Aliases for LYSMD4 Gene

Aliases for LYSMD4 Gene

  • LysM Domain Containing 4 2 3 5
  • LysM And Putative Peptidoglycan-Binding Domain-Containing Protein 4 3 4
  • LysM, Putative Peptidoglycan-Binding, Domain Containing 4 2 3
  • FLJ33008 2
  • LYSMD4 5

External Ids for LYSMD4 Gene

Previous GeneCards Identifiers for LYSMD4 Gene

  • GC15M098086
  • GC15M100256
  • GC15M076397
  • GC15M099715

Summaries for LYSMD4 Gene

GeneCards Summary for LYSMD4 Gene

LYSMD4 (LysM Domain Containing 4) is a Protein Coding gene. Diseases associated with LYSMD4 include Ichthyosis, Congenital, Autosomal Recessive 9 and Autosomal Recessive Congenital Ichthyosis. An important paralog of this gene is LYSMD3.

Additional gene information for LYSMD4 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 LYSMD4 Gene

Genomics for LYSMD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LYSMD4 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
GH15J099731 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 625.3 +0.4 419 4.3 SP1 GATAD2A PRDM10 NFKBIZ BACH1 LARP7 RBFOX2 POLR2A RXRB NR2C1 LYSMD4 lnc-LYSMD4-1 LRRC28 TTC23 DNM1P46 MN297332 MEF2A
GH15J099702 Promoter/Enhancer 1.2 Ensembl ENCODE 24.4 +29.8 29843 2.1 CEBPG CREB1 CTCF ATF7 PRDM10 ZNF629 ZNF692 POLR2A JUND FOXA1 LYSMD4 5MWI_A-056 ENSG00000201724 MEF2A
GH15J099563 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 9.2 +166.4 166360 7.2 RNF2 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 TFE3 RFX1 LEF1 MEF2A lnc-LRRC28-7 CERS3-AS1 ENSG00000259921 TTC23 PRKXP1 HSP90B2P LYSMD4 piR-38423-021
GH15J099715 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas 20.4 +14.6 14613 6.1 SP1 FOXA1 RELA IKZF2 PKNOX1 EED ARID3A HMBOX1 RUNX3 BCLAF1 LYSMD4 MEF2A 5MWI_A-056 MN297332 lnc-LYSMD4-1
GH15J099706 Enhancer 0.7 ENCODE 25.1 +25.8 25782 3.5 JUND PHF21A SP1 HMBOX1 EGR1 RUNX3 FOXA2 NR3C1 NR2C2 FOS LYSMD4 5MWI_A-056 ENSG00000201724 MEF2A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LYSMD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LYSMD4

Genomic Locations for LYSMD4 Gene

Genomic Locations for LYSMD4 Gene
chr15:99,714,798-99,733,561
(GRCh38/hg38)
Size:
18,764 bases
Orientation:
Minus strand
chr15:100,255,902-100,273,766
(GRCh37/hg19)
Size:
17,865 bases
Orientation:
Minus strand

Genomic View for LYSMD4 Gene

Genes around LYSMD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYSMD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYSMD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYSMD4 Gene

Proteins for LYSMD4 Gene

  • Protein details for LYSMD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5XG99-LYSM4_HUMAN
    Recommended name:
    LysM and putative peptidoglycan-binding domain-containing protein 4
    Protein Accession:
    Q5XG99
    Secondary Accessions:
    • A6NII6
    • A8K2N1
    • Q96LY7

    Protein attributes for LYSMD4 Gene

    Size:
    296 amino acids
    Molecular mass:
    32066 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB71528.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for LYSMD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYSMD4 Gene

Post-translational modifications for LYSMD4 Gene

  • Glycosylation at Asn30
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LYSMD4 Gene

Domains & Families for LYSMD4 Gene

Gene Families for LYSMD4 Gene

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

Protein Domains for LYSMD4 Gene

InterPro:
Blocks:
  • Peptidoglycan-binding LysM
ProtoNet:

Suggested Antigen Peptide Sequences for LYSMD4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ42862 fis, clone BRHIP2013699, moderately similar to Mus musculus LysM, putative peptidoglycan-binding, domain containing 4 (Lysmd4), mRNA (B3KWE4_HUMAN)
  • LysM and putative peptidoglycan-binding domain-containing protein 4 (LYSM4_HUMAN)
genes like me logo Genes that share domains with LYSMD4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LYSMD4 Gene

Function for LYSMD4 Gene

Phenotypes From GWAS Catalog for LYSMD4 Gene

genes like me logo Genes that share phenotypes with LYSMD4: view

Animal Model Products

CRISPR Products

miRNA for LYSMD4 Gene

miRTarBase miRNAs that target LYSMD4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYSMD4

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 LYSMD4 Gene

Localization for LYSMD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LYSMD4 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 LYSMD4 gene
Compartment Confidence
plasma membrane 2
cytoskeleton 2
mitochondrion 2
cytosol 2
extracellular 0
nucleus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LYSMD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LYSMD4: view

Pathways & Interactions for LYSMD4 Gene

PathCards logo

SuperPathways for LYSMD4 Gene

No Data Available

Interacting Proteins for LYSMD4 Gene

Gene Ontology (GO) - Biological Process for LYSMD4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LYSMD4 Gene

Drugs & Compounds for LYSMD4 Gene

No Compound Related Data Available

Transcripts for LYSMD4 Gene

mRNA/cDNA for LYSMD4 Gene

7 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
11 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 LYSMD4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYSMD4 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g
SP1: - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: - - - - - - -
SP6: - - - -
SP7: - - - - -
SP8: - -
SP9: - - - - - - -
SP10: - - - - - -

Relevant External Links for LYSMD4 Gene

GeneLoc Exon Structure for
LYSMD4

Expression for LYSMD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LYSMD4 Gene

Protein differential expression in normal tissues from HIPED for LYSMD4 Gene

This gene is overexpressed in Pancreatic juice (53.7) and Peripheral blood mononuclear cells (15.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LYSMD4 Gene



Protein tissue co-expression partners for LYSMD4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LYSMD4

SOURCE GeneReport for Unigene cluster for LYSMD4 Gene:

Hs.562568

Evidence on tissue expression from TISSUES for LYSMD4 Gene

  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with LYSMD4: 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 LYSMD4 Gene

Orthologs for LYSMD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for LYSMD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LYSMD4 31
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LYSMD4 30 31
  • 84.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LYSMD4 30
  • 83.11 (n)
MGC155141 31
  • 69 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lysmd4 30
  • 77.74 (n)
Mouse
(Mus musculus)
Mammalia Lysmd4 30 17 31
  • 76.94 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LYSMD4 31
  • 46 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LYSMD4 31
  • 41 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LYSMD4 30 31
  • 63.55 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LYSMD4 31
  • 31 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lysmd4 30
  • 56.49 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13092 30
Zebrafish
(Danio rerio)
Actinopterygii lysmd4 30 31
  • 55.65 (n)
OneToOne
zgc77861 30
Worm
(Caenorhabditis elegans)
Secernentea lmd-1 31
  • 19 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.343 31
  • 21 (a)
OneToMany
Species where no ortholog for LYSMD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 Vase (Ciona intestinalis)
  • 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 LYSMD4 Gene

ENSEMBL:
Gene Tree for LYSMD4 (if available)
TreeFam:
Gene Tree for LYSMD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYSMD4: view image

Paralogs for LYSMD4 Gene

Paralogs for LYSMD4 Gene

(1) SIMAP similar genes for LYSMD4 Gene using alignment to 3 proteins:

  • LYSM4_HUMAN
  • B3KWE4_HUMAN
  • C9J1B9_HUMAN

Pseudogenes.org Pseudogenes for LYSMD4 Gene

genes like me logo Genes that share paralogs with LYSMD4: view

Variants for LYSMD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LYSMD4 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs2061007 - p.Ala180Gly
rs8041078 - p.Ala161Val
rs8041089 - p.Ala157Val

Additional dbSNP identifiers (rs#s) for LYSMD4 Gene

Structural Variations from Database of Genomic Variants (DGV) for LYSMD4 Gene

Variant ID Type Subtype PubMed ID
dgv4769n54 CNV gain 21841781
esv3637430 CNV gain 21293372
nsv1045838 CNV gain 25217958
nsv428313 CNV gain 18775914

Variation tolerance for LYSMD4 Gene

Residual Variation Intolerance Score: 92.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.37; 95.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYSMD4 Gene

Human Gene Mutation Database (HGMD)
LYSMD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYSMD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYSMD4 Gene

Disorders for LYSMD4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LYSMD4 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LYSMD4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LYSMD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LYSMD4 Gene

Publications for LYSMD4 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. 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
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  5. Genetics of coronary artery calcification among African Americans, a meta-analysis. (PMID: 23870195) Wojczynski MK … Reilly MP (BMC medical genetics 2013) 3

Products for LYSMD4 Gene

Sources for LYSMD4 Gene