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
  • Ly6/PLAUR Domain-Containing Protein 3 3 4
  • Matrigel-Induced Gene C4 Protein 3 4
  • MIG-C4 3 4
  • C4.4A 3 4
  • GPI-Anchored Metastasis-Associated Protein Homolog 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. Diseases associated with LYPD3 include Atrial Septal Defect 6 and Mal De Meleda. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. Gene Ontology (GO) annotations related to this gene include laminin binding. An important paralog of this gene is LYPD5.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for LYPD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LYPD3 Gene

Genomics for LYPD3 Gene

GeneHancer (GH) Regulatory Elements for LYPD3 Gene

Promoters and enhancers for LYPD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J043462 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 515.5 +0.9 878 4.4 ZNF217 TCF12 NRF1 POLR2G PHF8 ZFX ZNF639 ZNF10 POLR2A ZBTB10 LYPD3 ZNF223 ZNF225 ZNF235 ZNF226 ZNF575 ZNF227 ZNF45 ENSG00000270679 PHLDB3
GH19J043437 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 12.3 +27.1 27078 4.4 ZNF217 RBAK JUND KLF4 CUX1 TOE1 EP300 ZNF274 GATAD2B CTBP1 piR-31462-020 PHLDB3 LYPD3 ZNF575 PLAUR KCNN4 SMG9 RF00017-2990
GH19J043425 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.3 +39.5 39513 1.5 CTCF ZNF639 ZIC2 RFX1 HINFP WT1 ZBTB17 ZSCAN18 ZNF207 YY1 ZNF45 ZNF224 ZNF234 ZNF155 LYPD3 PHLDB3 ZNF284 ZNF428 piR-31462-020 RF02543-026
GH19J043454 Enhancer 1 Ensembl ENCODE dbSUPER 12 +10.3 10279 2.8 ZNF217 ZNF10 CUX1 CTBP1 SIN3A PBX2 ELF1 GATA3 FOXA1 DPF2 ZNF575 LYPD3 ETHE1 PHLDB3 L13714-243 AY940853-001
GH19J043443 Enhancer 0.8 Ensembl 12.3 +20.7 20678 3.2 HINFP NCOR1 RELA NFIC ZNF592 ARNT ZNF524 TBP PBX2 SPI1 IRGQ LYPD3 PHLDB3 ZNF575 ZNF576 RF00017-2990 L13714-243
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYPD3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LYPD3

Top Transcription factor binding sites by QIAGEN in the LYPD3 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • Sp1

Genomic Locations for LYPD3 Gene

Genomic Locations for LYPD3 Gene
chr19:43,460,787-43,465,679
(GRCh38/hg38)
Size:
4,893 bases
Orientation:
Minus strand
chr19:43,964,939-43,969,831
(GRCh37/hg19)
Size:
4,893 bases
Orientation:
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:
    O95274-LYPD3_HUMAN
    Recommended name:
    Ly6/PLAUR domain-containing protein 3
    Protein Accession:
    O95274
    Secondary Accessions:
    • Q9UJ74

    Protein attributes for LYPD3 Gene

    Size:
    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 Asn118, Asn163, Asn176, Asn183, Ser289, and Thr297
  • 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for LYPD3 Gene

Blocks:
  • CD59 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LYPD3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ95643, Homo sapiens GPI-anchored metastasis-associated protein homolog(C4.4A), mRNA (B2RBR3_HUMAN)
  • Matrigel-induced gene C4 protein (LYPD3_HUMAN)
genes like me logo Genes that share domains with LYPD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LYPD3 Gene

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.

Phenotypes From GWAS Catalog for LYPD3 Gene

Gene Ontology (GO) - Molecular Function for LYPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043236 laminin binding IBA 21873635
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:
  • Lypd3 Lypd3<tm1.1(KOMP)Vlcg>
  • Lypd3 Lypd3<tm1(KOMP)Vlcg>

Animal Model Products

  • Taconic Biosciences Mouse Models for LYPD3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYPD3

Clone 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

COMPARTMENTS
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
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LYPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space HDA 16502470
GO:0005886 plasma membrane IBA,TAS --
GO:0016020 membrane IEA --
GO:0016021 integral 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 IBA 21873635
genes like me logo Genes that share ontologies with LYPD3: view

No data available for SIGNOR curated interactions for LYPD3 Gene

Drugs & Compounds for LYPD3 Gene

No Compound Related Data Available

Transcripts for LYPD3 Gene

mRNA/cDNA for LYPD3 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYPD3

Clone Products

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

No ASD Table

Relevant External Links for LYPD3 Gene

GeneLoc Exon Structure for
LYPD3

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 and MOPED for LYPD3 Gene



Protein tissue co-expression partners for LYPD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LYPD3

SOURCE GeneReport for Unigene cluster for LYPD3 Gene:

Hs.631594

mRNA Expression by UniProt/SwissProt for LYPD3 Gene:

O95274-LYPD3_HUMAN
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.

Evidence on tissue expression from TISSUES for LYPD3 Gene

  • Skin(4.6)
genes like me logo Genes that share expression patterns with LYPD3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LYPD3 Gene

Orthologs for LYPD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LYPD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYPD3 31 30
  • 99.6 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LYPD3 31 30
  • 82.99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LYPD3 31 30
  • 81.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lypd3 17 31 30
  • 78.56 (n)
rat
(Rattus norvegicus)
Mammalia Lypd3 30
  • 78.46 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LYPD3 31
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LYPD3 31
  • 35 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489124 30
  • 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

ENSEMBL:
Gene Tree for LYPD3 (if available)
TreeFam:
Gene Tree for LYPD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYPD3: view image

Paralogs for LYPD3 Gene

Paralogs for LYPD3 Gene

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

  • LYPD3_HUMAN
  • B2RBR3_HUMAN
genes like me logo Genes that share paralogs with LYPD3: view

Variants for LYPD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LYPD3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
769015 Benign: not provided 43,461,375(-) G/A SYNONYMOUS_VARIANT
771523 Benign: not provided 43,465,515(-) C/T SYNONYMOUS_VARIANT
780573 Benign: not provided 43,461,652(-) G/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for LYPD3 Gene

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)

Additional Variant Information for LYPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYPD3

SNP Genotyping and Copy Number Assay Products

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

Disorders for LYPD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LYPD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
atrial septal defect 6
  • asd6
mal de meleda
  • mdm
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search LYPD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LYPD3

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

No data available for 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 BA … Southgate J (Cancer research 2001) 2 3 4 23 54
  2. Structural analysis and tissue localization of human C4.4A: a protein homologue of the urokinase receptor. (PMID: 15012588) Hansen LV … Ploug M (The Biochemical journal 2004) 3 4 23 54
  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 GC … Terrett JA (British journal of cancer 2003) 3 4 23 54
  4. Cloning of the human homologue of the metastasis-associated rat C4.4A. (PMID: 11179665) Würfel J … Zöller M (Gene 2001) 2 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for LYPD3 Gene

Sources for LYPD3 Gene