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Aliases for LYSMD2 Gene

Aliases for LYSMD2 Gene

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

External Ids for LYSMD2 Gene

Previous GeneCards Identifiers for LYSMD2 Gene

  • GC15M049803
  • GC15M052015
  • GC15M028845
  • GC15M052412
  • GC15M052683
  • GC15M054182
  • GC15M054932
  • GC15M055373
  • GC15M055820
  • GC15M056257
  • GC15M056704

Summaries for LYSMD2 Gene

GeneCards Summary for LYSMD2 Gene

LYSMD2 (LysM Domain Containing 2) is a Protein Coding gene. An important paralog of this gene is LYSMD1.

Additional gene information for LYSMD2 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 LYSMD2 Gene

Genomics for LYSMD2 Gene

GeneHancer (GH) Regulatory Elements for LYSMD2 Gene

Promoters and enhancers for LYSMD2 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
GH15J051728 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 687.5 +17.7 17709 9.9 PKNOX1 SIN3A IRF4 YY1 ZNF766 ZNF207 ZNF143 JUNB REST ZNF592 LYSMD2 DMXL2 SCG3 TMOD3 MAPK6 TMOD2 ENSG00000259296
GH15J051751 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 684.2 -0.1 -121 1.4 HDAC1 PKNOX1 RB1 SIN3A ETS1 ZNF335 ZNF766 GLIS2 EGR1 SCRT2 LYSMD2 TMOD2 ENSG00000259377
GH15J051750 Enhancer 0.5 FANTOM5 dbSUPER 701.3 +1.2 1211 0.4 POLR2A LYSMD2 TMOD2 TMOD3 ENSG00000259296
GH15J051828 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29 -78.4 -78448 4 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 TMOD3 MAPK6 LYSMD2 LOC100422556 DMXL2 GNB5 ENSG00000274954
GH15J051841 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 38.1 -93.1 -93053 6.9 PKNOX1 SMAD1 ATF1 SIN3A FEZF1 BRCA1 ZNF766 ATF7 FOS RUNX3 LYSMD2 TMOD2 TMOD3 DMXL2 MAPK6 ENSG00000259178 MYO5C ENSG00000277677 ENSG00000274954
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LYSMD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LYSMD2 gene promoter:
  • AREB6
  • ISGF-3
  • Roaz
  • NF-kappaB2
  • NF-kappaB
  • NF-kappaB1
  • Lmo2
  • Cart-1
  • HNF-1A

Genomic Locations for LYSMD2 Gene

Genomic Locations for LYSMD2 Gene
chr15:51,723,011-51,751,585
(GRCh38/hg38)
Size:
28,575 bases
Orientation:
Minus strand
chr15:52,015,208-52,043,782
(GRCh37/hg19)
Size:
28,575 bases
Orientation:
Minus strand

Genomic View for LYSMD2 Gene

Genes around LYSMD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LYSMD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LYSMD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LYSMD2 Gene

Proteins for LYSMD2 Gene

  • Protein details for LYSMD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IV50-LYSM2_HUMAN
    Recommended name:
    LysM and putative peptidoglycan-binding domain-containing protein 2
    Protein Accession:
    Q8IV50
    Secondary Accessions:
    • Q5CZ88
    • Q8WTV3

    Protein attributes for LYSMD2 Gene

    Size:
    215 amino acids
    Molecular mass:
    23463 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LYSMD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LYSMD2 Gene

Post-translational modifications for LYSMD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LYSMD2 Gene

No data available for DME Specific Peptides for LYSMD2 Gene

Domains & Families for LYSMD2 Gene

Gene Families for LYSMD2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LYSMD2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LYSMD2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LYSMD2: view

No data available for UniProtKB/Swiss-Prot for LYSMD2 Gene

Function for LYSMD2 Gene

Phenotypes From GWAS Catalog for LYSMD2 Gene

genes like me logo Genes that share phenotypes with LYSMD2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYSMD2

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LYSMD2 Gene

Localization for LYSMD2 Gene

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 LYSMD2 gene
Compartment Confidence
mitochondrion 2
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nuclear bodies (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LYSMD2 Gene

Pathways & Interactions for LYSMD2 Gene

SuperPathways for LYSMD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LYSMD2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LYSMD2 Gene

Drugs & Compounds for LYSMD2 Gene

No Compound Related Data Available

Transcripts for LYSMD2 Gene

mRNA/cDNA for LYSMD2 Gene

Unigene Clusters for LYSMD2 Gene

LysM, putative peptidoglycan-binding, domain containing 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LYSMD2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LYSMD2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c · 5d
SP1: -
SP2:
SP3: - -
SP4: - - -

Relevant External Links for LYSMD2 Gene

GeneLoc Exon Structure for
LYSMD2
ECgene alternative splicing isoforms for
LYSMD2

Expression for LYSMD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LYSMD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LYSMD2 Gene

This gene is overexpressed in Tlymphocyte (13.9), Peripheral blood mononuclear cells (12.7), Lymph node (9.2), and Monocytes (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LYSMD2 Gene



Protein tissue co-expression partners for LYSMD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LYSMD2 Gene:

LYSMD2

SOURCE GeneReport for Unigene cluster for LYSMD2 Gene:

Hs.603629
genes like me logo Genes that share expression patterns with LYSMD2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LYSMD2 Gene

Orthologs for LYSMD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LYSMD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LYSMD2 34 33
  • 99.69 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LYSMD2 34
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LYSMD2 34 33
  • 90.34 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lysmd2 16 34 33
  • 87.29 (n)
rat
(Rattus norvegicus)
Mammalia Lysmd2 33
  • 86.56 (n)
oppossum
(Monodelphis domestica)
Mammalia LYSMD2 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves LYSMD2 34 33
  • 76.16 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LYSMD2 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lysmd2 33
  • 68.83 (n)
Str.2664 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8367 33
zebrafish
(Danio rerio)
Actinopterygii lysmd2 34 33
  • 63.62 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG12207 34
  • 14 (a)
OneToMany
Species where no ortholog for LYSMD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 LYSMD2 Gene

ENSEMBL:
Gene Tree for LYSMD2 (if available)
TreeFam:
Gene Tree for LYSMD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LYSMD2: view image

Paralogs for LYSMD2 Gene

Paralogs for LYSMD2 Gene

(1) SIMAP similar genes for LYSMD2 Gene using alignment to 2 proteins:

  • LYSM2_HUMAN
  • H0YK98_HUMAN
genes like me logo Genes that share paralogs with LYSMD2: view

Variants for LYSMD2 Gene

Sequence variations from dbSNP and Humsavar for LYSMD2 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000060921 -- 51,749,206(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000101765 -- 51,752,420(-) T/A upstream_transcript_variant
rs1000233169 -- 51,734,327(-) G/T intron_variant
rs1000293593 -- 51,728,334(-) A/G intron_variant
rs1000345366 -- 51,728,541(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LYSMD2 Gene

Variant ID Type Subtype PubMed ID
nsv569409 CNV loss 21841781
nsv471243 CNV gain 18288195
nsv1144735 CNV deletion 24896259
esv3581701 CNV loss 25503493

Variation tolerance for LYSMD2 Gene

Residual Variation Intolerance Score: 81.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.51; 55.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LYSMD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LYSMD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LYSMD2 Gene

Disorders for LYSMD2 Gene

Additional Disease Information for LYSMD2

No disorders were found for LYSMD2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LYSMD2 Gene

Publications for LYSMD2 Gene

  1. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 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. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4 58

Products for LYSMD2 Gene

Sources for LYSMD2 Gene

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