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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. Gene Ontology (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

Additional gene information for LYPD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies 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 2.4 EPDnew Ensembl ENCODE dbSUPER 665.2 +1.1 1147 3.6 HDGF PKNOX1 SIN3A YY1 ZNF416 FOS KLF13 SP3 ZHX2 SMARCB1 LYPD3 ZNF225 ZNF235 ZNF223 ZNF45 ZNF284 ZNF226 ZNF227 PINLYP ZNF155
GH19J043437 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 12.2 +26.7 26685 3.4 PKNOX1 FOXA2 SIN3A ZNF121 TCF12 SCRT2 FOS RCOR1 GATAD2B ELF1 ZNF45 ZNF224 ZNF155 ZNF234 ZNF225 ZNF284 MRPS15P2 ZNF283 PHLDB3 ZNF112
GH19J043425 Enhancer 1 ENCODE dbSUPER 11.3 +39.4 39415 1.3 SIN3A ZNF2 RAD21 ZNF614 ZNF366 SCRT2 ZNF207 ZNF654 SP3 ZNF362 ZNF45 ZNF224 ZNF234 ZNF155 LYPD3 PHLDB3 ZNF284 ZNF428 GC19M043399
GH19J043457 Enhancer 0.7 dbSUPER 11.8 +7.8 7838 0.9 BCOR MEIS2 LEF1 ZNF316 FOXK2 NFE2 PRDM10 MAFK CBFA2T3 MAFG LYPD3 PINLYP ZNF575 GC19M043399
GH19J043555 Enhancer 0.7 ENCODE 10.4 -89.7 -89700 0.2 HDGF CTCF ARID4B ERF ZNF2 RAD21 GLIS2 ZNF366 ARID2 SMC3 GC19M043549 ENSG00000269177 XRCC1 PINLYP IRGQ ZNF576 SRRM5 ZNF227 ZNF575 ETHE1
- 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

Top Transcription factor binding sites by QIAGEN in the LYPD3 gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • 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 posLast=289289, isoforms=183, posLast=176176, posLast=163163, and posLast=118118
  • 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

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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 --
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

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

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 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:0006501 C-terminal protein lipidation TAS --
GO:0007160 cell-matrix adhesion IBA --
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 :
(9) Additional mRNA sequences :
(131) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LYPD3 Gene

LY6/PLAUR domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for LYPD3 Gene

GeneLoc Exon Structure for
LYPD3
ECgene alternative splicing isoforms for
LYPD3

Expression for LYPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of LYPD3 Gene:

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 34 33
  • 99.6 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LYPD3 34 33
  • 82.99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LYPD3 34 33
  • 81.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lypd3 16 34 33
  • 78.56 (n)
rat
(Rattus norvegicus)
Mammalia Lypd3 33
  • 78.46 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LYPD3 34
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LYPD3 34
  • 35 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489124 33
  • 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 from dbSNP and Humsavar for LYPD3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000008650 -- 43,462,424(-) G/C intron_variant
rs1000062519 -- 43,462,778(-) C/T intron_variant
rs1000579335 -- 43,467,039(-) C/T upstream_transcript_variant
rs1001009941 -- 43,461,184(-) A/C/G 3_prime_UTR_variant
rs1001138918 -- 43,465,130(-) T/C 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)

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

Additional Disease Information for LYPD3

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 BA … Southgate J (Cancer research 2001) 2 3 4 22 58
  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 22 58
  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 22 58
  4. Cloning of the human homologue of the metastasis-associated rat C4.4A. (PMID: 11179665) Würfel J … Zöller M (Gene 2001) 2 3 4 58
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58

Products for LYPD3 Gene

Sources for LYPD3 Gene

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