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Q12309

- CLF1_YEAST

UniProt

Q12309 - CLF1_YEAST

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Protein

Pre-mRNA-splicing factor CLF1

Gene

CLF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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).5 Publications

GO - Molecular functioni

  1. chromatin binding Source: SGD
  2. DNA replication origin binding Source: SGD

GO - Biological processi

  1. cis assembly of pre-catalytic spliceosome Source: SGD
  2. DNA replication initiation Source: SGD
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciYEAST:G3O-32262-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:CLF1
Synonyms:NTC77, SYF3
Ordered Locus Names:YLR117C
ORF Names:L2952
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XII

Organism-specific databases

CYGDiYLR117c.
SGDiS000004107. CLF1.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. chromatin Source: SGD
  2. Prp19 complex Source: SGD
  3. U2-type catalytic step 1 spliceosome Source: SGD
  4. U2-type catalytic step 2 spliceosome Source: SGD
  5. U2-type post-mRNA release spliceosomal complex Source: SGD
  6. U2-type prespliceosome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 687687Pre-mRNA-splicing factor CLF1PRO_0000205753Add
BLAST

Proteomic databases

MaxQBiQ12309.
PaxDbiQ12309.
PRIDEiQ12309.

Expressioni

Gene expression databases

GenevestigatoriQ12309.

Interactioni

Subunit structurei

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.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CEF1Q036549EBI-484,EBI-476
ISY1P213745EBI-484,EBI-9382
NTC20P383026EBI-484,EBI-20921
PRP19P325239EBI-484,EBI-493
SNT309Q060915EBI-484,EBI-818
SYF1Q040485EBI-484,EBI-540
SYF2P532772EBI-484,EBI-23308

Protein-protein interaction databases

BioGridi31389. 78 interactions.
DIPiDIP-1685N.
IntActiQ12309. 35 interactions.
MINTiMINT-385873.
STRINGi4932.YLR117C.

Structurei

3D structure databases

ProteinModelPortaliQ12309.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati45 – 7733HAT 1Add
BLAST
Repeati79 – 11133HAT 2Add
BLAST
Repeati113 – 14533HAT 3Add
BLAST
Repeati147 – 17832HAT 4Add
BLAST
Repeati180 – 21132HAT 5Add
BLAST
Repeati213 – 24735HAT 6Add
BLAST
Repeati251 – 28333HAT 7Add
BLAST
Repeati300 – 33233HAT 8Add
BLAST
Repeati337 – 36933HAT 9Add
BLAST
Repeati383 – 41634HAT 10Add
BLAST
Repeati451 – 48333HAT 11Add
BLAST
Repeati525 – 55733HAT 12Add
BLAST
Repeati629 – 66133HAT 13Add
BLAST

Sequence similaritiesi

Belongs to the crooked-neck family.Curated
Contains 13 HAT repeats.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiNOG327505.
GeneTreeiENSGT00550000074931.
HOGENOMiHOG000207972.
InParanoidiQ12309.
KOiK12869.
OMAiEGSLAKC.
OrthoDBiEOG7TF7JJ.

Family and domain databases

Gene3Di1.25.40.10. 3 hits.
InterProiIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
[Graphical view]
PfamiPF02184. HAT. 1 hit.
[Graphical view]
SMARTiSM00386. HAT. 12 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12309-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK
60 70 80 90 100
RTEYEGYLKR NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP
110 120 130 140 150
LWIRYIDAEL KVKCINHARN LMNRAISTLP RVDKLWYKYL IVEESLNNVE
160 170 180 190 200
IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK NWNGVREIYS KYVMAHPQMQ
210 220 230 240 250
TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD MEVAKLVNSF
260 270 280 290 300
AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET
310 320 330 340 350
ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR
360 370 380 390 400
PKELSKNVQW KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH
410 420 430 440 450
FTFSKIWLMY AKFLIRHDDV PKARKILGKA IGLCPKAKTF KGYIELEVKL
460 470 480 490 500
KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL EENLGDWDRV RGIYTIALDE
510 520 530 540 550
NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL NQYSPQSWIE
560 570 580 590 600
FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV
610 620 630 640 650
FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG
660 670 680
VEEEFVDYIF PDDIDDDKPK PSKFLELAKK WKQEQAL
Length:687
Mass (Da):82,445
Last modified:November 1, 1996 - v1
Checksum:iAE7D5EC5B3979E00
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89514 Genomic DNA. Translation: CAA61696.1.
U53877 Genomic DNA. Translation: AAB82364.1.
Z73289 Genomic DNA. Translation: CAA97685.1.
BK006945 Genomic DNA. Translation: DAA09431.1.
PIRiS64954.
RefSeqiNP_013218.1. NM_001182004.1.

Genome annotation databases

EnsemblFungiiYLR117C; YLR117C; YLR117C.
GeneIDi850808.
KEGGisce:YLR117C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89514 Genomic DNA. Translation: CAA61696.1 .
U53877 Genomic DNA. Translation: AAB82364.1 .
Z73289 Genomic DNA. Translation: CAA97685.1 .
BK006945 Genomic DNA. Translation: DAA09431.1 .
PIRi S64954.
RefSeqi NP_013218.1. NM_001182004.1.

3D structure databases

ProteinModelPortali Q12309.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31389. 78 interactions.
DIPi DIP-1685N.
IntActi Q12309. 35 interactions.
MINTi MINT-385873.
STRINGi 4932.YLR117C.

Proteomic databases

MaxQBi Q12309.
PaxDbi Q12309.
PRIDEi Q12309.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLR117C ; YLR117C ; YLR117C .
GeneIDi 850808.
KEGGi sce:YLR117C.

Organism-specific databases

CYGDi YLR117c.
SGDi S000004107. CLF1.

Phylogenomic databases

eggNOGi NOG327505.
GeneTreei ENSGT00550000074931.
HOGENOMi HOG000207972.
InParanoidi Q12309.
KOi K12869.
OMAi EGSLAKC.
OrthoDBi EOG7TF7JJ.

Enzyme and pathway databases

BioCyci YEAST:G3O-32262-MONOMER.

Miscellaneous databases

NextBioi 967040.
PROi Q12309.

Gene expression databases

Genevestigatori Q12309.

Family and domain databases

Gene3Di 1.25.40.10. 3 hits.
InterProi IPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
[Graphical view ]
Pfami PF02184. HAT. 1 hit.
[Graphical view ]
SMARTi SM00386. HAT. 12 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.
    , 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  13. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiCLF1_YEAST
AccessioniPrimary (citable) accession number: Q12309
Secondary accession number(s): D6VYB5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: November 1, 1996
Last modified: November 26, 2014
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2140 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

External Data

Dasty 3