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   24-JAN-2024, entry version 159.
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.
DR   AlphaFoldDB; Q9JIL3; -.
DR   SMR; Q9JIL3; -.
DR   BioGRID; 249972; 3.
DR   CORUM; Q9JIL3; -.
DR   IntAct; Q9JIL3; 2.
DR   STRING; 10116.ENSRNOP00000073179; -.
DR   iPTMnet; Q9JIL3; -.
DR   PhosphoSitePlus; Q9JIL3; -.
DR   jPOST; Q9JIL3; -.
DR   PaxDb; 10116-ENSRNOP00000009354; -.
DR   GeneID; 84472; -.
DR   KEGG; rno:84472; -.
DR   UCSC; RGD:619734; rat. [Q9JIL3-1]
DR   AGR; RGD:619734; -.
DR   CTD; 3609; -.
DR   RGD; 619734; Ilf3.
DR   eggNOG; KOG3792; Eukaryota.
DR   InParanoid; Q9JIL3; -.
DR   OrthoDB; 4565640at2759; -.
DR   PhylomeDB; Q9JIL3; -.
DR   Reactome; R-RNO-9833482; PKR-mediated signaling.
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:0001618; F:virus receptor activity; ISO:RGD.
DR   GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR   GO; GO:0045892; P:negative regulation of DNA-templated transcription; 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 DNA-templated transcription; ISO:RGD.
DR   GO; GO:0006479; P:protein methylation; IDA:MGI.
DR   GO; GO:0006468; P:protein phosphorylation; ISS:UniProtKB.
DR   CDD; cd19910; DSRM_ILF3_rpt1; 1.
DR   CDD; cd19912; DSRM_ILF3_rpt2; 1.
DR   Gene3D; 1.10.1410.40; -; 1.
DR   Gene3D; 3.30.160.20; -; 2.
DR   Gene3D; 3.30.460.10; Beta Polymerase, domain 2; 2.
DR   InterPro; IPR014720; dsRBD_dom.
DR   InterPro; IPR033099; DSRM1_ILF3.
DR   InterPro; IPR006561; DZF_dom.
DR   InterPro; IPR049402; DZF_dom_C.
DR   InterPro; IPR049401; DZF_dom_N.
DR   InterPro; IPR043519; NT_sf.
DR   PANTHER; PTHR45762:SF4; INTERLEUKIN ENHANCER-BINDING FACTOR 3; 1.
DR   PANTHER; PTHR45762; ZINC FINGER RNA-BINDING PROTEIN; 1.
DR   Pfam; PF00035; dsrm; 2.
DR   Pfam; PF20965; DZF_C; 1.
DR   Pfam; PF07528; DZF_N; 1.
DR   SMART; SM00358; DSRM; 2.
DR   SMART; SM00572; DZF; 1.
DR   SUPFAM; SSF54768; dsRNA-binding domain-like; 2.
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
//