P29539 (RIF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Telomere length regulator protein RIF1

Alternative name(s):
RAP1-interacting factor 1

Gene names

Name:	RIF1
Ordered Locus Names:	YBR275C
ORF Names:	YBR1743

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1916 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Negatively regulates telomere length by preventing telomere elongation or promoting degradation of the telomere ends. Recruited to telomeres by interaction with the C-terminus of RAP1, which binds directly to telomeric repeat DNA. This may create a negative feedback loop in which the addition of new telomere repeats creates binding sites for inhibitors of telomere length extension. May also influence the balance of transcriptional silencing at telomeres and the silent mating type locus HMR, which is mediated by SIR (Silent Information Regulator) proteins including SIR3 and SIR4. RIF1 competes with SIR proteins for binding to the C-terminus of RAP1. In the absence of RIF1, a limiting cellular pool of SIR proteins may preferentially associate with RAP1 at sub-telomeric loci, causing enhanced telomeric silencing and attenuated silencing of the HMR locus. Ref.1 Ref.5 Ref.6 Ref.8 Ref.10
Subunit structure	Interacts with RIF2 and RAP1. Ref.1 Ref.6
Subcellular location	Nucleus. Chromosome › telomere. Note: Localizes to telomeres. Telomere association begins in G1/S, attains a peak during late G2/S phase of the cell cycle, and is lost during telophase. Localization to telomeres may be increased by telomere uncapping caused by expression of a mutant telomerase RNA subunit (TLC1). Ref.7 Ref.8 Ref.9

Ontologies

Keywords
Biological process	Cell cycle
Cellular component	Chromosome Nucleus Telomere
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW chromatin silencing at silent mating-type cassette Inferred from mutant phenotype Ref.1. Source: SGD telomere capping Inferred from mutant phenotype PubMed 20523746. Source: SGD
Cellular_component	nuclear telomere cap complex Inferred from direct assay Ref.7. Source: SGD
Molecular_function	telomeric DNA binding Inferred from direct assay PubMed 17656141. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1916	1916	Telomere length regulator protein RIF1		PRO_0000097336
Amino acid modifications
	Modified residue	97	1	Phosphoserine Ref.14
	Modified residue	159	1	Phosphoserine Ref.14
	Modified residue	1351	1	Phosphoserine; by ATM or ATR Ref.13
	Modified residue	1360	1	Phosphoserine Ref.14
	Modified residue	1362	1	Phosphoserine Ref.13 Ref.14
	Modified residue	1375	1	Phosphoserine Ref.14
	Modified residue	1567	1	Phosphoserine Ref.14
	Modified residue	1637	1	Phosphoserine Ref.11 Ref.12 Ref.13 Ref.14
	Modified residue	1668	1	Phosphothreonine Ref.14
	Modified residue	1795	1	Phosphoserine Ref.14
Experimental info
	Sequence conflict	580	1	C → S in CAA47121. Ref.1
	Sequence conflict	732	1	A → T in CAA85238. Ref.2
	Sequence conflict	732	1	A → T in CAA53638. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P29539 [UniParc]. Last modified July 27, 2011. Version 3. Checksum: 07070AF02361D96F	FASTA	1,916	217,931
	10 20 30 40 50 60 MSKDFSDKKK HTIDRIDQHI LRRSQHDNYS NGSSPWMKTN LPPPSPQAHM HIQSDLSPTP 70 80 90 100 110 120 KRRKLASSSD CENKQFDLSA INKNLYPEDT GSRLMQSLPE LSASNSDNVS PVTKSVAFSD 130 140 150 160 170 180 RIESSPIYRI PGSSPKPSPS SKPGKSILRN RLPSVRTVSD LSYNKLQYTQ HKLHNGNIFT 190 200 210 220 230 240 SPYKETRVNP RALEYWVSGE IHGLVDNESV SEFKEIIEGG LGILRQESED YVARRFEVYA 250 260 270 280 290 300 TFNNIIPILT TKNVNEVDQK FNILIVNIES IIEICIPHLQ IAQDTLLSSS EKKNPFVIRL 310 320 330 340 350 360 YVQIVRFFSA IMSNFKIVKW LTKRPDLVNK LKVIYRWTTG ALRNENSNKI IITAQVSFLR 370 380 390 400 410 420 DEKFGTFFLS NEEIKPIIST FTEIMEINSH NLIYEKLLLI RGFLSKYPKL MIETVTSWLP 430 440 450 460 470 480 GEVLPRIIIG DEIYSMKILI TSIVVLLELL KKCLDFVDEH ERIYQCIMLS PVCETIPEKF 490 500 510 520 530 540 LSKLPLNSYD SANLDKVTIG HLLTQQIKNY IVVKNDNKIA MDLWLSMTGL LYDSGKRVYD 550 560 570 580 590 600 LTSESNKVWF DLNNLCFINN HPKTRLMSIK VWRIITYCIC TKISQKNQEG NKSLLSLLRT 610 620 630 640 650 660 PFQMTLPYVN DPSAREGIIY HLLGVVYTAF TSNKNLSTDM FELFWDHLIT PIYEDYVFKY 670 680 690 700 710 720 DSIHLQNVLF TVLHLLIGGK NADVALERKY KKHIHPMSVI ASEGVKLKDI SSLPPQIIKR 730 740 750 760 770 780 EYDKIMKVVF QAVEVAISNV NLAHDLILTS LKHLPEDRKD QTHLESFSSL ILKVTQNNKD 790 800 810 820 830 840 TPIFRDFFGA VTSSFVYTFL DLFLRKNDSS LVNFNIQISK VGISQGNMTL DLLKDVIRKA 850 860 870 880 890 900 RNETSEFLII EKFLELDDKK TEVYAQNWVG STLLPPNISF REFQSLANIV NKVPNENSIE 910 920 930 940 950 960 NFLDLCLKLS FPVNLFTLLH VSMWSNNNFI YFIQSYVSKN ENKLNVDLIT LLKTSLPGNP 970 980 990 1000 1010 1020 ELFSGLLPFL RRNKFMDILE YCIHSNPNLL NSIPDLNSDL LLKLLPRSRA SYFAANIKLF 1030 1040 1050 1060 1070 1080 KCSEQLTLVR WLLKGQQLEQ LNQNFSEIEN VLQNASDSEL EKSEIIRELL HLAMANPIEP 1090 1100 1110 1120 1130 1140 LFSGLLNFCI KNNMADHLDE FCGNMTSEVL FKISPELLLK LLTYKEKPNG KLLAAVIEKI 1150 1160 1170 1180 1190 1200 ENGDDDYILE LLEKIIIQKE IQILEKLKEP LLVFFLNPVS SNMQKHKKST NMLRELVLLY 1210 1220 1230 1240 1250 1260 LTKPLSRSAA KKFFSMLISI LPPNPNYQTI DMVNLLIDLI KSHNRKFKDK RTYNATLKTI 1270 1280 1290 1300 1310 1320 GKWIQESGVV HQGDSSKEIE AIPDTKSMYI PCEGSENKLS NLQRKVDSQD IQVPATQGMK 1330 1340 1350 1360 1370 1380 EPPSSIQISS QISAKDSDSI SLKNTAIMNS SQQESHANRS RSIDDETLEE VDNESIREID 1390 1400 1410 1420 1430 1440 QQMKSTQLDK NVANHSNICS TKSDEVDVTE LHESIDTQSS EVNAYQPIEV LTSELKAVTN 1450 1460 1470 1480 1490 1500 RSIKTNPDHN VVNSDNPLKR PSKETPTSEN KRSKGHETMV DVLVSEEQAV SPSSDVICTN 1510 1520 1530 1540 1550 1560 IKSIANEESS LALRNSIKVE TNCNENSLNV TLDLDQQTIT KEDGKGQVEH VQRQENQESM 1570 1580 1590 1600 1610 1620 NKINSKSFTQ DNIAQYKSVK KARPNNEGEN NDYACNVEQA SPVRNEVPGD GIQIPSGTIL 1630 1640 1650 1660 1670 1680 LNSSKQTEKS KVDDLRSDED EHGTVAQEKH QVGAINSRNK NNDRMDSTPI QGTEEESREV 1690 1700 1710 1720 1730 1740 VMTEEGINVR LEDSGTCELN KNLKGPLKGD KDANINDDFV PVEENVRDEG FLKSMEHAVS 1750 1760 1770 1780 1790 1800 KETGLEEQPE VADISVLPEI RIPIFNSLKM QGSKSQIKEK LKKRLQRNEL MPPDSPPRMT 1810 1820 1830 1840 1850 1860 ENTNINAQNG LDTVPKTIGG KEKHHEIQLG QAHTEADGEP LLGGDGNEDA TSREATPSLK 1870 1880 1890 1900 1910 VHFFSKKSRR LVARLRGFTP GDLNGISVEE RRNLRIELLD FMMRLEYYSN RDNDMN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation." Hardy C.F.J., Sussel L., Shore D. Genes Dev. 6:801-814(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH RAP1. Strain: ATCC 204510 / AB320.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 732. Strain: ATCC 204508 / S288c.
[4]	"The sequence of a 32,420 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae." Holmstroem K., Brandt T., Kallesoe T. Yeast 10:S47-S62(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1096. Strain: ATCC 204508 / S288c.
[5]	"Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast." Buck S.W., Shore D. Genes Dev. 9:370-384(1995) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae." Wotton D., Shore D. Genes Dev. 11:748-760(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAP1 AND RIF2.
[7]	"Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo." Bourns B.D., Alexander M.K., Smith A.M., Zakian V.A. Mol. Cell. Biol. 18:5600-5608(1998) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins." Mishra K., Shore D. Curr. Biol. 9:1123-1126(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]	"Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae." Smith C.D., Smith D.L., DeRisi J.L., Blackburn E.H. Mol. Biol. Cell 14:556-570(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[10]	"Counting of Rif1p and Rif2p on Saccharomyces cerevisiae telomeres regulates telomere length." Levy D.L., Blackburn E.H. Mol. Cell. Biol. 24:10857-10867(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1637, MASS SPECTROMETRY. Strain: ADR376.
[12]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1637, MASS SPECTROMETRY.
[13]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1351; SER-1362 AND SER-1637, MASS SPECTROMETRY.
[14]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-97; SER-159; SER-1360; SER-1362; SER-1375; SER-1567; SER-1637; THR-1668 AND SER-1795, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X66501 Genomic DNA. Translation: CAA47121.1. Z36144 Genomic DNA. Translation: CAA85238.1. Z36145 Genomic DNA. Translation: CAA85240.1. X76053 Genomic DNA. Translation: CAA53638.1. BK006936 Genomic DNA. Translation: DAA07391.2.
PIR	S46157.
RefSeq	NP_009834.4. NM_001178623.4.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-801N.
IntAct	P29539. 7 interactions.
MINT	MINT-2780441.
STRING	4932.YBR275C.
Proteomic databases
PaxDb	P29539.
PeptideAtlas	P29539.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YBR275C; YBR275C; YBR275C.
GeneID	852578.
KEGG	sce:YBR275C. sce:YBR280C.
Organism-specific databases
CYGD	YBR275c.
SGD	S000000479. RIF1.
Phylogenomic databases
eggNOG	NOG73322.
KO	K11118. K15072.
OrthoDB	EOG4TB7KX.
Gene expression databases
Genevestigator	P29539.
GermOnline	YBR275C. Saccharomyces cerevisiae.
Family and domain databases
ProtoNet	Search...
Other
NextBio	971718.

Entry information

Entry name

RIF1_YEAST

Accession

Primary (citable) accession number: P29539
Secondary accession number(s): D6VQS1, P89507

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	July 27, 2011
Last modified:	April 3, 2013
This is version 102 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program