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LYSMD1 LysM domain containing 1 [ Homo sapiens (human) ]

Gene ID: 388695, updated on 2-Nov-2024

Summary

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Official Symbol
LYSMD1provided by HGNC
Official Full Name
LysM domain containing 1provided by HGNC
Primary source
HGNC:HGNC:32070
See related
Ensembl:ENSG00000163155 AllianceGenome:HGNC:32070
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
Also known as
SB145
Summary
Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in spleen (RPKM 7.3), lymph node (RPKM 5.9) and 25 other tissues See more
Orthologs
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Genomic context

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See LYSMD1 in Genome Data Viewer
Location:
1q21.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151148496..151165902, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150272196..150289846, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151132224..151138378, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151104130-151104914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1313 Neighboring gene semaphorin 6C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1315 Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene sodium channel modifier 1 Neighboring gene tropomodulin 4 Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710

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 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. A conserved acetylation switch enables pharmacological control of tubby-like protein stability. Kerek EM, et al. J Biol Chem, 2021 Jan-Jun. PMID 33187986, Free PMC Article
  2. The DNA sequence and biological annotation of human chromosome 1. Gregory SG, et al. Nature, 2006 May 18. PMID 16710414
  3. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article
  4. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article
  5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

See all (11) 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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Markers

Homology

Clone Names

  • MGC35223

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
lysM and putative peptidoglycan-binding domain-containing protein 1
Names
LysM, putative peptidoglycan-binding, domain containing 1
RP11-68I18.5

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_001136543.2 → NP_001130015.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region and uses an upstream start codon, compared to variant 1. Isoform b has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK298706, BX647911
    Consensus CDS
    CCDS44218.1
    UniProtKB/Swiss-Prot
    Q96S90
    Related
    ENSP00000404059.2, ENST00000440902.2

  2. NM_212551.5 → NP_997716.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_997716.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AL592424, BX647911, DA176882
    Consensus CDS
    CCDS986.1
    UniProtKB/Swiss-Prot
    B4DQA1, Q69YX9, Q96S90
    UniProtKB/TrEMBL
    B4DQI5
    Related
    ENSP00000357904.5, ENST00000368908.10
    Conserved Domains (1) summary
    cd00118
    Location:42 → 84
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    151148496..151165902 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420112.1 → XP_047276068.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DQA1, Q69YX9, Q96S90

  2. XM_047420105.1 → XP_047276061.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DQA1, Q69YX9, Q96S90

  3. XM_047420115.1 → XP_047276071.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DQA1, Q69YX9, Q96S90

  4. XM_047420118.1 → XP_047276074.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150272196..150289846 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336526.1 → XP_054192501.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DQA1, Q69YX9, Q96S90

  2. XM_054336527.1 → XP_054192502.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X3

  3. XM_054336528.1 → XP_054192503.1  lysM and putative peptidoglycan-binding domain-containing protein 1 isoform X2

RNA

  1. XR_008486045.1 RNA Sequence

  2. XR_008486044.1 RNA Sequence

  3. XR_008486046.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96S90.1 GenPept UniProtKB/Swiss-Prot:Q96S90

Gene LinkOut

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