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    smpd1 sphingomyelin phosphodiesterase 1 [ Danio rerio (zebrafish) ]

    Gene ID: 556700, updated on 17-Aug-2024

    Summary

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    Official Symbol
    smpd1provided by ZNC
    Official Full Name
    sphingomyelin phosphodiesterase 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-110411-222
    See related
    Ensembl:ENSDARG00000076121 AllianceGenome:ZFIN:ZDB-GENE-110411-222
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    si:ch211-287a12.10
    Summary
    Predicted to enable acid sphingomyelin phosphodiesterase activity. Predicted to be involved in ceramide biosynthetic process and sphingomyelin catabolic process. Predicted to be located in extracellular region and membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space and lysosome. Human ortholog(s) of this gene implicated in Niemann-Pick disease; Niemann-Pick disease type A; and Niemann-Pick disease type B. Orthologous to human SMPD1 (sphingomyelin phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    chromosome: 10
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (24710470..24724366, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (24741018..24754914, complement)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene fibrinogen like 1B Neighboring gene transmembrane phosphatase with tensin homology Neighboring gene integrin-linked kinase Neighboring gene translocase of inner mitochondrial membrane 10 homolog B (yeast)

    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 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. Reverse genetic screen reveals that Il34 facilitates yolk sac macrophage distribution and seeding of the brain. Kuil LE, et al. Dis Model Mech, 2019 Mar 8. PMID 30765415, Free PMC Article
    2. Molecular evolution of melatonin receptor genes (mtnr) in vertebrates and its shedding light on mtnr1c. Li Y, et al. Gene, 2021 Feb 15. PMID 33164759
    3. The spatial-temporal expression and functional divergence of bach homologs in zebrafish Danio rerio. Luo Q, et al. J Fish Biol, 2016 Apr. PMID 26992035
    4. 3-ketodihydrosphingosine reductase mutation induces steatosis and hepatic injury in zebrafish. Park KH, et al. Sci Rep, 2019 Feb 4. PMID 30718751, 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 (8) 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 acid sphingomyelin phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity, acting on glycosyl bonds IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sphingomyelin phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingomyelin catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sphingomyelin catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sphingomyelin phosphodiesterase
    Names
    sphingomyelin phosphodiesterase 1, acid lysosomal
    NP_001313465.1

    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_001326536.1 → NP_001313465.1  sphingomyelin phosphodiesterase precursor

      Status: VALIDATED

      Source sequence(s)
      AL928852
      UniProtKB/TrEMBL
      A0A8M1P933
      Related
      ENSDARP00000124101.1, ENSDART00000148582.2
      Conserved Domains (3) summary
      smart00741
      Location:54 → 127
      SapB; Saposin (B) Domains
      cd00842
      Location:168 → 464
      MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
      pfam00149
      Location:221 → 429
      Metallophos; Calcineurin-like phosphoesterase

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007121.7 Reference GRCz11 Primary Assembly

      Range
      24710470..24724366 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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