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LYPD3 Gene

protein-coding   GIFtS: 52
GCID: GC19M043964

LY6/PLAUR Domain Containing 3

  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
LY6/PLAUR Domain Containing 31 2     GPI-Anchored Metastasis-Associated Protein C4.4A Homolog2 3
Matrigel-Induced Gene C4 Protein2 3     2310061G07Rik2
C4.4A2 3     GPI-Anchored Metastasis-Associated Protein Homolog2
MIG-C42 3     Ly6/PLAUR Domain-Containing Protein 32

External Ids:    HGNC: 248801   Entrez Gene: 270762   Ensembl: ENSG000001244667   OMIM: 6094845   UniProtKB: O952743   

Export aliases for LYPD3 gene to outside databases

Previous GC identifers: GC19M048660 GC19M040394


(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 LYPD3 Gene:
LYPD3 (LY6/PLAUR domain containing 3) is a protein-coding gene. Diseases associated with LYPD3 include esophageal squamous cell carcinoma, and transitional cell carcinoma. GO annotations related to this gene include laminin binding.

UniProtKB/Swiss-Prot: LYPD3_HUMAN, O95274
Function: Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in
tumor progression

Gene Wiki entry for LYPD3 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:
NC_000019.10  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the LYPD3 gene promoter:
         Sp1   AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLYPD3 promoter sequence
   Search Chromatin IP Primers for LYPD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LYPD3


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

Entrez Gene cytogenetic band: 19q13.31   Ensembl cytogenetic band:  19q13.31   HGNC cytogenetic band: 19q13.31

LYPD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYPD3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M043964:  view genomic region     (about GC identifiers)

Start:
43,964,939 bp from pter      End:
43,969,831 bp from pter
Size:
4,893 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, 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LYPD3_HUMAN, O95274 (See protein sequence)
Recommended Name: Ly6/PLAUR domain-containing protein 3 precursor  
Size: 346 amino acids; 35971 Da
Subunit: Binds laminin-1 and laminin-5. Interacts with LGALS3 (By similarity). Interacts with AGR2 and AGR3
Mass spectrometry: Mass=21442.9; Method=MALDI; Range=1-204; Source=PubMed:15012588;
Secondary accessions: Q9UJ74

Explore the universe of human proteins at neXtProt for LYPD3: NX_O95274

Explore proteomics data for LYPD3 at MOPED

Post-translational modifications: 

  • N-glycosylated and O-glycosylated1
  • Glycosylation2 at Asn118, Asn163, Asn176, Asn183, Ser289, Thr297
  • Modification sites at PhosphoSitePlus

  • See LYPD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055215.2  
    ENSEMBL proteins: 
     ENSP00000244333  

    LYPD3 Human Recombinant Protein Products:

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    Cloud-Clone Corp. CLIAs for LYPD3


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR016054 LY6_UPA_recep-like
     IPR001526 LY6_UPAR

    Graphical View of Domain Structure for InterPro Entry O95274

    ProtoNet protein and cluster: O95274

    1 Blocks protein domain: IPB001526 CD59 antigen

    UniProtKB/Swiss-Prot: LYPD3_HUMAN, O95274
    Similarity: Contains 2 UPAR/Ly6 domains


    LYPD3 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: LYPD3_HUMAN, O95274
    Function: Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in
    tumor progression
    Induction: Up-regulated in migrating keratinocytes during epithelisation of incisional skin wounds

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0043236laminin binding IEA--
         
    LYPD3 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI phenotypic allele for Lypd3 (no phenotypes)

    LYPD3 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LYPD3
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LYPD3
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    miRNA
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    miRTarBase miRNAs that target LYPD3:
    hsa-mir-7-5p (MIRT025845), hsa-mir-335-5p (MIRT018038)

    Block miRNA regulation of human, mouse, rat LYPD3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LYPD3 (see all 17):
    hsa-miR-3194-5p hsa-miR-185* hsa-miR-128 hsa-miR-298 hsa-miR-28-5p hsa-miR-455-5p hsa-miR-922 hsa-miR-27a
    SwitchGear 3'UTR luciferase reporter plasmidLYPD3 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYPD3


    (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
    LYPD3_HUMAN, O95274: Cell membrane; Lipid-anchor, GPI-anchor
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular3

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--
    GO:0046658anchored component of plasma membrane TAS15012588

    LYPD3 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 LYPD3
    Interactions:

        Search GeneGlobe Interaction Network for LYPD3

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for LYPD3 (O952743 ENSP000002443334) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    AGR3Q8TD063, ENSP000003086064I2D: score=1 STRING: ENSP00000308606
    CTRB1ENSP000003542944STRING: ENSP00000354294
    AGR2ENSP000003914904STRING: ENSP00000391490
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006928cellular component movement IEA--
    GO:0007160cell-matrix adhesion IEA--

    LYPD3 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 LYPD3



    (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,
    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 LYPD3 gene: 
    NM_014400.2  

    Unigene Cluster for LYPD3:

    LY6/PLAUR domain containing 3
    Hs.631594  [show with all ESTs]
    Unigene Representative Sequence: AL832153
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000244333(uc002owl.1 uc002owm.3) ENST00000597741 ENST00000594326
    ENST00000595970
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate LYPD3 (see all 17):
    hsa-miR-3194-5p hsa-miR-185* hsa-miR-128 hsa-miR-298 hsa-miR-28-5p hsa-miR-455-5p hsa-miR-922 hsa-miR-27a
    SwitchGear 3'UTR luciferase reporter plasmidLYPD3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat LYPD3
      QuantiFast Probe-based Assays in human, mouse, rat LYPD3

    Additional mRNA sequence: 

    AF082889.1 AJ223603.2 AK075464.1 AK290905.1 AK314773.1 AL832153.1 AY359006.1 BC039167.1 
    BC041061.1 

    7 DOTS entries:

    DT.114327  DT.121431170  DT.100022646  DT.100717886  DT.95163099  DT.95304365  DT.100814164 

    Selected AceView cDNA sequences (see all 131):

    CR611777 BC041061 AW450151 N57021 BG679186 BE713165 AA479609 BG740590 
    BU682308 AI680020 CR610737 BU179573 BM672653 AJ223603 BM018299 AK075464 
    AA369339 BQ011687 AI202455 AI206356 BE713074 CR620698 CR622986 CA487679 

    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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    LYPD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCAGCGCCAA
    LYPD3 Expression
    About this image


    LYPD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Hair (Integumentary System)
             Bulge Stem Cells Bulge
     
     Tonsil (Hematopoietic System)
    LYPD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LYPD3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631594

    UniProtKB/Swiss-Prot: LYPD3_HUMAN, O95274
    Tissue specificity: Expressed in placenta, skin and urothelium. Found in suprabasal keratinocytes of chronic
    wounds. Weak expression is found in esophagus and peripheral blood mononuclear cells. Found in the majority of
    primary and metastatic transitional cell carcinomas (TCCs) and as well in breast cancer tissues, but not in
    adjacent normal tissues. High expression is found in the tumor component of some noninvasive superficial lesions
    and in invasive and metastatic urothelial cancers

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    In Situ
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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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    This gene was present in the common ancestor of chordates.

    Orthologs for LYPD3 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lypd31 , 5 Ly6/Plaur domain containing 31, 5 78.56(n)1
    76.31(a)1
      7 (11.95 cM)5
    724341  NM_133743.11  NP_598504.11 
     246365705 
    lizard
    (Anolis carolinensis)
    Reptilia LYPD36
    LY6/PLAUR domain containing 3
    35(a)
    1 ↔ 1
    LGf(994218-1009914)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004891241 ly6/PLAUR domain-containing protein 3-like 47.45(n)
    39.41(a)
      100489124  XM_002939130.2  XP_002939176.2 


    ENSEMBL Gene Tree for LYPD3 (if available)
    TreeFam Gene Tree for LYPD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LYPD3 gene
    1 SIMAP similar gene for LYPD3 using alignment to 2 protein entries:     LYPD3_HUMAN (see all proteins):
    DKFZp686D0114

    LYPD3 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 LYPD3 (see all 203)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1489482321,2
    --43964483(+) TAAAAG/TTAGCC 1 -- int10--------
    rs1842625281,2
    --43964515(+) TAGTCC/TCAGCT 1 -- int10--------
    rs1895690961,2
    --43964646(+) AGGCGA/GGTGGA 1 -- int10--------
    rs1811888041,2
    --43964757(+) GTCTCC/TCCCTC 1 -- int10--------
    rs1428803801,2
    C--43964768(+) ACCAGC/TGGGAC 1 -- int10--------
    rs454858921,2
    C,F--43964846(+) AGGTCC/GCATAT 1 -- int11Minor allele frequency- G:0.03NA 120
    rs1510784201,2
    C--43964862(+) CCGTTA/GAAGGC 1 -- int10--------
    rs1856293921,2
    --43964898(+) TAGAGC/TGGTTA 1 -- int10--------
    rs1410441961,2
    C--43964907(+) TATTGC/TGAGAA 1 -- int10--------
    rs1996193071,2
    --43964948(+) ATACA-/AAGT  
            
    AATTA
    1 -- ut310--------

    HapMap Linkage Disequilibrium report for LYPD3 (43964939 - 43969831 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for LYPD3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509744CNV Insertion20534489
    nsv2501CNV Loss18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LYPD3
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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.)
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    OMIM gene information: 609484    OMIM disorders: --

    7 diseases for LYPD3:    
    About MalaCards
    esophageal squamous cell carcinoma    transitional cell carcinoma    esophagitis    squamous cell carcinoma
    lung cancer    colorectal cancer    breast cancer


    LYPD3 for disorders           About GeneDecksing


    Export disorders for LYPD3 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 LYPD3 gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with LYPD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of genes involved in human urothelial cell-matrix interactions: implications for the progression pathways of malignant urothelium. (PubMed id 11245483)1, 2, 3, 9 Smith B.A....Southgate J. (Cancer Res. 2001)
    2. Cloning of the human homologue of the metastasis-associated rat C4.4A. (PubMed id 11179665)1, 2, 3 Wuerfel J.... Zoeller M. (Gene 2001)
    3. Structural analysis and tissue localization of human C4.4A: a protein homologue of the urokinase receptor. (PubMed id 15012588)1, 2, 9 Hansen L.V.... Ploug M. (Biochem. Eng. J. 2004)
    4. hAG-2 and hAG-3, human homologues of genes involved in differentiation, are associated with oestrogen receptor-positive breast tumours and interact with metastasis gene C4.4a and dystroglycan. (PubMed id 12592373)1, 2, 9 Fletcher G.C....Terrett J.A. (Br. J. Cancer 2003)
    5. 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)
    6. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)
    7. 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 Clark H.F.... Gray A.M. (Genome Res. 2003)
    8. Concurrent expression of C4.4A and Tenascin-C in tumor cells relates to poor prognosis of esophageal squamous cell carcinoma. (PubMed id 23708783)1 Ohtsuka M....Mori M. (Int. J. Oncol. 2013)
    9. Membrane-bound and exosomal metastasis-associated C4.4A promotes migration by associating with the I+(6)I^(4) integrin and MT1-MMP. (PubMed id 22431918)1 Ngora H....ZAPller M. (Neoplasia 2012)
    10. C4.4A is associated with tumor budding and epithelial-mesenchymal transition of colorectal cancer. (PubMed id 22404718)1 Oshiro R....Mori M. (Cancer Sci. 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 27076 HGNC: 24880 AceView: C4.4A Ensembl:ENSG00000124466 euGenes: HUgn27076
    ECgene: LYPD3 H-InvDB: LYPD3

    (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 LYPD3 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LYPD3 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LYPD3 gene:
    Search GeneIP for patents involving LYPD3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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