SMG5_DANRE
ID SMG5_DANRE Reviewed; 1099 AA.
AC F1R7R1; Q4V9C7;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=Nonsense-mediated mRNA decay factor SMG5 {ECO:0000312|ZFIN:ZDB-GENE-050913-144};
DE AltName: Full=EST1-like protein B {ECO:0000250|UniProtKB:Q9UPR3};
DE AltName: Full=SMG-5 homolog {ECO:0000250|UniProtKB:Q9UPR3};
GN Name=smg5; Synonyms=est1b {ECO:0000250|UniProtKB:Q9UPR3};
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:CAX32465.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION
RP 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).
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:AAH96955.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Olfactory epithelium {ECO:0000312|EMBL:AAH96955.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Plays a role in nonsense-mediated mRNA decay (By similarity).
CC Does not have RNase activity by itself (By similarity). Promotes
CC dephosphorylation of UPF1 (By similarity). Together with SMG7 is
CC thought to provide a link to the mRNA degradation machinery involving
CC exonucleolytic pathways, and to serve as an adapter for UPF1 to protein
CC phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation (By
CC similarity). Necessary for TERT activity (By similarity). Required for
CC normal embryonic development (PubMed:19414594).
CC {ECO:0000250|UniProtKB:Q9UPR3, ECO:0000269|PubMed:19414594}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9UPR3}. Nucleus
CC {ECO:0000250|UniProtKB:Q9UPR3}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F1R7R1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F1R7R1-2; Sequence=VSP_061250;
CC -!- DEVELOPMENTAL STAGE: Expressed during early cleavage, gastrulation and
CC at 1 day post-fertilization. {ECO:0000269|PubMed:19414594}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown leads to phenotypes ranging
CC in severity from weak to severe that are developmentally delayed with
CC disturbed brain patterning, necrosis in areas of the brain, aberrant
CC eye development, impaired somitogenesis resulting in stacked somites,
CC perturbed yolk sac extension and posterior axis extension with a high
CC mortality rate of 88% at 5 days post-fertilization.
CC {ECO:0000269|PubMed:19414594}.
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DR EMBL; FM993108; CAX32465.1; -; mRNA.
DR EMBL; CR848669; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC096955; AAH96955.1; -; mRNA.
DR RefSeq; NP_001020094.1; NM_001024923.1.
DR AlphaFoldDB; F1R7R1; -.
DR SMR; F1R7R1; -.
DR STRING; 7955.ENSDARP00000060808; -.
DR PaxDb; F1R7R1; -.
DR Ensembl; ENSDART00000060809; ENSDARP00000060808; ENSDARG00000041481. [F1R7R1-1]
DR GeneID; 553261; -.
DR KEGG; dre:553261; -.
DR CTD; 23381; -.
DR ZFIN; ZDB-GENE-050913-144; smg5.
DR eggNOG; KOG2162; Eukaryota.
DR GeneTree; ENSGT00940000154566; -.
DR HOGENOM; CLU_011872_0_0_1; -.
DR InParanoid; F1R7R1; -.
DR OMA; FQIIECC; -.
DR OrthoDB; 184090at2759; -.
DR PhylomeDB; F1R7R1; -.
DR TreeFam; TF327119; -.
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 16.
DR Bgee; ENSDARG00000041481; Expressed in mature ovarian follicle and 22 other tissues.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005697; C:telomerase holoenzyme complex; IBA:GO_Central.
DR GO; GO:0070034; F:telomerase RNA binding; IBA:GO_Central.
DR GO; GO:0042162; F:telomeric DNA binding; IBA:GO_Central.
DR GO; GO:0043009; P:chordate embryonic development; IMP:ZFIN.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IBA:GO_Central.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR018834; DNA/RNA-bd_Est1-type.
DR InterPro; IPR045153; Est1/Ebs1-like.
DR InterPro; IPR019458; Est1_N.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR PANTHER; PTHR15696; PTHR15696; 1.
DR Pfam; PF10374; EST1; 1.
DR Pfam; PF10373; EST1_DNA_bind; 1.
DR Pfam; PF13638; PIN_4; 1.
DR SMART; SM00670; PINc; 1.
DR SUPFAM; SSF48452; SSF48452; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cytoplasm; Nonsense-mediated mRNA decay; Nucleus;
KW Reference proteome.
FT CHAIN 1..1099
FT /note="Nonsense-mediated mRNA decay factor SMG5"
FT /id="PRO_0000454182"
FT DOMAIN 938..1061
FT /note="PINc"
FT /evidence="ECO:0000255"
FT REGION 403..631
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 663..722
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 403..429
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 438..454
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 455..486
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 508..525
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 557..571
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 595..631
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 679..705
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 706..722
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 825..829
FT /note="IAHRR -> VAHRC (in isoform 2)"
FT /id="VSP_061250"
FT CONFLICT 673
FT /note="S -> L (in Ref. 1; CAX32465 and 3; AAH96955)"
FT /evidence="ECO:0000305"
FT CONFLICT 708
FT /note="N -> D (in Ref. 1; CAX32465 and 3; AAH96955)"
FT /evidence="ECO:0000305"
FT CONFLICT 815
FT /note="M -> V (in Ref. 1; CAX32465 and 3; AAH96955)"
FT /evidence="ECO:0000305"
FT CONFLICT 1031
FT /note="M -> T (in Ref. 1; CAX32465 and 3; AAH96955)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1099 AA; 123812 MW; 082F2B8F51C01278 CRC64;
MSGPSQDSEP EAKVLHIKRL YRAVVETVHK LDIIISGKSS YREVFKPENI SLRNKLRELC
VKLMFLHPVD YGRKAEELLW RKVYYEVIQV IKTNKKHIHS RSALECAYRT HLIAGVGFFQ
HLLLYIQSHY QLELQDCIDW THVTDPLIGR KKPVSATSKE MEWAQMACHR CLVYLGDLAR
YQNELAGVEA EQLAERFYHQ ALSVAPHVGM PFNQLGTLAG SKFYNVEATY YYLRCIQSET
PFDGAYGNLK RLFDKASKMY HQVKKQEMKK LSPSRQRSKD IKRLLVSFMY LQSLLQPKNS
LMETELTSLC QSVLEDFNLV LFYLPLPAHG SQSASEEEEE HDSVGSVLPD SLIFKMVVIC
LMVVHSLKRG ASKQYSASIA FTLALFSHLV NHVNIRLQAE LEEGESDVPA LRTDNTDDAD
ARDHSSAALS EERTLQNGSL EEDDDEEEEE KENGEDEPKG NGRTVATKKN QEKKRSAEEK
QKQKRKFSRL SMLRRRRCAH KEDESDLSEG FESDEEEEEE EEGGGGGLVD GLGAPRVQMN
SLGRDTRKGP LPEDGGWESG SEEDEGGTAF DVETDSDMNS QESRSDLEDM EDAENAPQQP
QQEENEQPQT SREENATPPV TNGPSVSNDA SISSNLQAMS SQLFQAKRCF RLAPTFSNVL
LRPATTTPPA PESNPAPVQE ITPPTGETPR NTSPEIANGT NDKDPDSNSE GSEHSNHSFH
SEKTLSERLE ILTNQGLIQV VKVFLDWLRT NTDIILMCAQ SSQSLWNRLS VLLNLLPEGS
KILETDIGLN KDVTELLSEC EHPSLAQTLL LPEDMALRHL PALSIAHRRL DFTSQRPPLT
PLDECVVRVC CIRSFGHFLT NLQGNVLHFN PEAGIFTSIS QSEQDNLVQQ AKAQFRMAEE
EARRNRLMRD MAQLRLQLEV SQLEGSLQQP KAQSSMSPYL VPDTAVLCQH LGLLRQLAAS
GCFIIIIPRT VIDGLDMLKK ENSGARDGIR FLETEFRKGN RYIRCQKESG RSFERDKLKR
QDTEAWHLYK MVDSCRQLTG SQSSGDEDTA GMVTILTGHS LEELSERSAS MKAAVQAVAA
AGMELKNIIE FYRQWKEMG
