ILF3_RAT
ID ILF3_RAT Reviewed; 897 AA.
AC Q9JIL3;
DT 31-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 12-APR-2005, sequence version 2.
DT 25-MAY-2022, entry version 153.
DE RecName: Full=Interleukin enhancer-binding factor 3;
GN Name=Ilf3;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RX PubMed=10749851; DOI=10.1074/jbc.m000023200;
RA Tang J., Kao P.N., Herschman H.R.;
RT "Protein-arginine methyltransferase I, the predominant protein-arginine
RT methyltransferase in cells, interacts with and is regulated by interleukin
RT enhancer-binding factor 3.";
RL J. Biol. Chem. 275:19866-19876(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (ISOFORM 1).
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-67; SER-382; SER-476;
RP SER-477; SER-482 AND SER-486, AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: RNA-binding protein that plays an essential role in the
CC biogenesis of circular RNAs (circRNAs) which are produced by back-
CC splicing circularization of pre-mRNAs. Within the nucleus, promotes
CC circRNAs processing by stabilizing the regulatory elements residing in
CC the flanking introns of the circularized exons. Plays thereby a role in
CC the back-splicing of a subset of circRNAs. As a consequence,
CC participates in a wide range of transcriptional and post-
CC transcriptional processes. Binds to poly-U elements and AU-rich
CC elements (AREs) in the 3'-UTR of target mRNAs (By similarity). Upon
CC viral infection, ILF3 accumulates in the cytoplasm and participates in
CC the innate antiviral response. Mechanistically, ILF3 becomes
CC phosphorylated and activated by the double-stranded RNA-activated
CC protein kinase/PKR which releases ILF3 from cellular mature circRNAs.
CC In turn, unbound ILF3 molecules are able to interact with and thus
CC inhibit viral mRNAs. {ECO:0000250|UniProtKB:Q12906}.
CC -!- SUBUNIT: Identified in a IGF2BP1-dependent mRNP granule complex
CC containing untranslated mRNAs. Interacts with FUS and SMN. Interacts
CC (via C-terminus) with PRMT1. Forms a complex with ILF2. Can also bind
CC to PRKDC/XRCC7: this may stabilize the interaction of PRKDC/XRCC7 and
CC the heterodimeric complex of XRCC6/KU70 and XRCC5/KU80. Forms a
CC heteromeric complex with ZNF346 and ILF3. Found in a nuclear export
CC complex with XPO5, ILF3, Ran and double-stranded RNA or double-stranded
CC minihelix VA1 RNA. Found in a nuclear export complex with XPO5, RAN,
CC ILF3, ZNF346 and double-stranded RNA. Interacts with XPO5 and ZNF346.
CC Forms a complex with ILF2, YLPM1, KHDRBS1, RBMX, NCOA5 and PPP1CA.
CC Interacts with AGO1 and AGO2. Interacts with DHX36; this interaction
CC occurs in a RNA-dependent manner. Interacts with ELAVL1; this
CC interaction occurs in a RNA-dependent manner. Interacts with HAVCR2;
CC this interaction promotes ILF3 ubiquitination and subsequent
CC degradation (By similarity). {ECO:0000250|UniProtKB:Q12906}.
CC -!- INTERACTION:
CC Q9JIL3; Q63009: Prmt1; NbExp=2; IntAct=EBI-78714, EBI-78708;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q12906}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q12906}. Nucleus {ECO:0000250|UniProtKB:Q12906}.
CC Note=Localizes in the cytoplasm in response to viral infection. The
CC unphosphorylated form is retained in the nucleus by ILF2.
CC Phosphorylation at Thr-188 and Thr-315 causes the dissociation of ILF2
CC from the ILF2-ILF3 complex resulting in a cytoplasmic sequestration of
CC ILF3. Localized in cytoplasmic mRNP granules containing untranslated
CC mRNAs. {ECO:0000250|UniProtKB:Q12906}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9JIL3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9JIL3-2; Sequence=VSP_013409;
CC -!- PTM: Phosphorylated at Thr-188 and Thr-315 by PKR in response to RNA
CC viruses. This phosphorylation results in the dissociation of ILF2 from
CC the ILF2-ILF3 complex resulting in a cytoplasmic sequestration of ILF3
CC where it can bind to viral RNAs and impede viral replication.
CC {ECO:0000250|UniProtKB:Q12906}.
CC -!- PTM: Methylated by protein arginine N-methyltransferase 1.
CC {ECO:0000250|UniProtKB:Q12906}.
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DR EMBL; AF220102; AAF31446.1; -; mRNA.
DR EMBL; AABR03063190; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03065470; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_445864.1; NM_053412.1. [Q9JIL3-2]
DR AlphaFoldDB; Q9JIL3; -.
DR SMR; Q9JIL3; -.
DR BioGRID; 249972; 3.
DR CORUM; Q9JIL3; -.
DR IntAct; Q9JIL3; 2.
DR STRING; 10116.ENSRNOP00000009354; -.
DR iPTMnet; Q9JIL3; -.
DR PhosphoSitePlus; Q9JIL3; -.
DR jPOST; Q9JIL3; -.
DR PaxDb; Q9JIL3; -.
DR PRIDE; Q9JIL3; -.
DR GeneID; 84472; -.
DR KEGG; rno:84472; -.
DR UCSC; RGD:619734; rat. [Q9JIL3-1]
DR CTD; 3609; -.
DR RGD; 619734; Ilf3.
DR eggNOG; KOG3792; Eukaryota.
DR InParanoid; Q9JIL3; -.
DR OrthoDB; 612611at2759; -.
DR PhylomeDB; Q9JIL3; -.
DR PRO; PR:Q9JIL3; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; ISO:RGD.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; TAS:RGD.
DR GO; GO:0003725; F:double-stranded RNA binding; ISO:RGD.
DR GO; GO:0019899; F:enzyme binding; IPI:RGD.
DR GO; GO:0035925; F:mRNA 3'-UTR AU-rich region binding; ISS:UniProtKB.
DR GO; GO:0003727; F:single-stranded RNA binding; IBA:GO_Central.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0017148; P:negative regulation of translation; ISS:UniProtKB.
DR GO; GO:0045071; P:negative regulation of viral genome replication; ISS:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0006479; P:protein methylation; IDA:MGI.
DR GO; GO:0006468; P:protein phosphorylation; ISS:UniProtKB.
DR Gene3D; 3.30.460.10; -; 2.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR006561; DZF_dom.
DR InterPro; IPR033099; ILF3/NF90.
DR InterPro; IPR043519; NT_sf.
DR PANTHER; PTHR45762:SF4; PTHR45762:SF4; 3.
DR Pfam; PF00035; dsrm; 2.
DR Pfam; PF07528; DZF; 1.
DR SMART; SM00358; DSRM; 2.
DR SMART; SM00572; DZF; 1.
DR PROSITE; PS50137; DS_RBD; 2.
DR PROSITE; PS51703; DZF; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Antiviral defense; Cytoplasm;
KW DNA-binding; Isopeptide bond; Methylation; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; RNA-binding; Transcription;
KW Transcription regulation; Ubl conjugation.
FT CHAIN 1..897
FT /note="Interleukin enhancer-binding factor 3"
FT /id="PRO_0000126072"
FT DOMAIN 5..378
FT /note="DZF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01040"
FT DOMAIN 398..467
FT /note="DRBM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 524..590
FT /note="DRBM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 52..85
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 363..401
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 466..524
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 609..897
FT /note="Interaction with PRMT1"
FT REGION 624..662
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 720..897
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 371..389
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 67..85
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 372..399
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 504..521
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 741..897
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 67
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 100
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 188
FT /note="Phosphothreonine; by PKR"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 190
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 315
FT /note="Phosphothreonine; by PKR"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 382
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 384
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 460
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 476
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 477
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 482
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 486
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 794
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 812
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 814
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT MOD_RES 818
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT CROSSLNK 297
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT CROSSLNK 348
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO1)"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT CROSSLNK 396
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT CROSSLNK 489
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q12906"
FT VAR_SEQ 1
FT /note="M -> MALYHHHFITRRRR (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:10749851"
FT /id="VSP_013409"
SQ SEQUENCE 897 AA; 95935 MW; ACD800D1858539BB CRC64;
MRPMRIFVND DRHVMAKHSS VYPTQEELEA VQNMVSHTER ALKAVSDWID EQEKGNSELS
EAENMDTPPD DESKEGAGEQ KAEHMTRTLR GVMRVGLVAK GLLLKGDLDL ELVLLCKEKP
TTALLDKVAD NLAIQLTTVT EDKYEILQSV DDAAIVIKNT KEPPLSLTIH LTSPVVREEM
EKVLAGETLS VNDPPDVLDR QKCLAALASL RHAKWFQARA NGLKSCVIVI RVLRDLCTRV
PTWGPLRGWP LELLCEKSIG TANRPMGAGE ALRRVLECLA SGIVMPDGSG IYDPCEKEAT
DAIGHLDRQQ REDITQSAQH ALRLAAFGQL HKVLGMDPLP SKMPKKPKNE NPVDYTVQIP
PSTTYAITPM KRPMEEDGEE KSPSKKKKKI QKKEEKAEPP QAMNALMRLN QLKPGLQYKL
ISQTGPVHAP IFTMSVEVDG STFEASGPSK KTAKLHVAVK VLQDMGLPTG AEGRDSSKGE
DSAEESDGKP AVVAPPPVVE AVSNPSSVFP SDATTEQGPI LTKHGKNPVM ELNEKRRGLK
YELISETGGS HDKRFVMEVE VDGQKFQGAG SNKKVAKAYA ALAALEKLFP DAPLALEANK
KKRAPVPVRG GPKFAAKPHN PGFGMGGPMH NEAPPPPNIR GRGRGGNIRG RGRGRGFGGT
NHGGGYMNAG AGYGSYGYSS NSATAGYSQF YSNGGHYGNA GGGGSGGGGG SSSYSSYYQG
DSYNSPVPPK HAGKKPLHGG QQKPSYSSGY QSHQGQQQPY NQSQYSSYGT PQGKQKGYGH
GQGSYSSYSN SYNSPGGGGG SDYSYDSKFN YSGSGGRSGG NSYGSSGSSY NTGSHGGYGA
GSGGSSSYQG KQGGYSSQSN YSSPGSSQSY SGPASSYQSS QGGYSRNTEH SMNYQYR
