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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
    mouse all
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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

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

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