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    LYSMD3 LysM domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 116068, updated on 9-Dec-2024

    Summary

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    Official Symbol
    LYSMD3provided by HGNC
    Official Full Name
    LysM domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:26969
    See related
    Ensembl:ENSG00000176018 AllianceGenome:HGNC:26969
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables peptidoglycan binding activity. Involved in Golgi organization. Located in Golgi membrane and plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.6), adrenal (RPKM 8.4) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See LYSMD3 in Genome Data Viewer
    Location:
    5q14.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (90515626..90529584, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (91002230..91016199, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (89811443..89825401, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16167 Neighboring gene uncharacterized LOC731157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22779 Neighboring gene metallo-beta-lactamase domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:89820083-89820584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:89824672-89825172 Neighboring gene RNA polymerase III subunit G Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:89838485-89839226 Neighboring gene NANOG hESC enhancer GRCh37_chr5:89850082-89850882 Neighboring gene NANOG hESC enhancer GRCh37_chr5:89853234-89853735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16170 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:89900954-89901152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22781 Neighboring gene adhesion G protein-coupled receptor V1 Neighboring gene NANOG hESC enhancer GRCh37_chr5:89940736-89941239 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:89963673-89964204 Neighboring gene NANOG hESC enhancer GRCh37_chr5:89968220-89968777 Neighboring gene uncharacterized LOC105379077 Neighboring gene NANOG hESC enhancer GRCh37_chr5:90033573-90034074 Neighboring gene MPRA-validated peak5350 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90190300 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90212892 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:90225253-90225805 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90264394 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90266068 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90269376 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90272756 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90276298 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90277675 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:90277863 Neighboring gene Sharpr-MPRA regulatory region 3426 Neighboring gene LYSET pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. LYSMD3: A mammalian pattern recognition receptor for chitin. He X, et al. Cell Rep, 2021 Jul 20. PMID 34289364, Free PMC Article
    2. LysMD3 is a type II membrane protein without an in vivo role in the response to a range of pathogens. Yokoyama CC, et al. J Biol Chem, 2018 Apr 20. PMID 29496999, Free PMC Article
    3. Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response. Serebrenik YV, et al. Mol Biol Cell, 2018 Jun 1. PMID 29851555, Free PMC Article
    4. Peptidoglycan recognition in Drosophila is mediated by LysMD3/4. Snee M, et al. J Biol Chem, 2023 Jun. PMID 37116706, Free PMC Article
    5. Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2. Planchais C, et al. Protein Sci, 2022 Nov. PMID 36305765, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LYSMD3: A mammalian pattern recognition receptor for chitin.
      Title: LYSMD3: A mammalian pattern recognition receptor for chitin.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • FLJ13542, DKFZp686F0735

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables peptidoglycan binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysM and putative peptidoglycan-binding domain-containing protein 3
    Names
    LysM, putative peptidoglycan-binding, domain containing 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001286812.1 → NP_001273741.1  lysM and putative peptidoglycan-binding domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001273741.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC027323, BC058027, BP873090
      Consensus CDS
      CCDS68911.1
      UniProtKB/Swiss-Prot
      Q7Z3D4
      Related
      ENSP00000427683.1, ENST00000509384.5

    2. NM_198273.2 → NP_938014.1  lysM and putative peptidoglycan-binding domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_938014.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL832721, BC136741, CR933624, DN994993
      Consensus CDS
      CCDS43338.1
      UniProtKB/Swiss-Prot
      Q5H9U0, Q6PEK0, Q7Z3D4, Q9NTE9
      UniProtKB/TrEMBL
      A8K613
      Related
      ENSP00000314518.6, ENST00000315948.11
      Conserved Domains (1) summary
      cd00118
      Location:69 → 109
      LysM; Lysine Motif is a small domain involved in binding peptidoglycan

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      90515626..90529584 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416694.1 → XP_047272650.1  lysM and putative peptidoglycan-binding domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      G5E9N8
      Related
      ENSP00000405507.2, ENST00000453259.2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      91002230..91016199 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351564.1 → XP_054207539.1  lysM and putative peptidoglycan-binding domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      G5E9N8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3D4.2 GenPept UniProtKB/Swiss-Prot:Q7Z3D4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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