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Q92541

- RTF1_HUMAN

UniProt

Q92541 - RTF1_HUMAN

Protein

RNA polymerase-associated protein RTF1 homolog

Gene

RTF1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 112 (01 Oct 2014)
      Sequence version 4 (30 Nov 2010)
      Previous versions | rss
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    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 similarity

    GO - Molecular functioni

    1. poly(A) RNA binding Source: UniProtKB
    2. protein binding Source: IntAct
    3. single-stranded DNA binding Source: UniProtKB

    GO - Biological processi

    1. DNA-templated transcription, initiation Source: InterPro
    2. endodermal cell fate commitment Source: UniProtKB
    3. histone H3-K4 trimethylation Source: Ensembl
    4. negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
    5. positive regulation of histone H3-K4 methylation Source: Ensembl
    6. positive regulation of transcription elongation from RNA polymerase II promoter Source: UniProtKB
    7. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
    8. stem cell maintenance Source: UniProtKB
    9. Wnt signaling pathway Source: UniProtKB-KW

    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
    Synonyms:KIAA0252
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 15

    Organism-specific databases

    HGNCiHGNC:28996. RTF1.

    Subcellular locationi

    Nucleusnucleoplasm By similarity

    GO - Cellular componenti

    1. Cdc73/Paf1 complex Source: UniProtKB
    2. nucleolus Source: Ensembl

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi401 – 4011R → E: Loss of binding to single-stranded DNA. 1 Publication
    Mutagenesisi410 – 4101E → K: Reduced binding to single-stranded DNA. 1 Publication
    Mutagenesisi429 – 4291R → E: Loss of binding to single-stranded DNA. 1 Publication
    Mutagenesisi434 – 4341Q → A: Reduced binding to single-stranded DNA. 1 Publication
    Mutagenesisi435 – 4351R → E: Loss of binding to single-stranded DNA. 1 Publication

    Organism-specific databases

    PharmGKBiPA134961778.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 710710RNA polymerase-associated protein RTF1 homologPRO_0000255936Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei53 – 531Phosphoserine2 Publications
    Modified residuei55 – 551Phosphothreonine1 Publication
    Modified residuei650 – 6501Phosphoserine1 Publication
    Modified residuei697 – 6971Phosphoserine2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ92541.
    PaxDbiQ92541.
    PRIDEiQ92541.

    PTM databases

    PhosphoSiteiQ92541.

    Miscellaneous databases

    PMAP-CutDBQ92541.

    Expressioni

    Gene expression databases

    ArrayExpressiQ92541.
    BgeeiQ92541.
    CleanExiHS_RTF1.
    GenevestigatoriQ92541.

    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

    Protein-protein interaction databases

    BioGridi116780. 28 interactions.
    IntActiQ92541. 15 interactions.
    MINTiMINT-6941890.
    STRINGi9606.ENSP00000374280.

    Structurei

    Secondary structure

    1
    710
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi356 – 3605
    Beta strandi362 – 3643
    Helixi366 – 3727
    Beta strandi373 – 3775
    Helixi378 – 3825
    Beta strandi386 – 3927
    Beta strandi395 – 3973
    Beta strandi399 – 41719
    Beta strandi420 – 43011
    Beta strandi433 – 4386
    Helixi439 – 4413
    Helixi449 – 46214
    Helixi469 – 47810

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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. Positions 353-482.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ92541.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini353 – 484132Plus3PROSITE-ProRule annotationAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili526 – 56035Sequence AnalysisAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi10 – 189Poly-Ala
    Compositional biasi135 – 17339Ser-richAdd
    BLAST
    Compositional biasi174 – 345172Glu-richAdd
    BLAST
    Compositional biasi214 – 30794Lys-richAdd
    BLAST

    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

    eggNOGiCOG5296.
    HOGENOMiHOG000231764.
    HOVERGENiHBG057331.
    InParanoidiQ92541.
    KOiK15178.
    OMAiSNSDDEW.
    OrthoDBiEOG7K0ZC9.
    PhylomeDBiQ92541.
    TreeFamiTF321360.

    Family and domain databases

    InterProiIPR004343. Plus-3.
    IPR018144. Plus3-dom_subgr.
    [Graphical view]
    PfamiPF03126. Plus-3. 1 hit.
    [Graphical view]
    SMARTiSM00719. Plus3. 1 hit.
    [Graphical view]
    PROSITEiPS51360. PLUS3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q92541-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV    50
    IDSDTEDSGS DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS 100
    DDEWTFGSNK NKKKGKARKI EKKGTMKKQA NKTASSGSSD KDSSAESSAP 150
    EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD GYGEDLMGDE EDRARLEQMT 200
    EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK KKQEEEQEKK 250
    KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL 300
    AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS 350
    QPVSLPEELN RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY 400
    RVAEITGVVE TAKVYQLGGT RTNKGLQLRH GNDQRVFRLE FVSNQEFTES 450
    EFMKWKEAMF SAGMQLPTLD EINKKELSIK EALNYKFNDQ DIEEIVKEKE 500
    RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN ELEERAEALD 550
    RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK 600
    PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS 650
    ASDLSEDLFK VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL 700
    EDYKKRRGLI 710
    Length:710
    Mass (Da):80,313
    Last modified:November 30, 2010 - v4
    Checksum:i54CC014655AA22B8
    GO

    Sequence cautioni

    The sequence AAH15052.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence BAA13382.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.

    Polymorphism databases

    DMDMi313104316.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC087721 Genomic DNA. No translation available.
    D87440 mRNA. Translation: BAA13382.2 . Different initiation.
    BC015052 mRNA. Translation: AAH15052.1 . Different initiation.
    CCDSi CCDS32200.2.
    RefSeqi NP_055953.3. NM_015138.4.
    UniGenei Hs.511096.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2BZE NMR - A 353-484 [» ]
    2DB9 NMR - A 347-482 [» ]
    3U1U X-ray 1.80 A/B 347-482 [» ]
    4L1P X-ray 2.12 A/B 353-484 [» ]
    4L1U X-ray 2.42 A/B/C/D/E/F 353-484 [» ]
    ProteinModelPortali Q92541.
    SMRi Q92541. Positions 353-482.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116780. 28 interactions.
    IntActi Q92541. 15 interactions.
    MINTi MINT-6941890.
    STRINGi 9606.ENSP00000374280.

    PTM databases

    PhosphoSitei Q92541.

    Polymorphism databases

    DMDMi 313104316.

    Proteomic databases

    MaxQBi Q92541.
    PaxDbi Q92541.
    PRIDEi Q92541.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000389629 ; ENSP00000374280 ; ENSG00000137815 .
    GeneIDi 23168.
    KEGGi hsa:23168.
    UCSCi uc001zny.3. human.

    Organism-specific databases

    CTDi 23168.
    GeneCardsi GC15P041709.
    H-InvDB HIX0012153.
    HGNCi HGNC:28996. RTF1.
    HPAi HPA006714.
    MIMi 611633. gene.
    neXtProti NX_Q92541.
    PharmGKBi PA134961778.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5296.
    HOGENOMi HOG000231764.
    HOVERGENi HBG057331.
    InParanoidi Q92541.
    KOi K15178.
    OMAi SNSDDEW.
    OrthoDBi EOG7K0ZC9.
    PhylomeDBi Q92541.
    TreeFami TF321360.

    Miscellaneous databases

    ChiTaRSi RTF1. human.
    EvolutionaryTracei Q92541.
    GeneWikii RTF1.
    GenomeRNAii 23168.
    NextBioi 44567.
    PMAP-CutDB Q92541.
    PROi Q92541.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q92541.
    Bgeei Q92541.
    CleanExi HS_RTF1.
    Genevestigatori Q92541.

    Family and domain databases

    InterProi IPR004343. Plus-3.
    IPR018144. Plus3-dom_subgr.
    [Graphical view ]
    Pfami PF03126. Plus-3. 1 hit.
    [Graphical view ]
    SMARTi SM00719. Plus3. 1 hit.
    [Graphical view ]
    PROSITEi PS51360. PLUS3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Analysis of the DNA sequence and duplication history of human chromosome 15."
      Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
      , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
      Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    2. "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain."
      Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O., Tanaka A., Kotani H., Miyajima N., Nomura N.
      DNA Res. 3:321-329(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 9-710.
      Tissue: Brain.
    3. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
      Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
      DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION.
    4. "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 14-710.
      Tissue: Uterus.
    5. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
      Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
      Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    6. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-697, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    7. Cited for: FUNCTION.
    8. "The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS."
      Kim J., Guermah M., Roeder R.G.
      Cell 140:491-503(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE PAF1 COMPLEX, COMPOSITION OF THE PAF1 COMPLEX, FUNCTION OF THE PAF1 COMPLEX.
    9. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53; SER-650 AND SER-697, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-53 AND THR-55, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "Solution structure of the plus-3 domain of human KIAA0252 protein."
      RIKEN structural genomics initiative (RSGI)
      Submitted (JUN-2006) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 347-482.
    13. Cited for: STRUCTURE BY NMR OF 353-484, DOMAIN PLUS3, DNA-BINDING, MUTAGENESIS OF ARG-401; GLU-410; ARG-429; GLN-434 AND ARG-435.

    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: October 1, 2014
    This is version 112 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

    External Data

    Dasty 3