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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

RTF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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 similarity2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation, Wnt signaling pathway

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000137815-MONOMER.
ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-112387. Elongation arrest and recovery.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-75955. RNA Polymerase II Transcription Elongation.

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
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:28996. RTF1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi401R → E: Loss of binding to single-stranded DNA. 1 Publication1
Mutagenesisi410E → K: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi429R → E: Loss of binding to single-stranded DNA. 1 Publication1
Mutagenesisi434Q → A: Reduced binding to single-stranded DNA. 1 Publication1
Mutagenesisi435R → E: Loss of binding to single-stranded DNA. 1 Publication1

Organism-specific databases

DisGeNETi23168.
OpenTargetsiENSG00000137815.
PharmGKBiPA134961778.

Polymorphism and mutation databases

BioMutaiRTF1.
DMDMi313104316.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002559361 – 710RNA polymerase-associated protein RTF1 homologAdd BLAST710

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei53PhosphoserineCombined sources1
Modified residuei55PhosphothreonineCombined sources1
Modified residuei626PhosphoserineCombined sources1
Modified residuei650PhosphoserineCombined sources1
Modified residuei655PhosphoserineCombined sources1
Modified residuei697PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ92541.
MaxQBiQ92541.
PaxDbiQ92541.
PeptideAtlasiQ92541.
PRIDEiQ92541.

PTM databases

iPTMnetiQ92541.
PhosphoSitePlusiQ92541.

Miscellaneous databases

PMAP-CutDBQ92541.

Expressioni

Gene expression databases

BgeeiENSG00000137815.
CleanExiHS_RTF1.
ExpressionAtlasiQ92541. baseline and differential.
GenevisibleiQ92541. HS.

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi116780. 39 interactors.
IntActiQ92541. 14 interactors.
MINTiMINT-6941890.
STRINGi9606.ENSP00000374280.

Structurei

Secondary structure

1710
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi356 – 360Combined sources5
Beta strandi362 – 364Combined sources3
Helixi366 – 372Combined sources7
Beta strandi373 – 377Combined sources5
Helixi378 – 382Combined sources5
Beta strandi386 – 392Combined sources7
Beta strandi395 – 397Combined sources3
Beta strandi399 – 417Combined sources19
Beta strandi420 – 430Combined sources11
Beta strandi433 – 438Combined sources6
Helixi439 – 441Combined sources3
Helixi449 – 462Combined sources14
Helixi469 – 478Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ92541.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini353 – 484Plus3PROSITE-ProRule annotationAdd BLAST132

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili526 – 560Sequence analysisAdd BLAST35

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 18Poly-Ala9
Compositional biasi135 – 173Ser-richAdd BLAST39
Compositional biasi174 – 345Glu-richAdd BLAST172
Compositional biasi214 – 307Lys-richAdd BLAST94

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

eggNOGiKOG2402. Eukaryota.
COG5296. LUCA.
GeneTreeiENSGT00390000012493.
HOGENOMiHOG000231764.
HOVERGENiHBG057331.
InParanoidiQ92541.
KOiK15178.
OMAiLKISDPF.
OrthoDBiEOG091G1817.
PhylomeDBiQ92541.
TreeFamiTF321360.

Family and domain databases

InterProiIPR004343. Plus-3_dom.
IPR031102. Rtf1.
[Graphical view]
PANTHERiPTHR13115. PTHR13115. 1 hit.
PfamiPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTiSM00719. Plus3. 1 hit.
[Graphical view]
SUPFAMiSSF159042. SSF159042. 1 hit.
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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA13382 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.

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.
CCDSiCCDS32200.2.
RefSeqiNP_055953.3. NM_015138.4.
UniGeneiHs.511096.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116780. 39 interactors.
IntActiQ92541. 14 interactors.
MINTiMINT-6941890.
STRINGi9606.ENSP00000374280.

PTM databases

iPTMnetiQ92541.
PhosphoSitePlusiQ92541.

Polymorphism and mutation databases

BioMutaiRTF1.
DMDMi313104316.

Proteomic databases

EPDiQ92541.
MaxQBiQ92541.
PaxDbiQ92541.
PeptideAtlasiQ92541.
PRIDEiQ92541.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi23168.
DisGeNETi23168.
GeneCardsiRTF1.
H-InvDBHIX0012153.
HGNCiHGNC:28996. RTF1.
HPAiHPA006714.
MIMi611633. gene.
neXtProtiNX_Q92541.
OpenTargetsiENSG00000137815.
PharmGKBiPA134961778.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2402. Eukaryota.
COG5296. LUCA.
GeneTreeiENSGT00390000012493.
HOGENOMiHOG000231764.
HOVERGENiHBG057331.
InParanoidiQ92541.
KOiK15178.
OMAiLKISDPF.
OrthoDBiEOG091G1817.
PhylomeDBiQ92541.
TreeFamiTF321360.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000137815-MONOMER.
ReactomeiR-HSA-112382. Formation of RNA Pol II elongation complex.
R-HSA-112387. Elongation arrest and recovery.
R-HSA-674695. RNA Polymerase II Pre-transcription Events.
R-HSA-75955. RNA Polymerase II Transcription Elongation.

Miscellaneous databases

ChiTaRSiRTF1. human.
EvolutionaryTraceiQ92541.
GeneWikiiRTF1.
GenomeRNAii23168.
PMAP-CutDBQ92541.
PROiQ92541.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000137815.
CleanExiHS_RTF1.
ExpressionAtlasiQ92541. baseline and differential.
GenevisibleiQ92541. HS.

Family and domain databases

InterProiIPR004343. Plus-3_dom.
IPR031102. Rtf1.
[Graphical view]
PANTHERiPTHR13115. PTHR13115. 1 hit.
PfamiPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTiSM00719. Plus3. 1 hit.
[Graphical view]
SUPFAMiSSF159042. SSF159042. 1 hit.
PROSITEiPS51360. PLUS3. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 30, 2016
This is version 132 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

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 one 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.