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Aliases for LYSMD1 Gene

Aliases for LYSMD1 Gene

  • LysM Domain Containing 1 2 3 5
  • LysM, Putative Peptidoglycan-Binding, Domain Containing 1 2 3
  • LysM And Putative Peptidoglycan-Binding Domain-Containing Protein 1 3
  • RP11-68I18.5 3
  • SB145 3

External Ids for LYSMD1 Gene

Previous GeneCards Identifiers for LYSMD1 Gene

  • GC01M147946
  • GC01M149398
  • GC01M122510

Summaries for LYSMD1 Gene

GeneCards Summary for LYSMD1 Gene

LYSMD1 (LysM Domain Containing 1) is a Protein Coding gene. An important paralog of this gene is LYSMD2.

Additional gene information for LYSMD1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LYSMD1 Gene

Genomics for LYSMD1 Gene

GeneHancer (GH) Regulatory Elements for LYSMD1 Gene

Promoters and enhancers for LYSMD1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I151164 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 561 -0.1 -101 3.1 CLOCK DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 LYSMD1 SCNM1 PRPF3 SETDB1 PI4KB ARNT UBE2D3P3 ZNF687 PIP5K1A CTSK
GH01I151940 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 67.9 -778.2 -778150 7.6 PKNOX1 CLOCK FOXA2 NEUROD1 SIN3A FEZF1 ZNF2 ZBTB7B ZNF416 FOS POGZ GABPB2 PI4KB MRPL9 PIP5K1A LYSMD1 ENSG00000229021 HRNR THEM4 ZNF687
GH01I151068 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 28.7 +95.5 95462 3.3 CLOCK FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 GABPB2 CDC42SE1 PRPF3 SETDB1 PI4KB PIP5K1A MRPL9 UBE2D3P3 ARNT CTSK
GH01I150626 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 22.4 +536.6 536577 4.9 HDGF PKNOX1 CLOCK SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A DMAP1 ENSA GC01P150630 SETDB1 PIP5K1A HORMAD1 ARNT PRPF3 RPRD2 UBE2D3P3 SF3B4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LYSMD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LYSMD1 gene promoter:

Genomic Locations for LYSMD1 Gene

Genomic Locations for LYSMD1 Gene
9,139 bases
Minus strand

Genomic View for LYSMD1 Gene

Genes around LYSMD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYSMD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYSMD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYSMD1 Gene

Proteins for LYSMD1 Gene

  • Protein details for LYSMD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LysM and putative peptidoglycan-binding domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • B4DQA1
    • Q69YX9

    Protein attributes for LYSMD1 Gene

    227 amino acids
    Molecular mass:
    25003 Da
    Quaternary structure:
    No Data Available
    • Sequence=CAH10716.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LYSMD1 Gene

    Alternative splice isoforms for LYSMD1 Gene


neXtProt entry for LYSMD1 Gene

Post-translational modifications for LYSMD1 Gene

No Post-translational modifications

Other Protein References for LYSMD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LYSMD1 Gene

Domains & Families for LYSMD1 Gene

Gene Families for LYSMD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LYSMD1 Gene

Suggested Antigen Peptide Sequences for LYSMD1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYSMD1: view

No data available for UniProtKB/Swiss-Prot for LYSMD1 Gene

Function for LYSMD1 Gene

Phenotypes From GWAS Catalog for LYSMD1 Gene

Gene Ontology (GO) - Molecular Function for LYSMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LYSMD1: view
genes like me logo Genes that share phenotypes with LYSMD1: view

Animal Model Products

CRISPR Products

miRNA for LYSMD1 Gene

miRTarBase miRNAs that target LYSMD1

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LYSMD1 Gene

Localization for LYSMD1 Gene

Subcellular locations from

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 LYSMD1 gene
Compartment Confidence
nucleus 4
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LYSMD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with LYSMD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LYSMD1 Gene

Pathways & Interactions for LYSMD1 Gene

SuperPathways for LYSMD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LYSMD1 Gene


No data available for Pathways by source and SIGNOR curated interactions for LYSMD1 Gene

Drugs & Compounds for LYSMD1 Gene

No Compound Related Data Available

Transcripts for LYSMD1 Gene

mRNA/cDNA for LYSMD1 Gene

Unigene Clusters for LYSMD1 Gene

LysM, putative peptidoglycan-binding, domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYSMD1 Gene

No ASD Table

Relevant External Links for LYSMD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LYSMD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYSMD1 Gene

Protein differential expression in normal tissues from HIPED for LYSMD1 Gene

This gene is overexpressed in Frontal cortex (29.3), Fetal Brain (27.0), and Retina (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LYSMD1 Gene

Protein tissue co-expression partners for LYSMD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LYSMD1 Gene:


SOURCE GeneReport for Unigene cluster for LYSMD1 Gene:


Evidence on tissue expression from TISSUES for LYSMD1 Gene

  • Muscle(2.3)
genes like me logo Genes that share expression patterns with LYSMD1: view

Primer Products

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 LYSMD1 Gene

Orthologs for LYSMD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LYSMD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LYSMD1 33 34
  • 99.56 (n)
(Bos Taurus)
Mammalia LYSMD1 33 34
  • 90.67 (n)
(Canis familiaris)
Mammalia LYSMD1 33 34
  • 89.72 (n)
(Rattus norvegicus)
Mammalia Lysmd1 33
  • 85.84 (n)
(Mus musculus)
Mammalia Lysmd1 33 16 34
  • 85.4 (n)
Gm9726 34
  • 84 (a)
(Monodelphis domestica)
Mammalia LYSMD1 34
  • 80 (a)
(Anolis carolinensis)
Reptilia LYSMD1 34
  • 53 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lysmd1 33
  • 57.44 (n)
(Danio rerio)
Actinopterygii lysmd1 33 34
  • 54.97 (n)
Dr.14388 33
fruit fly
(Drosophila melanogaster)
Insecta CG12207 34
  • 14 (a)
Species where no ortholog for LYSMD1 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)

Evolution for LYSMD1 Gene

Gene Tree for LYSMD1 (if available)
Gene Tree for LYSMD1 (if available)

Paralogs for LYSMD1 Gene

Paralogs for LYSMD1 Gene

(1) SIMAP similar genes for LYSMD1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LYSMD1: view

Variants for LYSMD1 Gene

Sequence variations from dbSNP and Humsavar for LYSMD1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000400084 -- 151,150,484(-) C/G genic_downstream_transcript_variant, intron_variant
rs1000448949 -- 151,151,677(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000543735 -- 151,151,343(-) C/G/T genic_downstream_transcript_variant, intron_variant
rs1000605489 -- 151,158,487(-) A/T genic_downstream_transcript_variant, intron_variant
rs1000901120 -- 151,164,922(-) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LYSMD1 Gene

Variant ID Type Subtype PubMed ID
dgv2n68 CNV loss 17160897
nsv522840 CNV gain 19592680

Variation tolerance for LYSMD1 Gene

Residual Variation Intolerance Score: 56% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.68; 32.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYSMD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYSMD1 Gene

Disorders for LYSMD1 Gene

Additional Disease Information for LYSMD1

No disorders were found for LYSMD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LYSMD1 Gene

Publications for LYSMD1 Gene

  1. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 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. 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 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58

Products for LYSMD1 Gene

Sources for LYSMD1 Gene

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