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Aliases for LYPD3 Gene

Aliases for LYPD3 Gene

  • LY6/PLAUR Domain Containing 3 2 3 5
  • GPI-Anchored Metastasis-Associated Protein C4.4A Homolog 3 4
  • Matrigel-Induced Gene C4 Protein 3 4
  • MIG-C4 3 4
  • C4.4A 3 4
  • GPI-Anchored Metastasis-Associated Protein Homolog 3
  • Ly6/PLAUR Domain-Containing Protein 3 3
  • 2310061G07Rik 3

External Ids for LYPD3 Gene

Previous GeneCards Identifiers for LYPD3 Gene

  • GC19M048660
  • GC19M043964
  • GC19M040394

Summaries for LYPD3 Gene

GeneCards Summary for LYPD3 Gene

LYPD3 (LY6/PLAUR Domain Containing 3) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. GO annotations related to this gene include laminin binding. An important paralog of this gene is LYPD5.

UniProtKB/Swiss-Prot for LYPD3 Gene

  • Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression.

Gene Wiki entry for LYPD3 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYPD3 Gene

Genomics for LYPD3 Gene

Regulatory Elements for LYPD3 Gene

Enhancers for LYPD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F043437 1.5 FANTOM5 Ensembl ENCODE 12.2 +26.7 26685 3.4 PKNOX1 SIN3A KAT2B ZNF121 SCRT2 RCOR1 FOS REST ZNF592 ZNF217 PHLDB3 LYPD3 ZNF575 PLAUR KCNN4 SMG9 GC19M043399
GH19F043462 1 ENCODE 15.2 +1.1 1147 3.6 HDGF ATF1 PKNOX1 ZNF133 SIN3A ZNF48 YY1 GLIS2 ZNF416 KLF7 PINLYP SRRM5 ZNF575 ZNF45 PHLDB3 ZNF225 ZNF223 CEACAMP10 LOC105372414 CEACAMP1
GH19F043425 1.1 Ensembl ENCODE 11.2 +39.4 39416 1.3 ZNF2 RAD21 ZNF366 SCRT2 ZNF207 ZNF391 ZNF362 ZNF654 ZNF280D SP3 ZNF45 ZNF224 ZNF234 ZNF155 LYPD3 PHLDB3 ZNF284 ZNF428 GC19M043399
GH19F043445 0.6 Ensembl 12.2 +20.6 20579 0.2 TFDP1 HDAC1 RNF2 GATA2 ADNP SPI1 LYPD3 PHLDB3 GC19M043399
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LYPD3 on UCSC Golden Path with GeneCards custom track

Promoters for LYPD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000142352 779 201 ZNF274 YY2 ZBTB48 IKZF1 ZNF512 ZNF416 PRDM10
ENSR00001817873 1979 1801 HDGF ATF1 PKNOX1 ZNF133 FEZF1 ZNF48 YY1 GLIS2 ZNF416 KLF7

Genomic Location for LYPD3 Gene

43,460,787 bp from pter
43,465,679 bp from pter
4,893 bases
Minus strand

Genomic View for LYPD3 Gene

Genes around LYPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYPD3 Gene

Proteins for LYPD3 Gene

  • Protein details for LYPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ly6/PLAUR domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q9UJ74

    Protein attributes for LYPD3 Gene

    346 amino acids
    Molecular mass:
    35971 Da
    Quaternary structure:
    • Binds laminin-1 and laminin-5. Interacts with LGALS3 (By similarity). Interacts with AGR2 and AGR3.

neXtProt entry for LYPD3 Gene

Post-translational modifications for LYPD3 Gene

  • N-glycosylated and O-glycosylated.
  • Glycosylation at Asn 118, Asn 163, Asn 176, Asn 183, and Ser 289
  • Modification sites at PhosphoSitePlus

Other Protein References for LYPD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LYPD3 Gene

Domains & Families for LYPD3 Gene

Gene Families for LYPD3 Gene

Protein Domains for LYPD3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Contains 2 UPAR/Ly6 domains.
  • Contains 2 UPAR/Ly6 domains.
genes like me logo Genes that share domains with LYPD3: view

Function for LYPD3 Gene

Molecular function for LYPD3 Gene

UniProtKB/Swiss-Prot Function:
Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression.
UniProtKB/Swiss-Prot Induction:
Up-regulated in migrating keratinocytes during epithelisation of incisional skin wounds.

Gene Ontology (GO) - Molecular Function for LYPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043236 laminin binding IEA,IBA --
genes like me logo Genes that share ontologies with LYPD3: view
genes like me logo Genes that share phenotypes with LYPD3: view

Animal Models for LYPD3 Gene

MGI Knock Outs for LYPD3:

Animal Model Products

  • Taconic Biosciences Mouse Models for LYPD3

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LYPD3 Gene

Localization for LYPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYPD3 Gene

Cell membrane; Lipid-anchor, GPI-anchor.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LYPD3 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for LYPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 16502470
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LYPD3: view

Pathways & Interactions for LYPD3 Gene

genes like me logo Genes that share pathways with LYPD3: view

Gene Ontology (GO) - Biological Process for LYPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007160 cell-matrix adhesion IEA,IBA --
genes like me logo Genes that share ontologies with LYPD3: view

No data available for SIGNOR curated interactions for LYPD3 Gene

Transcripts for LYPD3 Gene

Unigene Clusters for LYPD3 Gene

LY6/PLAUR domain containing 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYPD3 Gene

No ASD Table

Relevant External Links for LYPD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LYPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LYPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LYPD3 Gene

This gene is overexpressed in Esophagus - Mucosa (x15.6), Skin - Sun Exposed (Lower leg) (x10.1), Skin - Not Sun Exposed (Suprapubic) (x9.3), Vagina (x7.0), Minor Salivary Gland (x4.8), and Cervix - Ectocervix (x4.3).

Protein differential expression in normal tissues from HIPED for LYPD3 Gene

This gene is overexpressed in Cervix (28.4) and Hair follicle (19.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LYPD3 Gene

Protein tissue co-expression partners for LYPD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LYPD3 Gene:


SOURCE GeneReport for Unigene cluster for LYPD3 Gene:


mRNA Expression by UniProt/SwissProt for LYPD3 Gene:

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.
genes like me logo Genes that share expression patterns with LYPD3: view

Orthologs for LYPD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LYPD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LYPD3 34 35
  • 99.6 (n)
(Canis familiaris)
Mammalia LYPD3 34 35
  • 82.99 (n)
(Bos Taurus)
Mammalia LYPD3 34 35
  • 81.82 (n)
(Mus musculus)
Mammalia Lypd3 34 16 35
  • 78.56 (n)
(Rattus norvegicus)
Mammalia Lypd3 34
  • 78.46 (n)
(Ornithorhynchus anatinus)
Mammalia LYPD3 35
  • 44 (a)
(Anolis carolinensis)
Reptilia LYPD3 35
  • 35 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489124 34
  • 47.45 (n)
Species where no ortholog for LYPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LYPD3 Gene

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

Paralogs for LYPD3 Gene

Paralogs for LYPD3 Gene

(1) SIMAP similar genes for LYPD3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LYPD3: view

Variants for LYPD3 Gene

Sequence variations from dbSNP and Humsavar for LYPD3 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs10408009 -- 43,465,283(+) CAGCT(C/T)CCCTT intron-variant
rs10425610 -- 43,463,884(+) ACAGG(A/T)CCGAC intron-variant
rs1044539 -- 43,461,472(-) CCGCA(G/T)CAATT reference, missense
rs111270620 -- 43,465,649(+) AGGAT(C/G)AGTAA utr-variant-5-prime
rs111509010 -- 43,464,011(+) GGAGA(C/T)AGCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LYPD3 Gene

Variant ID Type Subtype PubMed ID
dgv3603n100 CNV gain 25217958
nsv1057657 CNV gain 25217958
nsv2501 CNV deletion 18451855
nsv509744 CNV insertion 20534489

Variation tolerance for LYPD3 Gene

Residual Variation Intolerance Score: 75.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.29; 53.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LYPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYPD3 Gene

Disorders for LYPD3 Gene

Relevant External Links for LYPD3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for LYPD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LYPD3 Gene

Publications for LYPD3 Gene

  1. Identification of genes involved in human urothelial cell-matrix interactions: implications for the progression pathways of malignant urothelium. (PMID: 11245483) Smith B.A. … Southgate J. (Cancer Res. 2001) 2 3 4 22 64
  2. Structural analysis and tissue localization of human C4.4A: a protein homologue of the urokinase receptor. (PMID: 15012588) Hansen L.V. … Ploug M. (Biochem. Eng. J. 2004) 3 4 22 64
  3. 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. (PMID: 12592373) Fletcher G.C. … Terrett J.A. (Br. J. Cancer 2003) 3 4 22 64
  4. Cloning of the human homologue of the metastasis-associated rat C4.4A. (PMID: 11179665) Wuerfel J. … Zoeller M. (Gene 2001) 2 3 4 64
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J. … Lucas S.M. (Nature 2004) 3 4 64

Products for LYPD3 Gene

Sources for LYPD3 Gene

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