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Q92541 (RTF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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:
RNA polymerase-associated protein RTF1 homolog
Gene names
Name:RTF1
Synonyms:KIAA0252
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length710 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex By similarity. Ref.7 Ref.8

Subunit structure

Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61; the association of RTF1 appears to be less stable than that of other subunits. At least in HeLa cells a N-terminal shorter form of RTF1 is also found in the complex. Ref.8

Subcellular location

Nucleusnucleoplasm By similarity.

Domain

The Plus3 domain mediates single-stranded DNA-binding. Ref.13

Sequence similarities

Contains 1 Plus3 domain.

Caution

It is uncertain whether Met-1 or Met-41 is the initiator.

Sequence caution

The sequence AAH15052.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAA13382.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
Wnt signaling pathway
   Cellular componentNucleus
   DomainCoiled coil
   LigandDNA-binding
   Molecular functionActivator
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA-templated transcription, initiation

Inferred from electronic annotation. Source: InterPro

Wnt signaling pathway

Inferred from electronic annotation. Source: UniProtKB-KW

endodermal cell fate commitment

Inferred from sequence or structural similarity. Source: UniProtKB

histone H3-K4 trimethylation

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of histone H3-K4 methylation

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription elongation from RNA polymerase II promoter

Inferred from direct assay Ref.8. Source: UniProtKB

positive regulation of transcription from RNA polymerase II promoter

Inferred from direct assay Ref.8. Source: UniProtKB

stem cell maintenance

Inferred from direct assay Ref.7. Source: UniProtKB

   Cellular_componentCdc73/Paf1 complex

Inferred from direct assay Ref.8. Source: UniProtKB

nucleolus

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionpoly(A) RNA binding

Inferred from direct assay PubMed 22658674. Source: UniProtKB

protein binding

Inferred from physical interaction PubMed 15923622PubMed 16024656PubMed 19410543Ref.8. Source: IntAct

single-stranded DNA binding

Inferred from direct assay Ref.13. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CDC73Q6P1J912EBI-1055239,EBI-930143
PAF1Q8N7H516EBI-1055239,EBI-2607770

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 710710RNA polymerase-associated protein RTF1 homolog
PRO_0000255936

Regions

Domain353 – 484132Plus3
Coiled coil526 – 56035 Potential
Compositional bias10 – 189Poly-Ala
Compositional bias135 – 17339Ser-rich
Compositional bias174 – 345172Glu-rich
Compositional bias214 – 30794Lys-rich

Amino acid modifications

Modified residue531Phosphoserine Ref.9 Ref.11
Modified residue551Phosphothreonine Ref.11
Modified residue6501Phosphoserine Ref.9
Modified residue6971Phosphoserine Ref.6 Ref.9

Experimental info

Mutagenesis4011R → E: Loss of binding to single-stranded DNA. Ref.13
Mutagenesis4101E → K: Reduced binding to single-stranded DNA. Ref.13
Mutagenesis4291R → E: Loss of binding to single-stranded DNA. Ref.13
Mutagenesis4341Q → A: Reduced binding to single-stranded DNA. Ref.13
Mutagenesis4351R → E: Loss of binding to single-stranded DNA. Ref.13

Secondary structure

........................ 710
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q92541 [UniParc].

Last modified November 30, 2010. Version 4.
Checksum: 54CC014655AA22B8

FASTA71080,313
        10         20         30         40         50         60 
MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV IDSDTEDSGS 

        70         80         90        100        110        120 
DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS DDEWTFGSNK NKKKGKARKI 

       130        140        150        160        170        180 
EKKGTMKKQA NKTASSGSSD KDSSAESSAP EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD 

       190        200        210        220        230        240 
GYGEDLMGDE EDRARLEQMT EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK 

       250        260        270        280        290        300 
KKQEEEQEKK KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL 

       310        320        330        340        350        360 
AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS QPVSLPEELN 

       370        380        390        400        410        420 
RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY RVAEITGVVE TAKVYQLGGT 

       430        440        450        460        470        480 
RTNKGLQLRH GNDQRVFRLE FVSNQEFTES EFMKWKEAMF SAGMQLPTLD EINKKELSIK 

       490        500        510        520        530        540 
EALNYKFNDQ DIEEIVKEKE RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN 

       550        560        570        580        590        600 
ELEERAEALD RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK 

       610        620        630        640        650        660 
PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS ASDLSEDLFK 

       670        680        690        700        710 
VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL EDYKKRRGLI 

« Hide

References

« Hide 'large scale' references
[1]"Analysis of the DNA sequence and duplication history of human chromosome 15."
Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A. expand/collapse author list , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]"Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain."
Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N.
DNA Res. 3:321-329(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 9-710.
Tissue: Brain.
[3]"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 14-710.
Tissue: Uterus.
[5]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[6]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-697, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity."
Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M., Heninger A.K., de Vries I., Kittler R., Junqueira M., Shevchenko A., Schulz H., Hubner N., Doss M.X., Sachinidis A., Hescheler J., Iacone R., Anastassiadis K., Stewart A.F., Pisabarro M.T. expand/collapse author list , Caldarelli A., Poser I., Theis M., Buchholz F.
Cell Stem Cell 4:403-415(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS."
Kim J., Guermah M., Roeder R.G.
Cell 140:491-503(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE PAF1 COMPLEX, COMPOSITION OF THE PAF1 COMPLEX, FUNCTION OF THE PAF1 COMPLEX.
[9]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53; SER-650 AND SER-697, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53 AND THR-55, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Solution structure of the plus-3 domain of human KIAA0252 protein."
RIKEN structural genomics initiative (RSGI)
Submitted (JUN-2006) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 347-482.
[13]"Structure and DNA binding of the human Rtf1 Plus3 domain."
de Jong R.N., Truffault V., Diercks T., Ab E., Daniels M.A., Kaptein R., Folkers G.E.
Structure 16:149-159(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 353-484, DOMAIN PLUS3, DNA-BINDING, MUTAGENESIS OF ARG-401; GLU-410; ARG-429; GLN-434 AND ARG-435.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AC087721 Genomic DNA. No translation available.
D87440 mRNA. Translation: BAA13382.2. Different initiation.
BC015052 mRNA. Translation: AAH15052.1. Different initiation.
CCDSCCDS32200.2.
RefSeqNP_055953.3. NM_015138.4.
UniGeneHs.511096.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2BZENMR-A353-484[»]
2DB9NMR-A347-482[»]
3U1UX-ray1.80A/B347-482[»]
4L1PX-ray2.12A/B353-484[»]
4L1UX-ray2.42A/B/C/D/E/F353-484[»]
ProteinModelPortalQ92541.
SMRQ92541. Positions 353-482.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116780. 28 interactions.
IntActQ92541. 15 interactions.
MINTMINT-6941890.
STRING9606.ENSP00000374280.

PTM databases

PhosphoSiteQ92541.

Polymorphism databases

DMDM313104316.

Proteomic databases

MaxQBQ92541.
PaxDbQ92541.
PRIDEQ92541.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000389629; ENSP00000374280; ENSG00000137815.
GeneID23168.
KEGGhsa:23168.
UCSCuc001zny.3. human.

Organism-specific databases

CTD23168.
GeneCardsGC15P041709.
H-InvDBHIX0012153.
HGNCHGNC:28996. RTF1.
HPAHPA006714.
MIM611633. gene.
neXtProtNX_Q92541.
PharmGKBPA134961778.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5296.
HOGENOMHOG000231764.
HOVERGENHBG057331.
InParanoidQ92541.
KOK15178.
OMASNSDDEW.
OrthoDBEOG7K0ZC9.
PhylomeDBQ92541.
TreeFamTF321360.

Gene expression databases

ArrayExpressQ92541.
BgeeQ92541.
CleanExHS_RTF1.
GenevestigatorQ92541.

Family and domain databases

InterProIPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view]
PfamPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTSM00719. Plus3. 1 hit.
[Graphical view]
PROSITEPS51360. PLUS3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSRTF1. human.
EvolutionaryTraceQ92541.
GeneWikiRTF1.
GenomeRNAi23168.
NextBio44567.
PMAP-CutDBQ92541.
PROQ92541.
SOURCESearch...

Entry information

Entry nameRTF1_HUMAN
AccessionPrimary (citable) accession number: Q92541
Secondary accession number(s): Q96BX6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 30, 2010
Last modified: July 9, 2014
This is version 111 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 15

Human chromosome 15: entries, gene names and cross-references to MIM