CLF1/YLR117C Summary Help

Standard Name CLF1 1
Systematic Name YLR117C
Alias SYF3 2 , NTC77 3 , 4
Feature Type ORF, Verified
Description 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 (1, 2, 5, 6, 7, 8 and see Summary Paragraph)
Name Description Crooked neck-Like Factor 1
Chromosomal Location
ChrXII:384534 to 382471 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All CLF1 GO evidence and references
  View Computational GO annotations for CLF1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 5 genes
Classical genetics
Large-scale survey
reduction of function
214 total interaction(s) for 78 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 133
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 20
  • Co-purification: 1
  • Reconstituted Complex: 3
  • Two-hybrid: 29

Genetic Interactions
  • Dosage Lethality: 1
  • Dosage Rescue: 3
  • Negative Genetic: 1
  • Phenotypic Suppression: 1
  • Positive Genetic: 2
  • Synthetic Growth Defect: 14
  • Synthetic Lethality: 3

Expression Summary
Length (a.a.) 687
Molecular Weight (Da) 82,444
Isoelectric Point (pI) 5.37
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXII:384534 to 382471 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2064 384534..382471 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000004107

About the NineTeen Complex

The nineteen complex (for prp NineTeen associated Complex and also referred to as the NTC) is a non-snRNA containing protein complex involved in splicing of nuclear RNAs via the spliceosome. It was originally isolated as a complex containing Prp19p and at least eight other proteins that complemented the splicing defect of extracts from prp19 mutant cells (9). Subsequent work has identified the genes encoding the additional members of the complex: NTC20 (10), SNT309 (11), ISY1 (10), SYF2 (2, 3), CWC2 (4), PRP46 (4), CLF1 (3, 4), CEF1 (12), and SYF1 (3, 4). The complex appears to be conserved as mammalian cells contain a functional equivalent called the Prp19/CDC5 complex composed of a similar, though not identical, set of proteins (13). The nineteen complex associates with the assembling splicesosome during or after the dissociation of the U4 snRNA, stabilizes the U5 and U6 snRNAs in the activated spliceosomal complex that is catalytic for the first step of splicing, and remains through the second step of splicing (14, 15). Following disassembly of the spliceosome, members of the nineteen complex have been found in association with the excised intron (16, 17).

The nineteen complex also appears to be involved in control of fidelity and efficiency of splicing. Mutations in isy1 suppress the relaxed fidelity of recognition of the conserved branchpoint sequence conferred by mutations in prp16, an ATP-dependent RNA helicase required for the second step of splicing, and an isy1 null mutation decreases accuracy of 3'-splice site usage (18). In addition, cells with mutations in prp45, a protein found in association with NineTeen complex members, are defective in splicing of introns with non-canonical sequences at the branchpoint or the 5' or 3' splice sites (19). Splicing efficiency of various transcripts is differentially affected by mutations in spliceosomal components, such as PRP19, suggesting that the spliceosome can distinguish between individual transcripts and possibly use these differences to specifically regulate gene expression via control of splicing (20). Interestingly, the Drosophila crooked neck protein (the homolog of CLF1) regulates glial cell differentiation by facilitating the splicing of specific target genes (21).

Mutational and genetic analysis of several nineteen complex subunits has suggested involvement in other cellular processes in addition to splicing, such as cell cycle regulation, cytoskeletal structure, DNA repair, and vesicular transport (5, 17, 22, 2, 23, 23 24). In most cases it appears that the primary defect is in splicing and the other defects are the result of failure to remove an intron from the transcript of a gene involved in that process. However Clf1p, and possibly also Prp19p, may have other direct roles in addition to splicing.

About CLF1

CLF1 was originally identified as the ortholog of the Drosophila crooked neck (crn) gene which when mutated causes embryonic lethality and severe developmental defects. It is composed almost entirely of fifteen tandem repeats of a 34 amino acid tetratricopeptide repeat (TPR) motif often involved in protein-protein interactions, with short non-TPR amino and carboxyl terminal sequences. CLF1 is essential and cells depleted of Clf1p arrest in G2/M and are defective in spliceosome assembly, specifically in the step of adding the tri-snRNP to the spliceosomal complex (17, 1). In addition to interacting directly with a number of nineteen complex members (Cef1p, Ntc20p, Ntc30p, Syf1p, and Prp46p), Clf1p interacts with the U1 proteins Prp40p and Mud2p (homolog of mammalian U2AF65; 4).

Clf1p-depleted cells arrest as large-budded cells, but with intact, fully formed spindles suggesting that failure to splice the TUB1 and TUB3 genes encoding tubulin is not the primary defect, unlike what is seen in other nineteen complex mutations that produce cell cycle arrest. This is further confirmed by genetic analysis with a mad2 spindle checkpoint mutant indicating that the arrest does not depend on an intact spindle checkpoint. CLF1 appears to have a direct role in initiation of DNA replication as clf1-1 mutants fail to initiate DNA replication, Clf1p interacts directly with the Orc2p component of the Origin Recognition Complex (ORC), and Clf1p localizes to chromatin and replication origins in an ORC-dependent manner (25). Clf1p also interacts with Csm1p, a protein involved in meiotic chromosome segregation and spore formation (26).

Last updated: 2009-12-11 Contact SGD

References cited on this page View Complete Literature Guide for CLF1
1) Chung S, et al.  (1999) Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition. RNA 5(8):1042-54
2) Ben-Yehuda S, et al.  (2000) Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics 156(4):1503-17
3) Chen CH, et al.  (2002) Functional and physical interactions between components of the Prp19p-associated complex. Nucleic Acids Res 30(4):1029-37
4) Ohi MD and Gould KL  (2002) Characterization of interactions among the Cef1p-Prp19p-associated splicing complex. RNA 8(6):798-815
5) Vincent K, et al.  (2003) Genetic interactions with CLF1 identify additional pre-mRNA splicing factors and a link between activators of yeast vesicular transport and splicing. Genetics 164(3):895-907
6) Wang Q, et al.  (2003) The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts. J Biol Chem 278(10):7875-83
7) Chen CH, et al.  (2006) Functional links between the Prp19-associated complex, U4/U6 biogenesis, and spliceosome recycling. RNA 12(5):765-74
8) Tardiff DF and Rosbash M  (2006) Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly. RNA 12(6):968-79
9) Tarn WY, et al.  (1994) Functional association of essential splicing factor(s) with PRP19 in a protein complex. EMBO J 13(10):2421-31
10) Chen CH, et al.  (2001) Identification and characterization of two novel components of the Prp19p-associated complex, Ntc30p and Ntc20p. J Biol Chem 276(1):488-94
11) Chen HR, et al.  (1998) Snt309p, a component of the Prp19p-associated complex that interacts with Prp19p and associates with the spliceosome simultaneously with or immediately after dissociation of U4 in the same manner as Prp19p. Mol Cell Biol 18(4):2196-204
12) Tsai WY, et al.  (1999) Cef1p is a component of the Prp19p-associated complex and essential for pre-mRNA splicing. J Biol Chem 274(14):9455-62
13) Wahl MC, et al.  (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136(4):701-18
14) Chan SP, et al.  (2003) The Prp19p-associated complex in spliceosome activation. Science 302(5643):279-82
15) Chan SP and Cheng SC  (2005) The Prp19-associated complex is required for specifying interactions of U5 and U6 with pre-mRNA during spliceosome activation. J Biol Chem 280(35):31190-9
16) Dix I, et al.  (1999) The identification and characterization of a novel splicing protein, Isy1p, of Saccharomyces cerevisiae. RNA 5(3):360-8
17) Russell CS, et al.  (2000) Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. RNA 6(11):1565-72
18) Villa T and Guthrie C  (2005) The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev 19(16):1894-904
19) Gahura O, et al.  (2009) Prp45 affects Prp22 partition in spliceosomal complexes and splicing efficiency of non-consensus substrates. J Cell Biochem 106(1):139-51
20) Pleiss JA, et al.  (2007) Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 5(4):e90
21) Edenfeld G, et al.  (2006) The splicing factor crooked neck associates with the RNA-binding protein HOW to control glial cell maturation in Drosophila. Neuron 52(6):969-80
22) Ohi R, et al.  (1998) Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes. Mol Cell Biol 18(7):4097-108
23) Dahan O and Kupiec M  (2002) Mutations in genes of Saccharomyces cerevisiae encoding pre-mRNA splicing factors cause cell cycle arrest through activation of the spindle checkpoint. Nucleic Acids Res 30(20):4361-70
24) Burns CG, et al.  (2002) Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae. Mol Cell Biol 22(3):801-15
25) Zhu W, et al.  (2002) Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA replication in Saccharomyces cerevisiae. Genetics 160(4):1319-33
26) Wysocka M, et al.  (2004) Saccharomyces cerevisiae CSM1 gene encoding a protein influencing chromosome segregation in meiosis I interacts with elements of the DNA replication complex. Exp Cell Res 294(2):592-602