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    CLF1 Clf1p [ Saccharomyces cerevisiae S288C ]

    Gene ID: 850808, updated on 29-Jun-2024

    Summary

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    Gene symbol
    CLF1
    Gene description
    Clf1p
    Primary source
    FungiDB:YLR117C
    Locus tag
    YLR117C
    See related
    SGD:S000004107; AllianceGenome:SGD:S000004107; VEuPathDB:YLR117C
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Saccharomyces cerevisiae S288C (strain: S288C)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
    Also known as
    NTC77; SYF3
    Summary
    Enables DNA replication origin binding activity and chromatin binding activity. Involved in DNA replication initiation and cis assembly of pre-catalytic spliceosome. Located in chromatin. Part of Prp19 complex and U2-type spliceosomal complex. 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, Apr 2022]
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    Genomic context

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    See CLF1 in Genome Data Viewer
    Location:
    chromosome: XII
    Exon count:
    1
    Sequence:
    Chromosome: XII; NC_001144.5 (382471..384534, complement)

    Chromosome XII - NC_001144.5Genomic Context describing neighboring genes Neighboring gene cleavage polyadenylation factor subunit CFT2 Neighboring gene mRNA splicing protein MSL5 Neighboring gene palmitoyl-(protein) hydrolase Neighboring gene ESCRT-I subunit protein SRN2

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001144.5

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains. Gasch A, et al. J Biol Chem, 2006 Jan 6. PMID 16253993
    2. Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA replication in Saccharomyces cerevisiae. Zhu W, et al. Genetics, 2002 Apr. PMID 11973290, Free PMC Article
    3. Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition. Chung S, et al. RNA, 1999 Aug. PMID 10445879, Free PMC Article
    4. A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast. Wang Q, et al. Nucleic Acids Res, 2008 May. PMID 18375978, Free PMC Article
    5. Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. Russell CS, et al. RNA, 2000 Nov. PMID 11105756, Free PMC Article

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. binding site for the N-terminal crooked neck tetratricopeptide repeat of Clf1 found for PRP40 protein
      Title: The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by SGD

    Function Evidence Code Pubs
    enables DNA replication origin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA replication initiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA replication initiation IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cis assembly of pre-catalytic spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cis assembly of pre-catalytic spliceosome IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in mRNA 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 Prp19 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type catalytic step 1 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type post-mRNA release spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type prespliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Clf1p
    NP_013218.1
    • Member of the NineTeen Complex (NTC); this complex contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs; homolog of Drosophila crooked neck protein; interacts with U1 snRNP proteins

    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_001144.5 Reference assembly

      Range
      382471..384534 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001182004.1 → NP_013218.1  TPA: Clf1p [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_013218.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VYB5, Q12309
      UniProtKB/TrEMBL
      A0A6A5PT67, B3LT82, C8ZD87, N1NY82
      Conserved Domains (4) summary
      pfam02184
      Location:186 → 211
      HAT; HAT (Half-A-TPR) repeat
      smart00386
      Location:451 → 483
      HAT; HAT (Half-A-TPR) repeats
      sd00006
      Location:404 → 432
      TPR; TPR repeat [structural motif]
      cl26712
      Location:64 → 157
      U3_assoc_6; U3 small nucleolar RNA-associated protein 6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12309.1

    Gene LinkOut

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