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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

Rtf1

Organism
Mus musculus (Mouse)
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. 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

GO - Molecular functioni

GO - Biological processi

  • blastocyst growth Source: MGI
  • DNA-templated transcription, initiation Source: InterPro
  • endodermal cell fate commitment Source: UniProtKB
  • histone H3-K4 trimethylation Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of histone H3-K4 methylation Source: UniProtKB
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • stem cell population maintenance Source: UniProtKB
  • transcription elongation from RNA polymerase II promoter Source: InterPro
  • 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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1309480. Rtf1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 715715RNA polymerase-associated protein RTF1 homologPRO_0000401196Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei58 – 581PhosphoserineBy similarity
Modified residuei60 – 601PhosphothreonineBy similarity
Modified residuei702 – 7021PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiA2AQ19.
MaxQBiA2AQ19.
PaxDbiA2AQ19.
PRIDEiA2AQ19.

PTM databases

PhosphoSiteiA2AQ19.

Expressioni

Gene expression databases

BgeeiA2AQ19.
GenevisibleiA2AQ19. MM.

Interactioni

Subunit structurei

Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61.By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000028767.

Structurei

3D structure databases

ProteinModelPortaliA2AQ19.
SMRiA2AQ19. Positions 358-487.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini358 – 489132Plus3PROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili531 – 56535Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi10 – 2314Poly-AlaAdd
BLAST
Compositional biasi140 – 17839Ser-richAdd
BLAST
Compositional biasi151 – 350200Glu-richAdd
BLAST
Compositional biasi219 – 31294Lys-richAdd
BLAST

Domaini

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

Sequence similaritiesi

Contains 1 Plus3 domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2402. Eukaryota.
COG5296. LUCA.
GeneTreeiENSGT00390000012493.
HOGENOMiHOG000231764.
HOVERGENiHBG057331.
InParanoidiA2AQ19.
KOiK15178.
OMAiLKISDPF.
OrthoDBiEOG7K0ZC9.
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.

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 AAI17849.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAI17850.1 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. Translation: CAM18078.1.
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.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL844536 Genomic DNA. Translation: CAM18078.1.
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. Positions 358-487.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000028767.

PTM databases

PhosphoSiteiA2AQ19.

Proteomic databases

EPDiA2AQ19.
MaxQBiA2AQ19.
PaxDbiA2AQ19.
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.
OMAiLKISDPF.
OrthoDBiEOG7K0ZC9.
TreeFamiTF321360.

Miscellaneous databases

ChiTaRSiRtf1. mouse.
NextBioi344845.
PROiA2AQ19.
SOURCEiSearch...

Gene expression databases

BgeeiA2AQ19.
GenevisibleiA2AQ19. MM.

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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. "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 51-715.
  3. "A differential phosphoproteomic analysis of retinoic acid-treated P19 cells."
    Smith J.C., Duchesne M.A., Tozzi P., Ethier M., Figeys D.
    J. Proteome Res. 6:3174-3186(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Teratocarcinoma.
  4. Cited for: FUNCTION.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Spleen and Testis.

Entry informationi

Entry nameiRTF1_MOUSE
AccessioniPrimary (citable) accession number: A2AQ19
Secondary accession number(s): Q08EC5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: February 20, 2007
Last modified: May 11, 2016
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.