RTRAF_HUMAN
ID RTRAF_HUMAN Reviewed; 244 AA.
AC Q9Y224;
DT 03-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=RNA transcription, translation and transport factor protein {ECO:0000312|HGNC:HGNC:23169};
DE AltName: Full=CLE7 homolog;
DE Short=CLE;
DE Short=hCLE {ECO:0000303|PubMed:26864902};
GN Name=RTRAF {ECO:0000312|HGNC:HGNC:23169};
GN Synonyms=C14orf166 {ECO:0000312|HGNC:HGNC:23169}; ORFNames=CGI-99;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Pituitary;
RA Song H., Peng Y., Dai M., Huang Q., Mao Y., Zhang Q., Mao M., Fu G.,
RA Luo M., Chen J., Hu R.;
RL Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=10810093; DOI=10.1101/gr.10.5.703;
RA Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.;
RT "Identification of novel human genes evolutionarily conserved in
RT Caenorhabditis elegans by comparative proteomics.";
RL Genome Res. 10:703-713(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Muscle;
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 [4]
RP INTERACTION WITH INFLUENZA A VIRUS PA (MICROBIAL INFECTION).
RX PubMed=11507205; DOI=10.1128/jvi.75.18.8597-8604.2001;
RA Huarte M., Sanz-Ezquerro J.J., Roncal F., Ortin J., Nieto A.;
RT "PA subunit from influenza virus polymerase complex interacts with a
RT cellular protein with homology to a family of transcriptional activators.";
RL J. Virol. 75:8597-8604(2001).
RN [5]
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INTERACTION WITH NIN.
RX PubMed=15147888; DOI=10.1016/j.febslet.2004.04.024;
RA Howng S.-L., Hsu H.-C., Cheng T.-S., Lee Y.-L., Chang L.-K., Lu P.-J.,
RA Hong Y.-R.;
RT "A novel ninein-interaction protein, CGI-99, blocks ninein phosphorylation
RT by GSK3beta and is highly expressed in brain tumors.";
RL FEBS Lett. 566:162-168(2004).
RN [6]
RP FUNCTION, AND INTERACTION WITH POLR2A.
RX PubMed=16950395; DOI=10.1016/j.jmb.2006.07.085;
RA Perez-Gonzalez A., Rodriguez A., Huarte M., Salanueva I.J., Nieto A.;
RT "hCLE/CGI-99, a human protein that interacts with the influenza virus
RT polymerase, is a mRNA transcription modulator.";
RL J. Mol. Biol. 362:887-900(2006).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-20; LYS-62 AND LYS-98, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [9]
RP INTERACTION WITH HEPATITIS C VIRUS CORE PROTEIN P19 (MICROBIAL INFECTION).
RX PubMed=21823664; DOI=10.1021/pr200338d;
RA Lee J.W., Liao P.C., Young K.C., Chang C.L., Chen S.S., Chang T.T.,
RA Lai M.D., Wang S.W.;
RT "Identification of hnRNPH1, NF45, and C14orf166 as novel host interacting
RT partners of the mature hepatitis C virus core protein.";
RL J. Proteome Res. 10:4522-4534(2011).
RN [10]
RP FUNCTION (MICROBIAL INFECTION), AND INTERACTION WITH INFLUENZA VIRUS PA;
RP PB1; PB2 AND NP (MICROBIAL INFECTION).
RX PubMed=21900157; DOI=10.1128/jvi.00684-11;
RA Rodriguez A., Perez-Gonzalez A., Nieto A.;
RT "Cellular human CLE/C14orf166 protein interacts with influenza virus
RT polymerase and is required for viral replication.";
RL J. Virol. 85:12062-12066(2011).
RN [11]
RP IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX.
RX PubMed=21311021; DOI=10.1126/science.1197847;
RA Popow J., Englert M., Weitzer S., Schleiffer A., Mierzwa B., Mechtler K.,
RA Trowitzsch S., Will C.L., Luhrmann R., Soll D., Martinez J.;
RT "HSPC117 is the essential subunit of a human tRNA splicing ligase
RT complex.";
RL Science 331:760-764(2011).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [13]
RP FUNCTION, AND IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX.
RX PubMed=24870230; DOI=10.1038/nature13284;
RA Popow J., Jurkin J., Schleiffer A., Martinez J.;
RT "Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing
RT factors.";
RL Nature 511:104-107(2014).
RN [14]
RP SUBCELLULAR LOCATION, SUBUNIT, INTERACTION WITH FAM98B; DDX1 AND RTCB,
RP RNA-BINDING, AND FUNCTION.
RX PubMed=24608264; DOI=10.1371/journal.pone.0090957;
RA Perez-Gonzalez A., Pazo A., Navajas R., Ciordia S., Rodriguez-Frandsen A.,
RA Nieto A.;
RT "hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel
RT transcription-dependent shuttling RNA-transporting complex.";
RL PLoS ONE 9:E90957-E90957(2014).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [16]
RP ASSOCIATION WITH INFLUENZA A VIRUS RNP AND RNA POLYMERASE SUBUNITS
RP (MICROBIAL INFECTION), SUBCELLULAR LOCATION (MICROBIAL INFECTION), AND
RP INDUCTION (MICROBIAL INFECTION).
RX PubMed=26864902; DOI=10.1038/srep20744;
RA Rodriguez-Frandsen A., de Lucas S., Perez-Gonzalez A., Perez-Cidoncha M.,
RA Roldan-Gomendio A., Pazo A., Marcos-Villar L., Landeras-Bueno S., Ortin J.,
RA Nieto A.;
RT "hCLE/C14orf166, a cellular protein required for viral replication, is
RT incorporated into influenza virus particles.";
RL Sci. Rep. 6:20744-20744(2016).
RN [17]
RP INTERACTION WITH FAM98A, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=28040436; DOI=10.1016/j.biocel.2016.12.013;
RA Akter K.A., Mansour M.A., Hyodo T., Senga T.;
RT "FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved
RT in colorectal cancer progression.";
RL Int. J. Biochem. Cell Biol. 84:1-13(2017).
CC -!- FUNCTION: RNA-binding protein involved in modulation of mRNA
CC transcription by Polymerase II (PubMed:16950395). Component of the
CC tRNA-splicing ligase complex and is required for tRNA ligation
CC (PubMed:24870230). May be required for RNA transport (PubMed:24608264).
CC {ECO:0000269|PubMed:16950395, ECO:0000269|PubMed:24608264,
CC ECO:0000269|PubMed:24870230}.
CC -!- FUNCTION: (Microbial infection) In case of infection by influenza virus
CC A (IVA), is involved in viral replication (PubMed:21900157).
CC {ECO:0000269|PubMed:21900157}.
CC -!- SUBUNIT: Homodimer (Probable). Interacts with FAM98A (via N- and C-
CC terminus) (PubMed:28040436). Interacts with NIN; which may prevent
CC phosphorylation of NIN (PubMed:15147888). Interacts with POLR2A
CC (PubMed:16950395). Component of a tRNA-splicing ligase complex with
CC FAM98B, DDX1 and RTCB (PubMed:21311021, PubMed:24870230,
CC PubMed:24608264). {ECO:0000269|PubMed:15147888,
CC ECO:0000269|PubMed:16950395, ECO:0000269|PubMed:21311021,
CC ECO:0000269|PubMed:24608264, ECO:0000269|PubMed:24870230,
CC ECO:0000269|PubMed:28040436, ECO:0000305|PubMed:24608264}.
CC -!- SUBUNIT: (Microbial infection) Interacts with influenza A virus (IAV)
CC RNA polymerase subunits PA, PB1 and PB2, and nucleocapsid NP
CC (PubMed:21900157, PubMed:26864902). Associates with IAV polymerase
CC complexes both in the nucleus and cytosol (PubMed:26864902). Associates
CC with IAV ribonucleoproteins (vRNP) packaged in virions
CC (PubMed:26864902). Interacts with hepatitis C virus core protein p19
CC (PubMed:21823664). {ECO:0000269|PubMed:21823664,
CC ECO:0000269|PubMed:21900157, ECO:0000269|PubMed:26864902}.
CC -!- INTERACTION:
CC Q9Y224; Q92499: DDX1; NbExp=3; IntAct=EBI-1104547, EBI-358474;
CC Q9Y224; Q8NCA5: FAM98A; NbExp=7; IntAct=EBI-1104547, EBI-1210765;
CC Q9Y224; Q52LJ0: FAM98B; NbExp=2; IntAct=EBI-1104547, EBI-1043130;
CC Q9Y224; Q8N4C6: NIN; NbExp=4; IntAct=EBI-1104547, EBI-1164022;
CC Q9Y224; Q9UIG4: PSORS1C2; NbExp=3; IntAct=EBI-1104547, EBI-11974061;
CC Q9Y224; Q9Y3I0: RTCB; NbExp=4; IntAct=EBI-1104547, EBI-2107208;
CC Q9Y224; Q9Y224: RTRAF; NbExp=5; IntAct=EBI-1104547, EBI-1104547;
CC Q9Y224; P31343: PA; Xeno; NbExp=4; IntAct=EBI-1104547, EBI-5800362;
CC Q9Y224; Q67020: PA; Xeno; NbExp=3; IntAct=EBI-1104547, EBI-11514477;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15147888,
CC ECO:0000269|PubMed:24608264}. Cytoplasm, cytosol
CC {ECO:0000269|PubMed:15147888, ECO:0000269|PubMed:24608264}. Cytoplasm,
CC perinuclear region {ECO:0000269|PubMed:15147888}. Cytoplasm,
CC cytoskeleton, microtubule organizing center, centrosome
CC {ECO:0000269|PubMed:15147888}. Note=May localize at the centrosome
CC during mitosis (PubMed:15147888). Shuttles between the cytosol and the
CC nucleus: enters into the nucleus in case of active transcription while
CC it accumulates in cytosol when transcription level is low
CC (PubMed:24608264). {ECO:0000269|PubMed:15147888,
CC ECO:0000269|PubMed:24608264}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:26864902}. Cytoplasm
CC {ECO:0000269|PubMed:26864902}. Note=(Microbial infection) Following
CC influenza A virus (IAV) infection, included in influenza A virions via
CC its association with packaged viral ribonucleoproteins (vRNP) in the
CC nucleus and cytoplasm (PubMed:21900157, PubMed:26864902).
CC {ECO:0000269|PubMed:21900157, ECO:0000269|PubMed:26864902}.
CC -!- TISSUE SPECIFICITY: Widely expressed. Expressed at high level in heart
CC and skeletal muscle. Expressed at intermediate level in liver,
CC pancreas, fetal brain and fetal lung. Weakly expressed in adult brain,
CC adult lung, placenta, fetal liver and fetal kidney. Overexpressed in
CC many brain tumors. {ECO:0000269|PubMed:15147888}.
CC -!- INDUCTION: (Microbial infection) Up-regulated specifically following
CC influenza A virus (IAV) infection in a viral replication-dependent
CC manner (at protein level) (PubMed:26864902).
CC {ECO:0000269|PubMed:26864902}.
CC -!- SIMILARITY: Belongs to the RTRAF family. {ECO:0000305}.
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DR EMBL; AF100755; AAD43019.1; -; mRNA.
DR EMBL; AF151857; AAD34094.1; -; mRNA.
DR EMBL; BC001722; AAH01722.1; -; mRNA.
DR CCDS; CCDS9705.1; -.
DR RefSeq; NP_057123.1; NM_016039.2.
DR PDB; 7P3A; X-ray; 2.00 A; A/B=2-101.
DR PDBsum; 7P3A; -.
DR AlphaFoldDB; Q9Y224; -.
DR SMR; Q9Y224; -.
DR BioGRID; 119650; 170.
DR ComplexPortal; CPX-6411; tRNA-splicing ligase complex.
DR CORUM; Q9Y224; -.
DR IntAct; Q9Y224; 89.
DR MINT; Q9Y224; -.
DR STRING; 9606.ENSP00000261700; -.
DR GlyGen; Q9Y224; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q9Y224; -.
DR MetOSite; Q9Y224; -.
DR PhosphoSitePlus; Q9Y224; -.
DR SwissPalm; Q9Y224; -.
DR BioMuta; RTRAF; -.
DR DMDM; 20138086; -.
DR REPRODUCTION-2DPAGE; Q9Y224; -.
DR EPD; Q9Y224; -.
DR jPOST; Q9Y224; -.
DR MassIVE; Q9Y224; -.
DR MaxQB; Q9Y224; -.
DR PaxDb; Q9Y224; -.
DR PeptideAtlas; Q9Y224; -.
DR PRIDE; Q9Y224; -.
DR ProteomicsDB; 85609; -.
DR TopDownProteomics; Q9Y224; -.
DR Antibodypedia; 10723; 317 antibodies from 27 providers.
DR DNASU; 51637; -.
DR Ensembl; ENST00000261700.8; ENSP00000261700.3; ENSG00000087302.9.
DR GeneID; 51637; -.
DR KEGG; hsa:51637; -.
DR MANE-Select; ENST00000261700.8; ENSP00000261700.3; NM_016039.3; NP_057123.1.
DR UCSC; uc010aod.4; human.
DR CTD; 51637; -.
DR DisGeNET; 51637; -.
DR GeneCards; RTRAF; -.
DR HGNC; HGNC:23169; RTRAF.
DR HPA; ENSG00000087302; Low tissue specificity.
DR MIM; 610858; gene.
DR neXtProt; NX_Q9Y224; -.
DR OpenTargets; ENSG00000087302; -.
DR PharmGKB; PA134953268; -.
DR VEuPathDB; HostDB:ENSG00000087302; -.
DR eggNOG; KOG4380; Eukaryota.
DR GeneTree; ENSGT00390000005163; -.
DR HOGENOM; CLU_075085_0_0_1; -.
DR InParanoid; Q9Y224; -.
DR OMA; NRKEFAS; -.
DR OrthoDB; 1239557at2759; -.
DR PhylomeDB; Q9Y224; -.
DR TreeFam; TF323606; -.
DR BioCyc; MetaCyc:ENSG00000087302-MON; -.
DR PathwayCommons; Q9Y224; -.
DR Reactome; R-HSA-6784531; tRNA processing in the nucleus.
DR SignaLink; Q9Y224; -.
DR BioGRID-ORCS; 51637; 444 hits in 1051 CRISPR screens.
DR ChiTaRS; C14orf166; human.
DR GeneWiki; C14orf166; -.
DR GenomeRNAi; 51637; -.
DR Pharos; Q9Y224; Tbio.
DR PRO; PR:Q9Y224; -.
DR Proteomes; UP000005640; Chromosome 14.
DR RNAct; Q9Y224; protein.
DR Bgee; ENSG00000087302; Expressed in secondary oocyte and 200 other tissues.
DR ExpressionAtlas; Q9Y224; baseline and differential.
DR Genevisible; Q9Y224; HS.
DR GO; GO:0005813; C:centrosome; IDA:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0072686; C:mitotic spindle; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IDA:UniProtKB.
DR GO; GO:0006469; P:negative regulation of protein kinase activity; IMP:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:UniProtKB.
DR GO; GO:0050658; P:RNA transport; TAS:UniProtKB.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IMP:UniProtKB.
DR InterPro; IPR019265; RTRAF.
DR PANTHER; PTHR15924; PTHR15924; 1.
DR Pfam; PF10036; RLL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Cytoskeleton; Host-virus interaction;
KW Nucleus; Reference proteome; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..244
FT /note="RNA transcription, translation and transport factor
FT protein"
FT /id="PRO_0000089956"
FT MOD_RES 20
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 62
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT MOD_RES 98
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:19608861"
FT HELIX 2..11
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 15..35
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 42..45
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 56..66
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 76..91
FT /evidence="ECO:0007829|PDB:7P3A"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:7P3A"
SQ SEQUENCE 244 AA; 28068 MW; EB2C3C5577A09A2A CRC64;
MFRRKLTALD YHNPAGFNCK DETEFRNFIV WLEDQKIRHY KIEDRGNLRN IHSSDWPKFF
EKYLRDVNCP FKIQDRQEAI DWLLGLAVRL EYGDNAEKYK DLVPDNSKTA DNATKNAEPL
INLDVNNPDF KAGVMALANL LQIQRHDDYL VMLKAIRILV QERLTQDAVA KANQTKEGLP
VALDKHILGF DTGDAVLNEA AQILRLLHIE ELRELQTKIN EAIVAVQAII ADPKTDHRLG
KVGR
