RTF1_MOUSE
ID RTF1_MOUSE Reviewed; 715 AA.
AC A2AQ19; Q08EC5;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 20-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=RNA polymerase-associated protein RTF1 homolog;
GN Name=Rtf1;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 51-715.
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Teratocarcinoma;
RX PubMed=17622165; DOI=10.1021/pr070122r;
RA Smith J.C., Duchesne M.A., Tozzi P., Ethier M., Figeys D.;
RT "A differential phosphoproteomic analysis of retinoic acid-treated P19
RT cells.";
RL J. Proteome Res. 6:3174-3186(2007).
RN [4]
RP FUNCTION.
RX PubMed=19345177; DOI=10.1016/j.stem.2009.03.009;
RA Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M., Heninger A.K.,
RA de Vries I., Kittler R., Junqueira M., Shevchenko A., Schulz H., Hubner N.,
RA Doss M.X., Sachinidis A., Hescheler J., Iacone R., Anastassiadis K.,
RA Stewart A.F., Pisabarro M.T., Caldarelli A., Poser I., Theis M.,
RA Buchholz F.;
RT "A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1
RT complex for embryonic stem cell identity.";
RL Cell Stem Cell 4:403-415(2009).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=27749823; DOI=10.1038/ncb3424;
RA Strikoudis A., Lazaris C., Trimarchi T., Galvao Neto A.L., Yang Y.,
RA Ntziachristos P., Rothbart S., Buckley S., Dolgalev I., Stadtfeld M.,
RA Strahl B.D., Dynlacht B.D., Tsirigos A., Aifantis I.;
RT "Regulation of transcriptional elongation in pluripotency and cell
RT differentiation by the PHD-finger protein Phf5a.";
RL Nat. Cell Biol. 18:1127-1138(2016).
CC -!- FUNCTION: Component of the PAF1 complex (PAF1C) which has multiple
CC functions during transcription by RNA polymerase II and is implicated
CC in regulation of development and maintenance of embryonic stem cell
CC pluripotency. PAF1C associates with RNA polymerase II through
CC interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-
CC 5'-phosphorylated forms and is involved in transcriptional elongation,
CC acting both independently and synergistically with TCEA1 and in
CC cooperation with the DSIF complex and HTATSF1. PAF1C is required for
CC transcription of Hox and Wnt target genes. PAF1C is involved in
CC hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1.
CC PAF1C is involved in histone modifications such as ubiquitination of
CC histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C
CC recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2
CC enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of
CC 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B
CC ubiquitination is proposed to be coupled to transcription. PAF1C is
CC involved in mRNA 3' end formation probably through association with
CC cleavage and poly(A) factors. Binds single-stranded DNA (By
CC similarity). Required for maximal induction of heat-shock genes.
CC Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on
CC genes involved in stem cell pluripotency; this function is synergistic
CC with CXXC1 indicative for an involvement of a SET1 complex.
CC {ECO:0000250, ECO:0000269|PubMed:19345177}.
CC -!- SUBUNIT: Component of the PAF1 complex, which consists of CDC73, PAF1,
CC LEO1, CTR9, RTF1 and WDR61. The PAF1 complex interacts with PHF5A
CC (PubMed:27749823). {ECO:0000250|UniProtKB:Q92541,
CC ECO:0000269|PubMed:27749823}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm {ECO:0000250}.
CC -!- DOMAIN: The Plus3 domain mediates single-stranded DNA-binding.
CC {ECO:0000250}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-46 is the initiator.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI17849.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAI17850.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL844536; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC117848; AAI17849.1; ALT_INIT; mRNA.
DR EMBL; BC117849; AAI17850.1; ALT_INIT; mRNA.
DR CCDS; CCDS50673.1; -.
DR RefSeq; NP_084388.2; NM_030112.2.
DR AlphaFoldDB; A2AQ19; -.
DR BMRB; A2AQ19; -.
DR SMR; A2AQ19; -.
DR BioGRID; 218047; 14.
DR IntAct; A2AQ19; 1.
DR STRING; 10090.ENSMUSP00000028767; -.
DR iPTMnet; A2AQ19; -.
DR PhosphoSitePlus; A2AQ19; -.
DR EPD; A2AQ19; -.
DR MaxQB; A2AQ19; -.
DR PaxDb; A2AQ19; -.
DR PeptideAtlas; A2AQ19; -.
DR PRIDE; A2AQ19; -.
DR ProteomicsDB; 256637; -.
DR Antibodypedia; 1858; 235 antibodies from 27 providers.
DR Ensembl; ENSMUST00000028767; ENSMUSP00000028767; ENSMUSG00000027304.
DR GeneID; 76246; -.
DR KEGG; mmu:76246; -.
DR UCSC; uc008lue.2; mouse.
DR CTD; 23168; -.
DR MGI; MGI:1309480; Rtf1.
DR VEuPathDB; HostDB:ENSMUSG00000027304; -.
DR eggNOG; KOG2402; Eukaryota.
DR GeneTree; ENSGT00390000012493; -.
DR HOGENOM; CLU_018644_0_1_1; -.
DR InParanoid; A2AQ19; -.
DR OMA; SGCKSAV; -.
DR OrthoDB; 607093at2759; -.
DR PhylomeDB; A2AQ19; -.
DR TreeFam; TF321360; -.
DR Reactome; R-MMU-112382; Formation of RNA Pol II elongation complex.
DR Reactome; R-MMU-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-MMU-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-MMU-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
DR BioGRID-ORCS; 76246; 23 hits in 75 CRISPR screens.
DR ChiTaRS; Rtf1; mouse.
DR PRO; PR:A2AQ19; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; A2AQ19; protein.
DR Bgee; ENSMUSG00000027304; Expressed in embryonic brain and 231 other tissues.
DR Genevisible; A2AQ19; MM.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IPI:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:MGI.
DR GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IBA:GO_Central.
DR GO; GO:0003697; F:single-stranded DNA binding; ISS:UniProtKB.
DR GO; GO:0001832; P:blastocyst growth; IMP:MGI.
DR GO; GO:0001711; P:endodermal cell fate commitment; IMP:UniProtKB.
DR GO; GO:0080182; P:histone H3-K4 trimethylation; IMP:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0051571; P:positive regulation of histone H3-K4 methylation; IMP:UniProtKB.
DR GO; GO:0019827; P:stem cell population maintenance; IMP:UniProtKB.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; ISS:UniProtKB.
DR GO; GO:0016055; P:Wnt signaling pathway; IEA:UniProtKB-KW.
DR Gene3D; 3.90.70.200; -; 1.
DR InterPro; IPR004343; Plus-3_dom.
DR InterPro; IPR036128; Plus3-like_sf.
DR Pfam; PF03126; Plus-3; 1.
DR SMART; SM00719; Plus3; 1.
DR SUPFAM; SSF159042; SSF159042; 1.
DR PROSITE; PS51360; PLUS3; 1.
PE 1: Evidence at protein level;
KW Activator; Coiled coil; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Transcription; Transcription regulation;
KW Wnt signaling pathway.
FT CHAIN 1..715
FT /note="RNA polymerase-associated protein RTF1 homolog"
FT /id="PRO_0000401196"
FT DOMAIN 358..489
FT /note="Plus3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00693"
FT REGION 28..218
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 233..362
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 632..654
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 679..715
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 531..565
FT /evidence="ECO:0000255"
FT COMPBIAS 72..88
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 116..130
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 136..174
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 175..190
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 191..218
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 243..258
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 266..305
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 329..353
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 700..715
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q92541"
FT MOD_RES 60
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q92541"
FT MOD_RES 631
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q92541"
FT MOD_RES 660
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q92541"
FT MOD_RES 702
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q92541"
SQ SEQUENCE 715 AA; 80797 MW; CC1E4523DB00008C CRC64;
MRGRLCVGRA AAVAAAVAAA AVAVPLAGGQ EGSQGGVRRG SRGTTMVKKR KGRVVIDSDT
EDSGSDENLD QELLSLAKRK RSDSEEKEPP VSQPAASSDS ETSDSDDEWT FGSNKNKKKG
KTRKVEKKGA MKKQANKAAS SGSSDRDSSA ESSAPEEGEV SDSESSSSSS SSDSDSSSED
EEFHDGYGED LMGDEEDRAR LEQMTEKERE QELFNRIEKR EVLKRRFEIK KKLKTAKKKE
KKEKKKKQEE EQEKKKLTQI QESQVTSHNK ERRSKRDEKL DKKSQAMEEL KAEREKRKNR
TAELLAKKQP LKTSEVYSDD EEEEDDDKSS EKSDRSSRTS SSDEEEEKEE IPPKSQPVSL
PEELNRVRLS RHKLERWCHM PFFAKTVTGC FVRIGIGNHN SKPVYRVAEI TGVVETAKVY
QLGGTRTNKG LQLRHGNDQR VFRLEFVSNQ EFTESEFMKW KEAMFSAGMQ LPTLDEINKK
ELSIKEALNY KFNDQDIEEI VKEKERFRKA PPNYAMKKTQ LLKEKAMAED LGDQDKAKQI
QDQLNELEER AEALDRQRTK NISAISYINQ RNREWNIVES EKALVAESHN MRNQQMDPFT
RRQCKPTIVS NSRDPAVQAA ILAQLNAKYG SGVLPDAPKE MSKGQGKDKD LNSKTASDLS
EDLFKVHDFD VKIDLQVPSS ESKALAITSK APPAKDGAPR RSLNLEDYKK RRGLI
