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

Gene ID: 116068, updated on 5-Mar-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
Involved in Golgi organization. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
5q14.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (90515626..90529584, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (91002230..91016199, complement)
105.20220307 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. Peptidoglycan recognition in Drosophila is mediated by LysMD3/4. Snee M, et al. J Biol Chem, 2023 Jun. PMID 37116706, 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. 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
  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 (21) 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)

Genotypes

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_2023_10

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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