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    lysmd3 LysM, putative peptidoglycan-binding, domain containing 3 [ Danio rerio (zebrafish) ]

    Gene ID: 415194, updated on 2-Nov-2024

    Summary

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    Official Symbol
    lysmd3provided by ZNC
    Official Full Name
    LysM, putative peptidoglycan-binding, domain containing 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040625-88
    See related
    Ensembl:ENSDARG00000024693 AllianceGenome:ZFIN:ZDB-GENE-040625-88
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    cb462; sb:cb462; zgc:86877; wu:fb75a04
    Summary
    Predicted to be involved in Golgi organization. Predicted to be located in plasma membrane. Predicted to be active in Golgi apparatus. Is expressed in anterior axial hypoblast; axial mesoderm; axis; central nervous system; and notochord. Orthologous to human LYSMD3 (LysM domain containing 3). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See lysmd3 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (48672553..48680461, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (48021042..48028950, complement)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene metallo-beta-lactamase domain containing 2 Neighboring gene polymerase (RNA) III (DNA directed) polypeptide G Neighboring gene adhesion G protein-coupled receptor V1 Neighboring gene arrestin domain containing 3a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. 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
    2. The embryonic expression patterns of zebrafish genes encoding LysM-domains. Laroche FJ, et al. Gene Expr Patterns, 2013 Oct. PMID 23567754
    3. The evolutionary legacy of size-selective harvesting extends from genes to populations. Uusi-Heikkilä S, et al. Evol Appl, 2015 Jul. PMID 26136825, Free PMC Article
    4. Shutdown corner, a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish. Casey MA, et al. G3 (Bethesda), 2022 Mar 4. PMID 35079792, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Golgi organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    lysM and putative peptidoglycan-binding domain-containing protein 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_001002104.1 → NP_001002104.1  lysM and putative peptidoglycan-binding domain-containing protein 3

      See identical proteins and their annotated locations for NP_001002104.1

      Status: PROVISIONAL

      Source sequence(s)
      BC071508
      UniProtKB/Swiss-Prot
      Q6IQA2
      Related
      ENSDARP00000038848.4, ENSDART00000031194.5
      Conserved Domains (1) summary
      cd00118
      Location:72 → 112
      LysM; Lysine Motif is a small domain involved in binding peptidoglycan

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007116.7 Reference GRCz11 Primary Assembly

      Range
      48672553..48680461 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6IQA2.1 GenPept UniProtKB/Swiss-Prot:Q6IQA2

    Gene LinkOut

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

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