Aliases for LYPD4 Gene

Aliases for LYPD4 Gene

  • LY6/PLAUR Domain Containing 4 2 3 5
  • Ly6/PLAUR Domain-Containing Protein 4 3 4
  • Testicular Tissue Protein Li 159 3
  • Sperm Membrane Receptor 3
  • SMR 3

External Ids for LYPD4 Gene

Previous GeneCards Identifiers for LYPD4 Gene

  • GC19M047033
  • GC19M042341
  • GC19M038774
  • GC19M041834

Summaries for LYPD4 Gene

GeneCards Summary for LYPD4 Gene

LYPD4 (LY6/PLAUR Domain Containing 4) is a Protein Coding gene. Diseases associated with LYPD4 include Retinitis Pigmentosa 42 and Conidiobolomycosis. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. An important paralog of this gene is CD177.

Additional gene information for LYPD4 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LYPD4 Gene

Genomics for LYPD4 Gene

GeneHancer (GH) Regulatory Elements for LYPD4 Gene

Promoters and enhancers for LYPD4 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
GH19J041845 Promoter 0.7 EPDnew 500.7 +0.2 159 0.1 SP2 E2F6 ZNF395 ZBTB33 KLF1 GABPB1 L3MBTL2 MAX CBX3 MGA DMRTC2 LYPD4 piR-58768
GH19J041844 Promoter 0.6 EPDnew 500.7 +0.3 272 0.1 ZNF395 ZBTB33 KLF1 L3MBTL2 DMRTC2 LYPD4 piR-58768
GH19J041846 Promoter 0.6 EPDnew 500.7 -0.2 -161 0.1 ZBTB33 GABPB1 L3MBTL2 CBX3 DMRTC2 LYPD4 RPS19
GH19J042267 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 8.8 -426.0 -426008 6.9 EP300 FOXK2 ZBTB40 ZNF217 SIN3A NRF1 TCF12 MYC POLR2G USF1 CIC piR-36065 ZNF526 ZNF574 DEDD2 MEGF8 CEACAM3 PAFAH1B3 PRR19 GSK3A
GH19J041732 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +110.1 110118 4.7 KLF4 CTBP1 FOXA1 PKNOX1 ZFP36 RNF2 E2F1 SMARCE1 BCL6B ZNF579 CEACAM7 CEACAM5 DMRTC2 LYPD4 L17043-001 CEACAM6 ENSG00000267881
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYPD4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LYPD4

Top Transcription factor binding sites by QIAGEN in the LYPD4 gene promoter:
  • GR
  • GR-alpha
  • GR-beta
  • p53
  • PPAR-alpha

Genomic Locations for LYPD4 Gene

Genomic Locations for LYPD4 Gene
chr19:41,833,686-41,844,862
(GRCh38/hg38)
Size:
11,177 bases
Orientation:
Minus strand
chr19:42,341,148-42,348,760
(GRCh37/hg19)
Size:
7,613 bases
Orientation:
Minus strand

Genomic View for LYPD4 Gene

Genes around LYPD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYPD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYPD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYPD4 Gene

Proteins for LYPD4 Gene

  • Protein details for LYPD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UWN0-LYPD4_HUMAN
    Recommended name:
    Ly6/PLAUR domain-containing protein 4
    Protein Accession:
    Q6UWN0
    Secondary Accessions:
    • Q8IYW0

    Protein attributes for LYPD4 Gene

    Size:
    246 amino acids
    Molecular mass:
    26763 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LYPD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYPD4 Gene

Post-translational modifications for LYPD4 Gene

  • Glycosylation at Asn117
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LYPD4 Gene

Domains & Families for LYPD4 Gene

Gene Families for LYPD4 Gene

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

Protein Domains for LYPD4 Gene

Blocks:
  • CD59 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LYPD4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ77180, highly similar to Homo sapiens LY6/PLAUR domain containing 4 (LYPD4), mRNA (A8K8E0_HUMAN)
  • Ly6/PLAUR domain-containing protein 4 (LYPD4_HUMAN)
genes like me logo Genes that share domains with LYPD4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LYPD4 Gene

Function for LYPD4 Gene

Phenotypes From GWAS Catalog for LYPD4 Gene

genes like me logo Genes that share phenotypes with LYPD4: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LYPD4

CRISPR Products

miRNA for LYPD4 Gene

miRTarBase miRNAs that target LYPD4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYPD4

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LYPD4 Gene

Localization for LYPD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYPD4 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 LYPD4 gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LYPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with LYPD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LYPD4 Gene

Pathways & Interactions for LYPD4 Gene

genes like me logo Genes that share pathways with LYPD4: view

Gene Ontology (GO) - Biological Process for LYPD4 Gene

None

No data available for SIGNOR curated interactions for LYPD4 Gene

Drugs & Compounds for LYPD4 Gene

No Compound Related Data Available

Transcripts for LYPD4 Gene

mRNA/cDNA for LYPD4 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
3 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 LYPD4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYPD4 Gene

No ASD Table

Relevant External Links for LYPD4 Gene

GeneLoc Exon Structure for
LYPD4

Expression for LYPD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LYPD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LYPD4 Gene

This gene is overexpressed in Testis (x52.6).

Protein differential expression in normal tissues from HIPED for LYPD4 Gene

This gene is overexpressed in Monocytes (54.6) and Testis (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LYPD4 Gene



Protein tissue co-expression partners for LYPD4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LYPD4

SOURCE GeneReport for Unigene cluster for LYPD4 Gene:

Hs.98660
genes like me logo Genes that share expression patterns with LYPD4: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYPD4 Gene

Orthologs for LYPD4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LYPD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYPD4 30
  • 88.41 (n)
dog
(Canis familiaris)
Mammalia LYPD4 30
  • 83.33 (n)
cow
(Bos Taurus)
Mammalia LYPD4 30
  • 79.59 (n)
mouse
(Mus musculus)
Mammalia Lypd4 17 30
  • 77.64 (n)
Species where no ortholog for LYPD4 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LYPD4 Gene

ENSEMBL:
Gene Tree for LYPD4 (if available)
TreeFam:
Gene Tree for LYPD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYPD4: view image

Paralogs for LYPD4 Gene

Paralogs for LYPD4 Gene

(1) SIMAP similar genes for LYPD4 Gene using alignment to 2 proteins:

  • LYPD4_HUMAN
  • A8K8E0_HUMAN
genes like me logo Genes that share paralogs with LYPD4: view

Variants for LYPD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LYPD4 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs35476281 - p.Thr184Ser

Additional dbSNP identifiers (rs#s) for LYPD4 Gene

Structural Variations from Database of Genomic Variants (DGV) for LYPD4 Gene

Variant ID Type Subtype PubMed ID
nsv522854 CNV gain 19592680

Variation tolerance for LYPD4 Gene

Residual Variation Intolerance Score: 60.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.03% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYPD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYPD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYPD4 Gene

Disorders for LYPD4 Gene

MalaCards: The human disease database

(7) MalaCards diseases for LYPD4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 42
  • rp42
conidiobolomycosis
  • infection by conidiobolus
podoconiosis
  • podoconiosis, susceptibility to
retinitis pigmentosa 4
  • rp4
kabuki syndrome 1
  • kms
- elite association - COSMIC cancer census association via MalaCards
Search LYPD4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LYPD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LYPD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LYPD4 Gene

Publications for LYPD4 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 54
  2. 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
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  4. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. (PMID: 27229929) Daakour S … Twizere JC (BMC cancer 2016) 3 54
  5. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. (PMID: 21083371) Chinn LW … O'Brien SJ (The Journal of infectious diseases 2010) 41 54

Products for LYPD4 Gene

Sources for LYPD4 Gene