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Aliases for LYSMD3 Gene

Aliases for LYSMD3 Gene

  • LysM Domain Containing 3 2 3 5
  • LysM, Putative Peptidoglycan-Binding, Domain Containing 3 2 3
  • LysM And Putative Peptidoglycan-Binding Domain-Containing Protein 3 3

External Ids for LYSMD3 Gene

Previous GeneCards Identifiers for LYSMD3 Gene

  • GC05M089848
  • GC05M085022

Summaries for LYSMD3 Gene

GeneCards Summary for LYSMD3 Gene

LYSMD3 (LysM Domain Containing 3) is a Protein Coding gene. An important paralog of this gene is LYSMD4.

Gene Wiki entry for LYSMD3 Gene

Additional gene information for LYSMD3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYSMD3 Gene

Genomics for LYSMD3 Gene

GeneHancer (GH) Regulatory Elements for LYSMD3 Gene

Promoters and enhancers for LYSMD3 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
GH05J090527 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.1 107 3.2 HDGF FOXA2 PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 LYSMD3 ADGRV1 LINC01339 ENSG00000214942 POLR3G
GH05J091277 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 10.9 -751.0 -750960 5.9 CLOCK FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 ZNF610 GLIS1 GC05M091281 GC05P091280 RPS18P7 ENSG00000241059 LYSMD3 LOC729040
GH05J090557 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 10 -29.1 -29102 1.5 CLOCK SIN3A ZNF2 ZBTB7B ZNF213 ZNF143 KLF13 SP3 REST SREBF1 ADGRV1 ARRDC3 LYSMD3 POLR3G LOC105379077
GH05J091376 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.6 -851.3 -851348 8.5 CLOCK DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D ARRDC3 ARRDC3-AS1 ENSG00000241059 RPS18P7 LYSMD3
GH05J090439 Enhancer 1 Ensembl ENCODE 11.8 +89.5 89508 1 MEIS2 CTCF NFATC3 ZNF384 ZNF644 RAD21 YY1 ZNF366 BRD9 ZNF143 LYSMD3 ADGRV1 POLR3G MBLAC2 CETN3 LOC731157
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYSMD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LYSMD3 gene promoter:
  • ARP-1
  • S8
  • HNF-1
  • HNF-1A
  • SRF
  • SRF (504 AA)
  • deltaCREB
  • HOXA3
  • PPAR-gamma2
  • CREB

Genomic Locations for LYSMD3 Gene

Genomic Locations for LYSMD3 Gene
chr5:90,515,611-90,529,584
(GRCh38/hg38)
Size:
13,974 bases
Orientation:
Minus strand
chr5:89,811,428-89,825,401
(GRCh37/hg19)
Size:
13,974 bases
Orientation:
Minus strand

Genomic View for LYSMD3 Gene

Genes around LYSMD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYSMD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYSMD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYSMD3 Gene

Proteins for LYSMD3 Gene

  • Protein details for LYSMD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z3D4-LYSM3_HUMAN
    Recommended name:
    LysM and putative peptidoglycan-binding domain-containing protein 3
    Protein Accession:
    Q7Z3D4
    Secondary Accessions:
    • Q5H9U0
    • Q6PEK0
    • Q9NTE9

    Protein attributes for LYSMD3 Gene

    Size:
    306 amino acids
    Molecular mass:
    34538 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAD97936.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for LYSMD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYSMD3 Gene

Post-translational modifications for LYSMD3 Gene

  • Glycosylation at isoforms=2, 37
  • Modification sites at PhosphoSitePlus

Other Protein References for LYSMD3 Gene

No data available for DME Specific Peptides for LYSMD3 Gene

Domains & Families for LYSMD3 Gene

Gene Families for LYSMD3 Gene

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

Protein Domains for LYSMD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LYSMD3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYSMD3: view

No data available for UniProtKB/Swiss-Prot for LYSMD3 Gene

Function for LYSMD3 Gene

Phenotypes From GWAS Catalog for LYSMD3 Gene

genes like me logo Genes that share phenotypes with LYSMD3: view

Animal Model Products

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 LYSMD3 Gene

Localization for LYSMD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYSMD3 Gene

Membrane; Single-pass membrane protein.

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 LYSMD3 gene
Compartment Confidence
cytosol 3
plasma membrane 2
extracellular 1
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LYSMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LYSMD3: view

Pathways & Interactions for LYSMD3 Gene

SuperPathways for LYSMD3 Gene

No Data Available

Interacting Proteins for LYSMD3 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000314518%0d%0a9606.ENSP00000357484%0d%0a9606.ENSP00000358464%0d%0a
Selected Interacting proteins: ENSP00000314518 Q7Z3D4-LYSM3_HUMAN for LYSMD3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for LYSMD3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LYSMD3 Gene

Drugs & Compounds for LYSMD3 Gene

No Compound Related Data Available

Transcripts for LYSMD3 Gene

mRNA/cDNA for LYSMD3 Gene

Unigene Clusters for LYSMD3 Gene

LysM, putative peptidoglycan-binding, domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYSMD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2: -
SP3: - -

Relevant External Links for LYSMD3 Gene

GeneLoc Exon Structure for
LYSMD3
ECgene alternative splicing isoforms for
LYSMD3

Expression for LYSMD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYSMD3 Gene

Protein differential expression in normal tissues from HIPED for LYSMD3 Gene

This gene is overexpressed in CD8 Tcells (37.1), Pancreas (18.4), Placenta (7.3), and Platelet (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LYSMD3 Gene



Protein tissue co-expression partners for LYSMD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of LYSMD3 Gene:

LYSMD3

SOURCE GeneReport for Unigene cluster for LYSMD3 Gene:

Hs.136235

Evidence on tissue expression from TISSUES for LYSMD3 Gene

  • Kidney(4.3)
  • Eye(4)
genes like me logo Genes that share expression patterns with LYSMD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYSMD3 Gene

Orthologs for LYSMD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LYSMD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYSMD3 34 33
  • 99.67 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LYSMD3 34 33
  • 91.37 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LYSMD3 34 33
  • 90.63 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lysmd3 16 34 33
  • 83.61 (n)
rat
(Rattus norvegicus)
Mammalia Lysmd3 33
  • 81.32 (n)
oppossum
(Monodelphis domestica)
Mammalia LYSMD3 34
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LYSMD3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves LYSMD3 34 33
  • 67.58 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LYSMD3 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lysmd3 33
  • 65.16 (n)
zebrafish
(Danio rerio)
Actinopterygii lysmd3 34 33
  • 56.26 (n)
OneToOne
sbcb462 33
worm
(Caenorhabditis elegans)
Secernentea lmd-1 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.343 34
  • 30 (a)
OneToMany
Species where no ortholog for LYSMD3 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)
  • 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)
  • 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 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)

Evolution for LYSMD3 Gene

ENSEMBL:
Gene Tree for LYSMD3 (if available)
TreeFam:
Gene Tree for LYSMD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYSMD3: view image

Paralogs for LYSMD3 Gene

Paralogs for LYSMD3 Gene

(1) SIMAP similar genes for LYSMD3 Gene using alignment to 3 proteins:

  • LYSM3_HUMAN
  • A8K613_HUMAN
  • G5E9N8_HUMAN
genes like me logo Genes that share paralogs with LYSMD3: view

Variants for LYSMD3 Gene

Sequence variations from dbSNP and Humsavar for LYSMD3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000879498 -- 90,521,381(-) G/C intron_variant
rs1001030342 -- 90,529,186(-) G/A 5_prime_UTR_variant, intron_variant
rs1001460754 -- 90,521,158(-) C/G intron_variant
rs1001566169 -- 90,528,776(-) A/G intron_variant
rs1002247854 -- 90,518,078(-) A/C 3_prime_UTR_variant

Variation tolerance for LYSMD3 Gene

Residual Variation Intolerance Score: 91.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.19; 39.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYSMD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYSMD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LYSMD3 Gene

Disorders for LYSMD3 Gene

Additional Disease Information for LYSMD3

No disorders were found for LYSMD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LYSMD3 Gene

Publications for LYSMD3 Gene

  1. LysMD3 is a type II membrane protein without an in vivo role in the response to a range of pathogens. (PMID: 29496999) Yokoyama CC … Virgin HW (The Journal of biological chemistry 2018) 2 3 58
  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 58
  3. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta GD … Pelletier L (Cell 2015) 3 58
  4. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H … Mohammed S (Journal of proteome research 2013) 4 58
  5. A quantitative atlas of mitotic phosphorylation. (PMID: 18669648) Dephoure N … Gygi SP (Proceedings of the National Academy of Sciences of the United States of America 2008) 4 58

Products for LYSMD3 Gene

Sources for LYSMD3 Gene

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