proteins. (PubMed id 16751776)1 Girard A....Carmell M.A. (Nature 2006)
    6. 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: 147719 HGNC: 28659 AceView: MGC42718 Ensembl:ENSG00000183103 euGenes: HUgn147719
    ECgene: LYPD4 H-InvDB: LYPD4

    (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 LYPD4 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 LYPD4 gene:
    Search GeneIP for patents involving LYPD4

    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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