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

    Gene ID: 256586, updated on 19-Sep-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (51723011..51751451, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49530506..49558957, complement)
    RS_2024_09 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 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    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_2024_08

    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

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

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