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LYSMD2 LysM domain containing 2 [ Homo sapiens (human) ]

Gene ID: 256586, updated on 5-Mar-2024

Summary

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Official Symbol
LYSMD2provided by HGNC
Official Full Name
LysM domain containing 2provided by HGNC
Primary source
HGNC:HGNC:28571
See related
Ensembl:ENSG00000140280 AllianceGenome:HGNC:28571
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
Expression
Ubiquitous expression in brain (RPKM 8.4), lymph node (RPKM 8.3) and 25 other tissues See more
Orthologs
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Genomic context

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See LYSMD2 in Genome Data Viewer
Location:
15q21.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (51723011..51751451, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49530506..49558957, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (52015208..52043648, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370816 Neighboring gene CRISPRi-validated cis-regulatory element chr15.1149 Neighboring gene CRISPRi-validated cis-regulatory element chr15.1151 Neighboring gene Sharpr-MPRA regulatory region 12802 Neighboring gene secretogranin III Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9406 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6440 Neighboring gene tropomodulin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:52079467-52079967 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39634 Neighboring gene MPRA-validated peak2338 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:52121755-52121909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6441 Neighboring gene tropomodulin 3 Neighboring gene UTP6, small subunit (SSU) processome component, homolog (yeast) pseudogene

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. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Rush J, et al. Nat Biotechnol, 2005 Jan. PMID 15592455
  2. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. Malinová A, et al. J Cell Biol, 2017 Jun 5. PMID 28515276, Free PMC Article
  3. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Hein MY, et al. Cell, 2015 Oct 22. PMID 26496610
  4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • MGC35274, DKFZp686I2243

General protein information

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Preferred Names
lysM and putative peptidoglycan-binding domain-containing protein 2
Names
LysM, putative peptidoglycan-binding, domain containing 2

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_001143917.2 → NP_001137389.1  lysM and putative peptidoglycan-binding domain-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001137389.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region because it has a different first exon, compared to variant 1. These differences result in translation initiation from a downstream in-frame start codon and a protein (isoform 2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC026770, BC022075, BC033515, BQ446302
    Consensus CDS
    CCDS45259.1
    UniProtKB/Swiss-Prot
    Q8IV50
    Related
    ENSP00000410424.2, ENST00000454181.6
    Conserved Domains (1) summary
    pfam10168
    Location:10 → 115
    Nup88; Nuclear pore component

  2. NM_001363969.2 → NP_001350898.1  lysM and putative peptidoglycan-binding domain-containing protein 2 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC026770
    Consensus CDS
    CCDS45259.1
    Related
    ENSP00000453933.1, ENST00000560491.2
    Conserved Domains (1) summary
    pfam10168
    Location:10 → 115
    Nup88; Nuclear pore component

  3. NM_153374.3 → NP_699205.1  lysM and putative peptidoglycan-binding domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_699205.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC026770, BC033515, BQ446302
    Consensus CDS
    CCDS10143.1
    UniProtKB/Swiss-Prot
    Q5CZ88, Q8IV50, Q8WTV3
    Related
    ENSP00000267838.3, ENST00000267838.7
    Conserved Domains (3) summary
    PRK10783
    Location:35 → 131
    mltD; membrane-bound lytic murein transglycosylase D; Provisional
    cd00118
    Location:71 → 115
    LysM; Lysin Motif is a small domain involved in binding peptidoglycan
    pfam10168
    Location:101 → 206
    Nup88; Nuclear pore component

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    51723011..51751451 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432340.1 → XP_047288296.1  lysM and putative peptidoglycan-binding domain-containing protein 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    49530506..49558957 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377669.1 → XP_054233644.1  lysM and putative peptidoglycan-binding domain-containing protein 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IV50.1 GenPept UniProtKB/Swiss-Prot:Q8IV50

Gene LinkOut

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