REN3B_DANRE
ID REN3B_DANRE Reviewed; 467 AA.
AC F1QNX7; A0A2R8QRF9; Q7SXF0;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 66.
DE RecName: Full=Regulator of nonsense transcripts 3B {ECO:0000250|UniProtKB:Q9BZI7};
DE AltName: Full=UPF3B regulator of nonsense mediated mRNA decay {ECO:0000312|ZFIN:ZDB-GENE-040426-1630};
DE AltName: Full=Up-frameshift suppressor 3 homolog B {ECO:0000250|UniProtKB:P48412};
GN Name=upf3b {ECO:0000312|ZFIN:ZDB-GENE-040426-1630};
GN Synonyms=rent3b {ECO:0000250|UniProtKB:Q9BZI7};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|Proteomes:UP000000437};
RN [1] {ECO:0000312|EMBL:CAX18773.1}
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=19414594; DOI=10.1128/mcb.00177-09;
RA Wittkopp N., Huntzinger E., Weiler C., Sauliere J., Schmidt S.,
RA Sonawane M., Izaurralde E.;
RT "Nonsense-mediated mRNA decay effectors are essential for zebrafish
RT embryonic development and survival.";
RL Mol. Cell. Biol. 29:3517-3528(2009).
RN [2] {ECO:0000312|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000312|Proteomes:UP000000437};
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3] {ECO:0000312|EMBL:AAH55632.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo {ECO:0000312|EMBL:AAH55632.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing
CC premature stop codons by associating with the nuclear exon junction
CC complex (EJC) and serving as link between the EJC core and NMD
CC machinery. Recruits UPF2 at the cytoplasmic side of the nuclear
CC envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance
CC complex (including UPF1 bound to release factors at the stalled
CC ribosome) is believed to activate NMD. In cooperation with UPF2
CC stimulates both ATPase and RNA helicase activities of UPF1. Binds
CC spliced mRNA upstream of exon-exon junctions.
CC {ECO:0000250|UniProtKB:Q9BZI7}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9BZI7}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q9BZI7}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F1QNX7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F1QNX7-2; Sequence=VSP_061248;
CC -!- DEVELOPMENTAL STAGE: Expressed during early cleavage, gastrulation and
CC at 1 day post-fertilization. {ECO:0000269|PubMed:19414594}.
CC -!- SIMILARITY: Belongs to the RENT3 family.
CC {ECO:0000250|UniProtKB:Q9BZI7}.
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DR EMBL; FM986820; CAX18773.1; -; mRNA.
DR EMBL; BX571981; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC055632; AAH55632.1; -; mRNA.
DR RefSeq; NP_957248.1; NM_200954.1.
DR AlphaFoldDB; F1QNX7; -.
DR SMR; F1QNX7; -.
DR STRING; 7955.ENSDARP00000011948; -.
DR PaxDb; F1QNX7; -.
DR Ensembl; ENSDART00000010019; ENSDARP00000011948; ENSDARG00000000489. [F1QNX7-1]
DR Ensembl; ENSDART00000193170; ENSDARP00000155673; ENSDARG00000116719. [F1QNX7-2]
DR GeneID; 393929; -.
DR KEGG; dre:393929; -.
DR CTD; 65109; -.
DR ZFIN; ZDB-GENE-040426-1630; upf3b.
DR eggNOG; KOG1295; Eukaryota.
DR GeneTree; ENSGT00390000017146; -.
DR HOGENOM; CLU_041202_1_0_1; -.
DR InParanoid; F1QNX7; -.
DR OMA; PPTLEYA; -.
DR OrthoDB; 737663at2759; -.
DR TreeFam; TF316034; -.
DR Reactome; R-DRE-159236; Transport of Mature mRNA derived from an Intron-Containing Transcript.
DR Reactome; R-DRE-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DRE-72187; mRNA 3'-end processing.
DR Reactome; R-DRE-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-DRE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 14.
DR Bgee; ENSDARG00000116719; Expressed in multicellular organism.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IBA:GO_Central.
DR GO; GO:0045727; P:positive regulation of translation; IBA:GO_Central.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR039722; Upf3.
DR InterPro; IPR005120; UPF3_dom.
DR PANTHER; PTHR13112; PTHR13112; 1.
DR Pfam; PF03467; Smg4_UPF3; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cytoplasm; Methylation; Nonsense-mediated mRNA decay;
KW Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..467
FT /note="Regulator of nonsense transcripts 3B"
FT /id="PRO_0000454180"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 197..467
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 197..420
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 449..467
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 76..118
FT /note="FPHLFARAYLNFKNQDDIVLFRDRFDGYVFIDNRGQEYPAIVE -> RTVGN
FT LS (in isoform 2)"
FT /id="VSP_061248"
FT CONFLICT 243
FT /note="F -> S (in Ref. 1; CAX18773 and 3; AAH55632)"
FT /evidence="ECO:0000305"
FT CONFLICT 271
FT /note="T -> A (in Ref. 1; CAX18773 and 3; AAH55632)"
FT /evidence="ECO:0000305"
FT CONFLICT 364
FT /note="N -> T (in Ref. 1; CAX18773 and 3; AAH55632)"
FT /evidence="ECO:0000305"
FT CONFLICT 465
FT /note="A -> G (in Ref. 1; CAX18773 and 3; AAH55632)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 467 AA; 55912 MW; DAE5ECCA00FA6F93 CRC64;
MKEDKENTRP REKKVEIKCD ENDKQEKPCK EKKEAMTKIV IRRLPPTLTK EDLEEQLQPL
PELDYLEFFS SDTSLFPHLF ARAYLNFKNQ DDIVLFRDRF DGYVFIDNRG QEYPAIVEFA
PFQKVAKKRS KKKDAKSGTI DDDADYKKFL EFYNGDEEKS PSNPEILLEE IEAKTKELSS
KKTTPLLDFL KNKQRIREEK KEERRRREIE RKRLREEERR KWREEDRRKR KEAEKLKKVE
KAFEKDKDQH KDEQPKIKLL RKPEKADDGE TEKPKDKPKK QDRERQKEDR PSGGDLKKRQ
NGEHREEKGG KPEDVGHKEY RDRDGERERD RDRERERRQK EKERIRRQDE ERRRRREHQD
GENNYRKREE EGKKDKERVW EKRKNEHTGE SSGSARPEKS SRDSKKEESA RKDRLRNKDR
PAIQLYQPGS RNRTRGGGGG GGTGGDGPAA EKRAEREAKK NQEKAAE
