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Q92541

- RTF1_HUMAN

UniProt

Q92541 - RTF1_HUMAN

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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

RTF1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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).By similarity

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB
  2. single-stranded DNA binding Source: UniProtKB

GO - Biological processi

  1. DNA-templated transcription, initiation Source: InterPro
  2. endodermal cell fate commitment Source: UniProtKB
  3. histone H3-K4 trimethylation Source: Ensembl
  4. negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  5. positive regulation of histone H3-K4 methylation Source: Ensembl
  6. positive regulation of transcription elongation from RNA polymerase II promoter Source: UniProtKB
  7. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  8. stem cell maintenance Source: UniProtKB
  9. Wnt signaling pathway Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation, Wnt signaling pathway

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein RTF1 homolog
Gene namesi
Name:RTF1
Synonyms:KIAA0252
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 15

Organism-specific databases

HGNCiHGNC:28996. RTF1.

Subcellular locationi

Nucleusnucleoplasm By similarity

GO - Cellular componenti

  1. Cdc73/Paf1 complex Source: UniProtKB
  2. nucleolus Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi401 – 4011R → E: Loss of binding to single-stranded DNA. 1 Publication
Mutagenesisi410 – 4101E → K: Reduced binding to single-stranded DNA. 1 Publication
Mutagenesisi429 – 4291R → E: Loss of binding to single-stranded DNA. 1 Publication
Mutagenesisi434 – 4341Q → A: Reduced binding to single-stranded DNA. 1 Publication
Mutagenesisi435 – 4351R → E: Loss of binding to single-stranded DNA. 1 Publication

Organism-specific databases

PharmGKBiPA134961778.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 710710RNA polymerase-associated protein RTF1 homologPRO_0000255936Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei53 – 531Phosphoserine2 Publications
Modified residuei55 – 551Phosphothreonine1 Publication
Modified residuei650 – 6501Phosphoserine1 Publication
Modified residuei697 – 6971Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ92541.
PaxDbiQ92541.
PRIDEiQ92541.

PTM databases

PhosphoSiteiQ92541.

Miscellaneous databases

PMAP-CutDBQ92541.

Expressioni

Gene expression databases

BgeeiQ92541.
CleanExiHS_RTF1.
ExpressionAtlasiQ92541. baseline and differential.
GenevestigatoriQ92541.

Organism-specific databases

HPAiHPA006714.

Interactioni

Subunit structurei

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.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q6P1J912EBI-1055239,EBI-930143
PAF1Q8N7H516EBI-1055239,EBI-2607770

Protein-protein interaction databases

BioGridi116780. 29 interactions.
IntActiQ92541. 15 interactions.
MINTiMINT-6941890.
STRINGi9606.ENSP00000374280.

Structurei

Secondary structure

1
710
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi356 – 3605Combined sources
Beta strandi362 – 3643Combined sources
Helixi366 – 3727Combined sources
Beta strandi373 – 3775Combined sources
Helixi378 – 3825Combined sources
Beta strandi386 – 3927Combined sources
Beta strandi395 – 3973Combined sources
Beta strandi399 – 41719Combined sources
Beta strandi420 – 43011Combined sources
Beta strandi433 – 4386Combined sources
Helixi439 – 4413Combined sources
Helixi449 – 46214Combined sources
Helixi469 – 47810Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ92541.
SMRiQ92541. Positions 353-482.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ92541.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini353 – 484132Plus3PROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili526 – 56035Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi10 – 189Poly-Ala
Compositional biasi135 – 17339Ser-richAdd
BLAST
Compositional biasi174 – 345172Glu-richAdd
BLAST
Compositional biasi214 – 30794Lys-richAdd
BLAST

Domaini

The Plus3 domain mediates single-stranded DNA-binding.1 Publication

Sequence similaritiesi

Contains 1 Plus3 domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiCOG5296.
GeneTreeiENSGT00390000012493.
HOGENOMiHOG000231764.
HOVERGENiHBG057331.
InParanoidiQ92541.
KOiK15178.
OMAiSNSDDEW.
OrthoDBiEOG7K0ZC9.
PhylomeDBiQ92541.
TreeFamiTF321360.

Family and domain databases

InterProiIPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view]
PfamiPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTiSM00719. Plus3. 1 hit.
[Graphical view]
PROSITEiPS51360. PLUS3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q92541-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV
60 70 80 90 100
IDSDTEDSGS DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS
110 120 130 140 150
DDEWTFGSNK NKKKGKARKI EKKGTMKKQA NKTASSGSSD KDSSAESSAP
160 170 180 190 200
EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD GYGEDLMGDE EDRARLEQMT
210 220 230 240 250
EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK KKQEEEQEKK
260 270 280 290 300
KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL
310 320 330 340 350
AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS
360 370 380 390 400
QPVSLPEELN RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY
410 420 430 440 450
RVAEITGVVE TAKVYQLGGT RTNKGLQLRH GNDQRVFRLE FVSNQEFTES
460 470 480 490 500
EFMKWKEAMF SAGMQLPTLD EINKKELSIK EALNYKFNDQ DIEEIVKEKE
510 520 530 540 550
RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN ELEERAEALD
560 570 580 590 600
RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK
610 620 630 640 650
PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS
660 670 680 690 700
ASDLSEDLFK VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL
710
EDYKKRRGLI
Length:710
Mass (Da):80,313
Last modified:November 30, 2010 - v4
Checksum:i54CC014655AA22B8
GO

Sequence cautioni

The sequence AAH15052.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA13382.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC087721 Genomic DNA. No translation available.
D87440 mRNA. Translation: BAA13382.2. Different initiation.
BC015052 mRNA. Translation: AAH15052.1. Different initiation.
CCDSiCCDS32200.2.
RefSeqiNP_055953.3. NM_015138.4.
UniGeneiHs.511096.

Genome annotation databases

EnsembliENST00000389629; ENSP00000374280; ENSG00000137815.
GeneIDi23168.
KEGGihsa:23168.
UCSCiuc001zny.3. human.

Polymorphism databases

DMDMi313104316.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC087721 Genomic DNA. No translation available.
D87440 mRNA. Translation: BAA13382.2 . Different initiation.
BC015052 mRNA. Translation: AAH15052.1 . Different initiation.
CCDSi CCDS32200.2.
RefSeqi NP_055953.3. NM_015138.4.
UniGenei Hs.511096.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2BZE NMR - A 353-484 [» ]
2DB9 NMR - A 347-482 [» ]
3U1U X-ray 1.80 A/B 347-482 [» ]
4L1P X-ray 2.12 A/B 353-484 [» ]
4L1U X-ray 2.42 A/B/C/D/E/F 353-484 [» ]
ProteinModelPortali Q92541.
SMRi Q92541. Positions 353-482.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 116780. 29 interactions.
IntActi Q92541. 15 interactions.
MINTi MINT-6941890.
STRINGi 9606.ENSP00000374280.

PTM databases

PhosphoSitei Q92541.

Polymorphism databases

DMDMi 313104316.

Proteomic databases

MaxQBi Q92541.
PaxDbi Q92541.
PRIDEi Q92541.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000389629 ; ENSP00000374280 ; ENSG00000137815 .
GeneIDi 23168.
KEGGi hsa:23168.
UCSCi uc001zny.3. human.

Organism-specific databases

CTDi 23168.
GeneCardsi GC15P041709.
H-InvDB HIX0012153.
HGNCi HGNC:28996. RTF1.
HPAi HPA006714.
MIMi 611633. gene.
neXtProti NX_Q92541.
PharmGKBi PA134961778.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG5296.
GeneTreei ENSGT00390000012493.
HOGENOMi HOG000231764.
HOVERGENi HBG057331.
InParanoidi Q92541.
KOi K15178.
OMAi SNSDDEW.
OrthoDBi EOG7K0ZC9.
PhylomeDBi Q92541.
TreeFami TF321360.

Miscellaneous databases

ChiTaRSi RTF1. human.
EvolutionaryTracei Q92541.
GeneWikii RTF1.
GenomeRNAii 23168.
NextBioi 44567.
PMAP-CutDB Q92541.
PROi Q92541.
SOURCEi Search...

Gene expression databases

Bgeei Q92541.
CleanExi HS_RTF1.
ExpressionAtlasi Q92541. baseline and differential.
Genevestigatori Q92541.

Family and domain databases

InterProi IPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view ]
Pfami PF03126. Plus-3. 1 hit.
[Graphical view ]
SMARTi SM00719. Plus3. 1 hit.
[Graphical view ]
PROSITEi PS51360. PLUS3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-697, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. 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. 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. 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.

Entry informationi

Entry nameiRTF1_HUMAN
AccessioniPrimary (citable) accession number: Q92541
Secondary accession number(s): Q96BX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 30, 2010
Last modified: November 26, 2014
This is version 114 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Caution

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3