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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

RTF1

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

Caution

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

GO - Molecular functioni

  • RNA binding Source: UniProtKB
  • RNA polymerase II C-terminal domain phosphoserine binding Source: GO_Central
  • single-stranded DNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding
Biological processTranscription, Transcription regulation, Wnt signaling pathway

Enzyme and pathway databases

ReactomeiR-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins

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

EuPathDBiHostDB:ENSG00000137815.14
HGNCiHGNC:28996 RTF1
MIMi611633 gene
neXtProtiNX_Q92541

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi75301

PTM databases

iPTMnetiQ92541
PhosphoSitePlusiQ92541

Miscellaneous databases

PMAP-CutDBiQ92541

Expressioni

Gene expression databases

BgeeiENSG00000137815 Expressed in 241 organ(s), highest expression level in testis
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 (PubMed:20178742). The PAF1 complex interacts with PHF5A (By similarity).By similarity1 Publication

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi116780, 62 interactors
IntActiQ92541, 16 interactors
MINTiQ92541
STRINGi9606.ENSP00000374280

Structurei

Secondary structure

1710
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Keywords - Domaini

Coiled coil

Phylogenomic databases

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

Family and domain databases

Gene3Di2.170.260.30, 1 hit
InterProiView protein in InterPro
IPR004343 Plus-3_dom
IPR036128 Plus3-like_sf
IPR031102 Rtf1
PANTHERiPTHR13115 PTHR13115, 1 hit
PfamiView protein in Pfam
PF03126 Plus-3, 1 hit
SMARTiView protein in SMART
SM00719 Plus3, 1 hit
SUPFAMiSSF159042 SSF159042, 1 hit
PROSITEiView protein in PROSITE
PS51360 PLUS3, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0YKX1H0YKX1_HUMAN
RNA polymerase-associated protein R...
RTF1
171Annotation score:

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

Similar proteinsi

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, 62 interactors
IntActiQ92541, 16 interactors
MINTiQ92541
STRINGi9606.ENSP00000374280

PTM databases

iPTMnetiQ92541
PhosphoSitePlusiQ92541

Polymorphism and mutation databases

BioMutaiRTF1
DMDMi313104316

Proteomic databases

EPDiQ92541
MaxQBiQ92541
PaxDbiQ92541
PeptideAtlasiQ92541
PRIDEiQ92541
ProteomicsDBi75301

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi23168
DisGeNETi23168
EuPathDBiHostDB:ENSG00000137815.14
GeneCardsiRTF1
H-InvDBiHIX0012153
HGNCiHGNC:28996 RTF1
HPAiHPA006714
MIMi611633 gene
neXtProtiNX_Q92541
OpenTargetsiENSG00000137815
PharmGKBiPA134961778
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins

Miscellaneous databases

ChiTaRSiRTF1 human
EvolutionaryTraceiQ92541
GeneWikiiRTF1
GenomeRNAii23168
PMAP-CutDBiQ92541
PROiPR:Q92541
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000137815 Expressed in 241 organ(s), highest expression level in testis
CleanExiHS_RTF1
ExpressionAtlasiQ92541 baseline and differential
GenevisibleiQ92541 HS

Family and domain databases

Gene3Di2.170.260.30, 1 hit
InterProiView protein in InterPro
IPR004343 Plus-3_dom
IPR036128 Plus3-like_sf
IPR031102 Rtf1
PANTHERiPTHR13115 PTHR13115, 1 hit
PfamiView protein in Pfam
PF03126 Plus-3, 1 hit
SMARTiView protein in SMART
SM00719 Plus3, 1 hit
SUPFAMiSSF159042 SSF159042, 1 hit
PROSITEiView protein in PROSITE
PS51360 PLUS3, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRTF1_HUMAN
AccessioniPrimary (citable) accession number: Q92541
Secondary accession number(s): Q96BX6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 30, 2010
Last modified: November 7, 2018
This is version 147 of the entry and version 4 of the sequence. See 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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