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Q12309 (CLF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pre-mRNA-splicing factor CLF1
Alternative name(s):
Crooked neck-like factor 1
PRP19-associated complex protein 77
Synthetic lethal with CDC40 protein 3
Gene names
Name:CLF1
Synonyms:NTC77, SYF3
Ordered Locus Names:YLR117C
ORF Names:L2952
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length687 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in pre-mRNA splicing and cell cycle progression. Required for the spliceosome assembly by promoting the functional integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a component of the NTC complex (or PRP19-associated complex). The association of the NTC complex to the spliceosome mediates conformational rearrangement or stabilizes the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Required for initiation of the DNA replication by binding the RNA replication origins, probably through its interaction with the origin recognition complex (ORC). Ref.5 Ref.6 Ref.7 Ref.8 Ref.11

Subunit structure

Belongs to the NTC complex (or PRP19-associated complex), composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2, and PRP19. The NTC complex associates with the spliceosome after the release of the U1 and U4 snRNAs and forms the CWC spliceosome subcomplex (or CEF1-associated complex) reminiscent of a late-stage spliceosome composed also of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8, PRP9, PRP11, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNU114, SPP2, RSE1 and YJU2. Interacts with CEF1, ISY1, MUD2, NTC20, PRP22, PRP40, PRP46, SYF1, SYF2, and the ORC2 subunit of the origin recognition complex. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11

Subcellular location

Nucleus Ref.12.

Miscellaneous

Present with 2140 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the crooked-neck family.

Contains 13 HAT repeats.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 687687Pre-mRNA-splicing factor CLF1
PRO_0000205753

Regions

Repeat45 – 7733HAT 1
Repeat79 – 11133HAT 2
Repeat113 – 14533HAT 3
Repeat147 – 17832HAT 4
Repeat180 – 21132HAT 5
Repeat213 – 24735HAT 6
Repeat251 – 28333HAT 7
Repeat300 – 33233HAT 8
Repeat337 – 36933HAT 9
Repeat383 – 41634HAT 10
Repeat451 – 48333HAT 11
Repeat525 – 55733HAT 12
Repeat629 – 66133HAT 13

Sequences

Sequence LengthMass (Da)Tools
Q12309 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: AE7D5EC5B3979E00

FASTA68782,445
        10         20         30         40         50         60 
MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK RTEYEGYLKR 

        70         80         90        100        110        120 
NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP LWIRYIDAEL KVKCINHARN 

       130        140        150        160        170        180 
LMNRAISTLP RVDKLWYKYL IVEESLNNVE IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK 

       190        200        210        220        230        240 
NWNGVREIYS KYVMAHPQMQ TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD 

       250        260        270        280        290        300 
MEVAKLVNSF AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET 

       310        320        330        340        350        360 
ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR PKELSKNVQW 

       370        380        390        400        410        420 
KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH FTFSKIWLMY AKFLIRHDDV 

       430        440        450        460        470        480 
PKARKILGKA IGLCPKAKTF KGYIELEVKL KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL 

       490        500        510        520        530        540 
EENLGDWDRV RGIYTIALDE NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL 

       550        560        570        580        590        600 
NQYSPQSWIE FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV 

       610        620        630        640        650        660 
FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG VEEEFVDYIF 

       670        680 
PDDIDDDKPK PSKFLELAKK WKQEQAL 

« Hide

References

« Hide 'large scale' references
[1]"Sequence analysis of a 37.6 kbp cosmid clone from the right arm of Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6, tRNA-Arg3 and 23 new open reading frames, among which several homologies to proteins involved in cell division control and to mammalian growth factors and other animal proteins are found."
Verhasselt P., Volckaert G.
Yeast 13:241-250(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 90840 / EAY235 / FY23.
[2]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. expand/collapse author list , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"Functional and physical interactions between components of the Prp19p-associated complex."
Chen C.-H., Yu W.-C., Tsao T.Y., Wang L.-Y., Chen H.-R., Lin J.-Y., Tsai W.-Y., Cheng S.-C.
Nucleic Acids Res. 30:1029-1037(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 15-25, IDENTIFICATION IN THE PRP19-ASSOCIATED COMPLEX.
[5]"Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition."
Chung S., McLean M.R., Rymond B.C.
RNA 5:1042-1054(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH MUD2 AND PRP40.
[6]"Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae."
Ben-Yehuda S., Dix I., Russell C.S., McGarvey M., Beggs J.D., Kupiec M.
Genetics 156:1503-1517(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CEF1; ISY1; NTC20; PRP22 AND SYF2.
[7]"Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae."
Russell C.S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J.D.
RNA 6:1565-1572(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, IDENTIFICATION IN THE SPLICEOSOME.
[8]"Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA replication in Saccharomyces cerevisiae."
Zhu W., Rainville I.R., Ding M., Bolus M., Heintz N.H., Pederson D.S.
Genetics 160:1319-1333(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ORC2.
[9]"Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs."
Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.
Mol. Cell. Biol. 22:2011-2024(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE CWC COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[10]"Characterization of interactions among the Cef1p-Prp19p-associated splicing complex."
Ohi M.D., Gould K.L.
RNA 8:798-815(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ISY1; NTC20; PRP46 AND SYF1.
[11]"The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts."
Wang Q., Hobbs K., Lynn B., Rymond B.C.
J. Biol. Chem. 278:7875-7883(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, IDENTIFICATION IN THE SPLICEOSOME.
[12]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[13]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X89514 Genomic DNA. Translation: CAA61696.1.
U53877 Genomic DNA. Translation: AAB82364.1.
Z73289 Genomic DNA. Translation: CAA97685.1.
BK006945 Genomic DNA. Translation: DAA09431.1.
PIRS64954.
RefSeqNP_013218.1. NM_001182004.1.

3D structure databases

ProteinModelPortalQ12309.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31389. 78 interactions.
DIPDIP-1685N.
IntActQ12309. 35 interactions.
MINTMINT-385873.
STRING4932.YLR117C.

Proteomic databases

PaxDbQ12309.
PRIDEQ12309.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR117C; YLR117C; YLR117C.
GeneID850808.
KEGGsce:YLR117C.

Organism-specific databases

CYGDYLR117c.
SGDS000004107. CLF1.

Phylogenomic databases

eggNOGNOG327505.
GeneTreeENSGT00550000074931.
HOGENOMHOG000207972.
KOK12869.
OMAEGSLAKC.
OrthoDBEOG7TF7JJ.

Enzyme and pathway databases

BioCycYEAST:G3O-32262-MONOMER.

Gene expression databases

GenevestigatorQ12309.

Family and domain databases

Gene3D1.25.40.10. 3 hits.
InterProIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical.
[Graphical view]
PfamPF02184. HAT. 1 hit.
[Graphical view]
SMARTSM00386. HAT. 12 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio967040.
PROQ12309.

Entry information

Entry nameCLF1_YEAST
AccessionPrimary (citable) accession number: Q12309
Secondary accession number(s): D6VYB5
Entry history
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XII

Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families