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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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