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    snd1 staphylococcal nuclease and tudor domain containing 1 [ Danio rerio (zebrafish) ]

    Gene ID: 324404, updated on 2-Nov-2024

    Summary

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    Official Symbol
    snd1provided by ZNC
    Official Full Name
    staphylococcal nuclease and tudor domain containing 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-3124
    See related
    Ensembl:ENSDARG00000006766 AllianceGenome:ZFIN:ZDB-GENE-030131-3124
    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
    SN4TDR; TDRD11; wu:fc27g10
    Summary
    Predicted to enable RNA binding activity and nuclease activity. Predicted to be involved in mRNA catabolic process. Located in cytoplasm. Orthologous to human SND1 (staphylococcal nuclease and tudor domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See snd1 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (19396945..19694156, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (19407969..19705180, complement)

    Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137491540 Neighboring gene uncharacterized LOC137491541 Neighboring gene leucine rich repeat containing 4.1 Neighboring gene uncharacterized LOC101883798 Neighboring gene paired box 4 Neighboring gene hepatocyte growth factor a

    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. A Tudor staphylococcal nuclease from Penaeus monodon: cDNA cloning and its involvement in RNA interference. Phetrungnapha A, et al. Fish Shellfish Immunol, 2011 Sep. PMID 21745576
    2. Two variants of zebrafish p100 are expressed during embryogenesis and regulated by Nodal signaling. Zhao CT, et al. FEBS Lett, 2003 May 22. PMID 12753931
    3. Structural analysis of cDNAs coding for 4SNc-Tudor domain protein from fish and their expression in yellowtail organs. Abe S, et al. Mar Biotechnol (NY), 2005 Nov-Dec. PMID 16132464
    4. A Tudor protein with multiple SNc domains from pea seedlings: cellular localization, partial characterization, sequence analysis, and phylogenetic relationships. Abe S, et al. J Exp Bot, 2003 Mar. PMID 12598568
    5. Comparative studies on duplicated tdrd7 paralogs in teleosts: Molecular evolution caused neo-functionalization. Wang B, et al. Comp Biochem Physiol Part D Genomics Proteomics, 2019 Jun. PMID 31059868

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Two alternative transcripts of p100 are expressed during embryogenesis and regulated by Nodal signaling.
      Title: Two variants of zebrafish p100 are expressed during embryogenesis and regulated by Nodal signaling.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulatory ncRNA-mediated gene silencing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of RNAi effector complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    staphylococcal nuclease domain-containing protein 1
    Names
    100 kDa coactivator
    4SNc-Tudor domain protein
    p100 co-activator
    staphylococcal nuclease domain containing 1
    NP_001280610.1
    NP_878285.3

    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_001293681.1 → NP_001280610.1  staphylococcal nuclease domain-containing protein 1 isoform p100S

      Status: VALIDATED

      Description
      Transcript Variant: This variant (p100S) lacks multiple 3' exons and extends beyond a splice site used in variant p100L. The resulting protein (isoform p100S) is shorter and has a distinct C-terminus compared to isoform p100L.
      Source sequence(s)
      BX855622, BX897731
      UniProtKB/Swiss-Prot
      Q7ZT42
      Related
      ENSDARP00000091746.4, ENSDART00000100974.5
      Conserved Domains (2) summary
      smart00318
      Location:18 → 167
      SNc; Staphylococcal nuclease homologues
      cd00175
      Location:351 → 499
      SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.

    2. NM_182865.3 → NP_878285.3  staphylococcal nuclease domain-containing protein 1 isoform p100L

      Status: VALIDATED

      Description
      Transcript Variant: This variant (p100L) represents the longer transcript and encodes the longer protein (isoform p100L).
      Source sequence(s)
      BX855622, BX890545, BX897731, CR931778
      UniProtKB/Swiss-Prot
      Q6DEI2, Q7SX79, Q7ZT42, Q7ZZS7, Q8AXL0
      UniProtKB/TrEMBL
      A0A8N7UZV3, Q5RGK8
      Related
      ENSDARP00000040404.6, ENSDART00000040405.8
      Conserved Domains (5) summary
      smart00333
      Location:732 → 787
      TUDOR; Tudor domain
      smart00318
      Location:18 → 167
      SNc; Staphylococcal nuclease homologues
      cd00175
      Location:351 → 499
      SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
      pfam00567
      Location:680 → 802
      TUDOR; Tudor domain
      cl00140
      Location:847 → 898
      SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.

    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_007115.7 Reference GRCz11 Primary Assembly

      Range
      19396945..19694156 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7ZT42.1 GenPept UniProtKB/Swiss-Prot:Q7ZT42

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