ID   REN3A_DANRE             Reviewed;         452 AA.
AC   B0S733; Q4VBI8;
DT   05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   05-MAY-2009, sequence version 2.
DT   03-AUG-2022, entry version 90.
DE   RecName: Full=Regulator of nonsense transcripts 3A {ECO:0000250|UniProtKB:Q9H1J1};
DE   AltName: Full=Up-frameshift suppressor 3 homolog A {ECO:0000250|UniProtKB:Q9H1J1};
GN   Name=upf3a {ECO:0000312|ZFIN:ZDB-GENE-060721-2}; ORFNames=si:dkey-21o13.6;
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;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
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   [2] {ECO:0000305, ECO:0000312|EMBL:CAQ15001.1}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-196.
RC   TISSUE=Larval eye {ECO:0000312|EMBL:AAH95761.1};
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (MAY-2005) to the EMBL/GenBank/DDBJ databases.
RN   [3] {ECO:0000305}
RP   IDENTIFICATION (ISOFORM 2).
RX   PubMed=16601204; DOI=10.1261/rna.12506;
RA   Kunz J.B., Neu-Yilik G., Hentze M.W., Kulozik A.E., Gehring N.H.;
RT   "Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and
RT   translation.";
RL   RNA 12:1015-1022(2006).
RN   [4]
RP   DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
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).
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. Binds spliced mRNA upstream of
CC       exon-exon junctions (By similarity). {ECO:0000250}.
CC   -!- INTERACTION:
CC       B0S733; Q7ZTX2: wdr5; NbExp=3; IntAct=EBI-21405307, EBI-21405335;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9H1J1}. Cytoplasm
CC       {ECO:0000250|UniProtKB:Q9H1J1}. Note=Shuttling between the nucleus and
CC       the cytoplasm. {ECO:0000250|UniProtKB:Q9H1J1}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=2 {ECO:0000269|PubMed:16601204};
CC         IsoId=B0S733-1; Sequence=Displayed;
CC       Name=1;
CC         IsoId=B0S733-2; Sequence=VSP_053070;
CC   -!- DEVELOPMENTAL STAGE: Expressed during early cleavage, gastrulation and
CC       at 1 day post-fertilization. {ECO:0000269|PubMed:19414594}.
CC   -!- DISRUPTION PHENOTYPE: Morpholino knockdown results in a weakly abnormal
CC       brain patterning during development that does not affect embryo
CC       viability at 5 days post-fertilization. {ECO:0000269|PubMed:19414594}.
CC   -!- SIMILARITY: Belongs to the RENT3 family. {ECO:0000255}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAH95761.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
CC       Sequence=CAQ15001.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; BX601644; CAQ15001.1; ALT_INIT; Genomic_DNA.
DR   EMBL; BC095761; AAH95761.1; ALT_SEQ; mRNA.
DR   RefSeq; NP_001189377.1; NM_001202448.1. [B0S733-2]
DR   RefSeq; XP_005167908.1; XM_005167851.3. [B0S733-1]
DR   RefSeq; XP_017213192.1; XM_017357703.1. [B0S733-2]
DR   AlphaFoldDB; B0S733; -.
DR   SMR; B0S733; -.
DR   IntAct; B0S733; 2.
DR   STRING; 7955.ENSDARP00000114416; -.
DR   Ensembl; ENSDART00000100728; ENSDARP00000091501; ENSDARG00000069297. [B0S733-1]
DR   Ensembl; ENSDART00000123005; ENSDARP00000105134; ENSDARG00000111067. [B0S733-1]
DR   Ensembl; ENSDART00000139608; ENSDARP00000114416; ENSDARG00000069297. [B0S733-2]
DR   GeneID; 566608; -.
DR   KEGG; dre:566608; -.
DR   CTD; 65110; -.
DR   ZFIN; ZDB-GENE-060721-2; upf3a.
DR   eggNOG; KOG1295; Eukaryota.
DR   GeneTree; ENSGT00390000017146; -.
DR   InParanoid; B0S733; -.
DR   OrthoDB; 737663at2759; -.
DR   PhylomeDB; B0S733; -.
DR   TreeFam; TF316034; -.
DR   Reactome; R-DRE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR   PRO; PR:B0S733; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 9.
DR   Bgee; ENSDARG00000069297; Expressed in brain and 6 other tissues.
DR   ExpressionAtlas; B0S733; baseline.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR   GO; GO:0032991; C:protein-containing complex; IPI:ZFIN.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0042162; F:telomeric DNA binding; IBA:GO_Central.
DR   GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR   GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
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   InterPro; IPR034978; UPF3A.
DR   PANTHER; PTHR13112; PTHR13112; 1.
DR   PANTHER; PTHR13112:SF2; PTHR13112:SF2; 1.
DR   Pfam; PF03467; Smg4_UPF3; 1.
DR   SUPFAM; SSF54928; SSF54928; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Cytoplasm; mRNA transport;
KW   Nonsense-mediated mRNA decay; Nucleus; Reference proteome; RNA-binding;
KW   Transport.
FT   CHAIN           1..452
FT                   /note="Regulator of nonsense transcripts 3A"
FT                   /id="PRO_0000370745"
FT   REGION          205..452
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        205..400
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   VAR_SEQ         397
FT                   /note="N -> NKSVLVHQEKRTSQSEGPDQIGGALPA (in isoform 1)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_053070"
SQ   SEQUENCE   452 AA;  54096 MW;  14118036565D09D8 CRC64;
     MRSEKEQRTG SRERGSVEIQ FRDCQDNAAV NPKHKEEKKE IFSKVVIRRL PPSLSKDQLQ
     EHLSPLPSFD YFEFFPADQS LYPHLFSRAY INFKNPEDII IFRDRFDGYV FIDNKGQEYP
     AVVEFAPFQK VSKKKLKKKD AKAGTIEEDP EYRRFLENYS CDEEKSMANP ETLLGEIEAK
     TRELIAKRTT PLLEYIKNKK LEKQRIREEK REERRRRELE KKRQREEEKR KRREEERQKR
     KEAEKQKKLS EKEIKIKLLK KCDRDDDVDS DRLKDKGDSG ETEKNRWEKP GGHTKSKDSK
     DNRSQMENDK EQREGHGRRQ RDKDHRGRDE ERKRQRHHYE FDKFMRRKEE TKWGKGYCQD
     RAKKDQHHGY SYCPETGDKL GKEDREDMGS RKERIRNKDR PAMQLYQPGA RNRKRMGSGN
     KTFDFPPISP EHAGEHCYKT VIGTGSEKSA DE