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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

Rtf1

Organism
Mus musculus (Mouse)
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. 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. Binds single-stranded DNA (By similarity). 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 similarity1 Publication

Caution

It is uncertain whether Met-1 or Met-46 is the initiator.Curated

GO - Molecular functioni

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

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein RTF1 homolog
Gene namesi
Name:Rtf1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1309480 Rtf1

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004011961 – 715RNA polymerase-associated protein RTF1 homologAdd BLAST715

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei58PhosphoserineBy similarity1
Modified residuei60PhosphothreonineBy similarity1
Modified residuei631PhosphoserineBy similarity1
Modified residuei660PhosphoserineBy similarity1
Modified residuei702PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiA2AQ19
MaxQBiA2AQ19
PaxDbiA2AQ19
PeptideAtlasiA2AQ19
PRIDEiA2AQ19

PTM databases

iPTMnetiA2AQ19
PhosphoSitePlusiA2AQ19

Expressioni

Gene expression databases

BgeeiENSMUSG00000027304 Expressed in 247 organ(s), highest expression level in cardiac ventricle
GenevisibleiA2AQ19 MM

Interactioni

Subunit structurei

Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. The PAF1 complex interacts with PHF5A (PubMed:27749823).By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

IntActiA2AQ19, 1 interactor
STRINGi10090.ENSMUSP00000028767

Structurei

3D structure databases

ProteinModelPortaliA2AQ19
SMRiA2AQ19
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini358 – 489Plus3PROSITE-ProRule annotationAdd BLAST132

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili531 – 565Sequence analysisAdd BLAST35

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 23Poly-AlaAdd BLAST14
Compositional biasi140 – 178Ser-richAdd BLAST39
Compositional biasi151 – 350Glu-richAdd BLAST200
Compositional biasi219 – 312Lys-richAdd BLAST94

Domaini

The Plus3 domain mediates single-stranded DNA-binding.By similarity

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2402 Eukaryota
COG5296 LUCA
GeneTreeiENSGT00390000012493
HOGENOMiHOG000231764
HOVERGENiHBG057331
InParanoidiA2AQ19
KOiK15178
OMAiSGCKSAV
OrthoDBiEOG091G1817
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

Sequencei

Sequence statusi: Complete.

A2AQ19-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRGRLCVGRA AAVAAAVAAA AVAVPLAGGQ EGSQGGVRRG SRGTTMVKKR
60 70 80 90 100
KGRVVIDSDT EDSGSDENLD QELLSLAKRK RSDSEEKEPP VSQPAASSDS
110 120 130 140 150
ETSDSDDEWT FGSNKNKKKG KTRKVEKKGA MKKQANKAAS SGSSDRDSSA
160 170 180 190 200
ESSAPEEGEV SDSESSSSSS SSDSDSSSED EEFHDGYGED LMGDEEDRAR
210 220 230 240 250
LEQMTEKERE QELFNRIEKR EVLKRRFEIK KKLKTAKKKE KKEKKKKQEE
260 270 280 290 300
EQEKKKLTQI QESQVTSHNK ERRSKRDEKL DKKSQAMEEL KAEREKRKNR
310 320 330 340 350
TAELLAKKQP LKTSEVYSDD EEEEDDDKSS EKSDRSSRTS SSDEEEEKEE
360 370 380 390 400
IPPKSQPVSL PEELNRVRLS RHKLERWCHM PFFAKTVTGC FVRIGIGNHN
410 420 430 440 450
SKPVYRVAEI TGVVETAKVY QLGGTRTNKG LQLRHGNDQR VFRLEFVSNQ
460 470 480 490 500
EFTESEFMKW KEAMFSAGMQ LPTLDEINKK ELSIKEALNY KFNDQDIEEI
510 520 530 540 550
VKEKERFRKA PPNYAMKKTQ LLKEKAMAED LGDQDKAKQI QDQLNELEER
560 570 580 590 600
AEALDRQRTK NISAISYINQ RNREWNIVES EKALVAESHN MRNQQMDPFT
610 620 630 640 650
RRQCKPTIVS NSRDPAVQAA ILAQLNAKYG SGVLPDAPKE MSKGQGKDKD
660 670 680 690 700
LNSKTASDLS EDLFKVHDFD VKIDLQVPSS ESKALAITSK APPAKDGAPR
710
RSLNLEDYKK RRGLI
Length:715
Mass (Da):80,797
Last modified:February 20, 2007 - v1
Checksum:iCC1E4523DB00008C
GO

Sequence cautioni

The sequence AAI17849 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI17850 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL844536 Genomic DNA No translation available.
BC117848 mRNA Translation: AAI17849.1 Different initiation.
BC117849 mRNA Translation: AAI17850.1 Different initiation.
CCDSiCCDS50673.1
RefSeqiNP_084388.2, NM_030112.2
UniGeneiMm.33437

Genome annotation databases

EnsembliENSMUST00000028767; ENSMUSP00000028767; ENSMUSG00000027304
GeneIDi76246
KEGGimmu:76246
UCSCiuc008lue.2 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL844536 Genomic DNA No translation available.
BC117848 mRNA Translation: AAI17849.1 Different initiation.
BC117849 mRNA Translation: AAI17850.1 Different initiation.
CCDSiCCDS50673.1
RefSeqiNP_084388.2, NM_030112.2
UniGeneiMm.33437

3D structure databases

ProteinModelPortaliA2AQ19
SMRiA2AQ19
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiA2AQ19, 1 interactor
STRINGi10090.ENSMUSP00000028767

PTM databases

iPTMnetiA2AQ19
PhosphoSitePlusiA2AQ19

Proteomic databases

EPDiA2AQ19
MaxQBiA2AQ19
PaxDbiA2AQ19
PeptideAtlasiA2AQ19
PRIDEiA2AQ19

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028767; ENSMUSP00000028767; ENSMUSG00000027304
GeneIDi76246
KEGGimmu:76246
UCSCiuc008lue.2 mouse

Organism-specific databases

CTDi23168
MGIiMGI:1309480 Rtf1

Phylogenomic databases

eggNOGiKOG2402 Eukaryota
COG5296 LUCA
GeneTreeiENSGT00390000012493
HOGENOMiHOG000231764
HOVERGENiHBG057331
InParanoidiA2AQ19
KOiK15178
OMAiSGCKSAV
OrthoDBiEOG091G1817
TreeFamiTF321360

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiRtf1 mouse
PROiPR:A2AQ19
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027304 Expressed in 247 organ(s), highest expression level in cardiac ventricle
GenevisibleiA2AQ19 MM

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_MOUSE
AccessioniPrimary (citable) accession number: A2AQ19
Secondary accession number(s): Q08EC5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: February 20, 2007
Last modified: November 7, 2018
This is version 94 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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