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    syf-3 TPR_REGION domain-containing protein [ Caenorhabditis elegans ]

    Gene ID: 178979, updated on 9-Dec-2024

    Summary

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    Official Symbol
    syf-3
    Official Full Name
    TPR_REGION domain-containing protein
    Primary source
    WormBase:WBGene00019762
    Locus tag
    CELE_M03F8.3
    See related
    AllianceGenome:WB:WBGene00019762
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to be involved in spliceosomal complex assembly. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Is expressed in several structures, including intestine; nervous system; non-striated muscle; pharyngeal-intestinal valve; and reproductive system. Human ortholog(s) of this gene implicated in basal cell carcinoma. Orthologous to human CRNKL1 (crooked neck pre-mRNA splicing factor 1). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See syf-3 in Genome Data Viewer
    Location:
    chromosome: V
    Exon count:
    5
    Sequence:
    Chromosome: V; NC_003283.11 (5940022..5943366)

    Chromosome V - NC_003283.11Genomic Context describing neighboring genes Neighboring gene Beta-1,4-galactosyltransferase galt-1 Neighboring gene Glycosyltransferase family 92 protein Neighboring gene G-protein coupled receptors family 1 profile domain-containing protein Neighboring gene Adenosine 3'-phospho 5'-phosphosulfate transporter 1 Neighboring gene ncRNA Neighboring gene Uncharacterized protein Neighboring gene Neur_chan_LBD domain-containing protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003283.11

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Proteomic analysis reveals CACN-1 is a component of the spliceosome in Caenorhabditis elegans. Doherty MF, et al. G3 (Bethesda), 2014 Jun 19. PMID 24948787, Free PMC Article
    2. A genomewide RNAi screen for genes that affect the stability, distribution and function of P granules in Caenorhabditis elegans. Updike DL, et al. Genetics, 2009 Dec. PMID 19805813, Free PMC Article
    3. RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans. LeGendre JB, et al. J Biol Chem, 2013 Jan 25. PMID 23195953, Free PMC Article
    4. Germline Maintenance Through the Multifaceted Activities of GLH/Vasa in Caenorhabditis elegans P Granules. Marnik EA, et al. Genetics, 2019 Nov. PMID 31506335, Free PMC Article
    5. Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules. Cipriani PG, et al. Elife, 2021 Jul 5. PMID 34223818, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of Prp19 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    TPR_REGION domain-containing protein
    NP_001122979.1
    • Confirmed by transcript evidence
    NP_504547.1
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003283.11 Reference assembly

      Range
      5940022..5943366
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001129507.5 → NP_001122979.1  TPR_REGION domain-containing protein [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001122979.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A9D4S6
      Conserved Domains (3) summary
      pfam02184
      Location:201 → 233
      HAT; HAT (Half-A-TPR) repeat
      TIGR02917
      Location:98 → 554
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:89 → 114
      TPR; TPR repeat [structural motif]

    2. NM_072146.6 → NP_504547.1  TPR_REGION domain-containing protein [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_504547.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      O16376
      Conserved Domains (4) summary
      pfam02184
      Location:201 → 233
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:100 → 132
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:89 → 114
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:89 → 216
      Suf; Suppressor of forked protein (Suf)
    Nucleotide Protein
    Heading Accession and Version

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