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Protein

RNA end formation protein 2

Gene

REF2

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

Functioni

RNA-binding component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Negative regulator of poly(A) synthesis. Component of the APT complex, which may be involved in polyadenylation-independent transcript 3'-end formation. REF2 is required for 3'-end formation of snoRNAs.4 Publications

GO - Molecular functioni

  • chromatin binding Source: SGD
  • RNA binding Source: SGD

GO - Biological processi

  • mRNA 3'-end processing Source: SGD
  • negative regulation of mRNA polyadenylation Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • termination of RNA polymerase II transcription, poly(A)-coupled Source: SGD
Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29782-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA end formation protein 2
Gene namesi
Name:REF2
Ordered Locus Names:YDR195W
ORF Names:YD9346.06
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome IV

Organism-specific databases

CYGDiYDR195w.
EuPathDBiFungiDB:YDR195W.
SGDiS000002603. REF2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mRNA cleavage and polyadenylation specificity factor complex Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 533533RNA end formation protein 2PRO_0000097239Add
BLAST

Proteomic databases

MaxQBiP42073.
PaxDbiP42073.

Expressioni

Gene expression databases

GenevestigatoriP42073.

Interactioni

Subunit structurei

Interacts with FIR1. Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Component of the APT complex, which is a subcomplex of CPF, and is composed of PTI1, SYC1, SSU72, GLC7, REF2, PTA1 and SWD2.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GLC7P325987EBI-14915,EBI-13715

Protein-protein interaction databases

BioGridi32247. 61 interactions.
DIPiDIP-871N.
IntActiP42073. 31 interactions.
MINTiMINT-394246.
STRINGi4932.YDR195W.

Structurei

3D structure databases

ProteinModelPortaliP42073.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi321 – 33111Ser/Thr-richAdd
BLAST

Phylogenomic databases

eggNOGiNOG46408.
InParanoidiP42073.
KOiK15543.
OMAiINIAHAM.
OrthoDBiEOG754HZP.

Sequencei

Sequence statusi: Complete.

P42073-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAPVPQLVN ISHALQASTI QQIRLDMVDF NKDCKLSSIQ LARIDKYIDS
60 70 80 90 100
LQAALNQFTK DNLHIERKEK NVTEADIQLY SGLKSMYLDY LNQLIKLKHE
110 120 130 140 150
KQHHSTPPIA NDVSLDFFVN QLPKFSPEER KNYIDNLILN KNSHNRLSKM
160 170 180 190 200
DGLVDAVINL CVLDTSVAEN VRSYMKLLDT LGFQKGSNST GTKANLKKKL
210 220 230 240 250
ASSKAKIKDS EKEKEKEKDK SKVKMKTKLK PSPLLNNDDK NSSPSPTAST
260 270 280 290 300
SSMKKLKSGL FNKNEAKSTE SLPTSSKKKL SFSKYLNKDD ADMTKLGTKR
310 320 330 340 350
SIDVDFKVNP EASTVASNII SSSTSGSSTT TVATPASSEE PLKKKTKISV
360 370 380 390 400
QDSNVQSILR NGKPKKARIS SIKFLDDSQL IKVYGDDLPN QGLQVSPTQL
410 420 430 440 450
KKILKPFKEG EPKEIILFED MSIKLKPLDL MFLKNTNSDD YMDISETKGG
460 470 480 490 500
PIHCETRTPL IYRKNFNHFN PDLNKRPPRE PIEFDLNGNT NSTPTIAKAF
510 520 530
GKNSLLLRKD RGGLPYKHVP IVKRNKYPPR PVH
Length:533
Mass (Da):59,819
Last modified:February 1, 1996 - v2
Checksum:i36B0982B005697C4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20261 Genomic DNA. Translation: AAA85866.1.
Z48784 Genomic DNA. Translation: CAA88708.1.
BK006938 Genomic DNA. Translation: DAA12038.1.
PIRiS52702.
RefSeqiNP_010481.3. NM_001180503.3.

Genome annotation databases

EnsemblFungiiYDR195W; YDR195W; YDR195W.
GeneIDi851776.
KEGGisce:YDR195W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20261 Genomic DNA. Translation: AAA85866.1.
Z48784 Genomic DNA. Translation: CAA88708.1.
BK006938 Genomic DNA. Translation: DAA12038.1.
PIRiS52702.
RefSeqiNP_010481.3. NM_001180503.3.

3D structure databases

ProteinModelPortaliP42073.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32247. 61 interactions.
DIPiDIP-871N.
IntActiP42073. 31 interactions.
MINTiMINT-394246.
STRINGi4932.YDR195W.

Proteomic databases

MaxQBiP42073.
PaxDbiP42073.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR195W; YDR195W; YDR195W.
GeneIDi851776.
KEGGisce:YDR195W.

Organism-specific databases

CYGDiYDR195w.
EuPathDBiFungiDB:YDR195W.
SGDiS000002603. REF2.

Phylogenomic databases

eggNOGiNOG46408.
InParanoidiP42073.
KOiK15543.
OMAiINIAHAM.
OrthoDBiEOG754HZP.

Enzyme and pathway databases

BioCyciYEAST:G3O-29782-MONOMER.

Miscellaneous databases

NextBioi969576.
PROiP42073.

Gene expression databases

GenevestigatoriP42073.

Family and domain databases

ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Russnak R.
    Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end formation."
    Russnak R., Nehrke K.W., Platt T.
    Mol. Cell. Biol. 15:1689-1697(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE OF 1-429, FUNCTION.
  5. "RNA binding analysis of yeast REF2 and its two-hybrid interaction with a new gene product, FIR1."
    Russnak R., Pereira S., Platt T.
    Gene Expr. 6:241-258(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH FIR1.
  6. "Pti1p and Ref2p found in association with the mRNA 3' end formation complex direct snoRNA maturation."
    Dheur S., Vo le T.A., Voisinet-Hakil F., Minet M., Schmitter J.-M., Lacroute F., Wyers F., Minvielle-Sebastia L.
    EMBO J. 22:2831-2840(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN SNORNA 3-END FORMATION.
  7. "Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends."
    Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C.L., Greenblatt J.
    J. Biol. Chem. 278:33000-33010(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CPF COMPLEX, COMPOSITION OF THE APT COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "Identification of factors regulating poly(A) tail synthesis and maturation."
    Mangus D.A., Smith M.M., McSweeney J.M., Jacobson A.
    Mol. Cell. Biol. 24:4196-4206(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  11. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiREF2_YEAST
AccessioniPrimary (citable) accession number: P42073
Secondary accession number(s): D6VSH8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: February 1, 1996
Last modified: April 29, 2015
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7450 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.