REN3B_HUMAN
ID REN3B_HUMAN Reviewed; 483 AA.
AC Q9BZI7; D3DWI3; D3DWI4; Q0VAK8; Q9H1J0;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Regulator of nonsense transcripts 3B {ECO:0000312|HGNC:HGNC:20439};
DE AltName: Full=Nonsense mRNA reducing factor 3B {ECO:0000312|HGNC:HGNC:20439};
DE AltName: Full=Up-frameshift suppressor 3 homolog B {ECO:0000250|UniProtKB:P48412};
DE Short=hUpf3B;
DE AltName: Full=Up-frameshift suppressor 3 homolog on chromosome X;
DE Short=hUpf3p-X;
GN Name=UPF3B {ECO:0000312|HGNC:HGNC:20439};
GN Synonyms=RENT3B {ECO:0000312|HGNC:HGNC:20439}, UPF3X;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION IN NONSENSE-MEDIATED MRNA
RP DECAY, INTERACTION WITH UPF1 AND UPF2, AND SUBCELLULAR LOCATION.
RX PubMed=11163187; DOI=10.1016/s0092-8674(00)00214-2;
RA Lykke-Andersen J., Shu M.-D., Steitz J.A.;
RT "Human Upf proteins target an mRNA for nonsense-mediated decay when bound
RT downstream of a termination codon.";
RL Cell 103:1121-1131(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH UPF2, MUTAGENESIS
RP OF 53-VAL--LEU-58 AND 117-TYR--PHE-119, SUBCELLULAR LOCATION, AND TISSUE
RP SPECIFICITY.
RC TISSUE=Cervix carcinoma;
RX PubMed=11113196; DOI=10.1128/mcb.21.1.209-223.2001;
RA Serin G., Gersappe A., Black J.D., Aronoff R., Maquat L.E.;
RT "Identification and characterization of human orthologues to Saccharomyces
RT cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4).";
RL Mol. Cell. Biol. 21:209-223(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP INTERACTION WITH RBM8A, IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX,
RP ASSOCIATION WITH THE EJC COMPLEX, AND RNA-BINDING.
RX PubMed=11546873; DOI=10.1126/science.1062829;
RA Kim V.N., Kataoka N., Dreyfuss G.;
RT "Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent
RT exon-exon junction complex.";
RL Science 293:1832-1836(2001).
RN [6]
RP IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX, AND ASSOCIATION WITH THE
RP EJC COMPLEX.
RX PubMed=11546874; DOI=10.1126/science.1062786;
RA Lykke-Andersen J., Shu M.-D., Steitz J.A.;
RT "Communication of the position of exon-exon junctions to the mRNA
RT surveillance machinery by the protein RNPS1.";
RL Science 293:1836-1839(2001).
RN [7]
RP FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, INTERACTION WITH RBM8A, AND
RP MUTAGENESIS OF ARG-430; ARG-432; 434-LYS--ARG-447; LYS-434; ASP-435;
RP ARG-436 AND LEU-441.
RX PubMed=12718880; DOI=10.1016/s1097-2765(03)00142-4;
RA Gehring N.H., Neu-Yilik G., Schell T., Hentze M.W., Kulozik A.E.;
RT "Y14 and hUpf3b form an NMD-activating complex.";
RL Mol. Cell 11:939-949(2003).
RN [8]
RP INTERACTION WITH EST1A.
RX PubMed=12554878; DOI=10.1261/rna.2137903;
RA Chiu S.-Y., Serin G., Ohara O., Maquat L.E.;
RT "Characterization of human Smg5/7a: a protein with similarities to
RT Caenorhabditis elegans SMG5 and SMG7 that functions in the
RT dephosphorylation of Upf1.";
RL RNA 9:77-87(2003).
RN [9]
RP FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, ASSOCIATION WITH THE EJC COMPLEX,
RP AND IDENTIFICATION IN A COMPLEX WITH UPF2 AND RNPS1.
RX PubMed=16209946; DOI=10.1016/j.molcel.2005.08.012;
RA Gehring N.H., Kunz J.B., Neu-Yilik G., Breit S., Viegas M.H., Hentze M.W.,
RA Kulozik A.E.;
RT "Exon-junction complex components specify distinct routes of nonsense-
RT mediated mRNA decay with differential cofactor requirements.";
RL Mol. Cell 20:65-75(2005).
RN [10]
RP FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, FUNCTION IN TRANSLATION
RP STIMULATION, ASSOCIATION WITH THE EJC COMPLEX, AND MUTAGENESIS OF ARG-432.
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 [11]
RP FUNCTION, AND RECONSTITUTION OF THE EJC CORE-UPF COMPLEX.
RX PubMed=18066079; DOI=10.1038/nsmb1330;
RA Chamieh H., Ballut L., Bonneau F., Le Hir H.;
RT "NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and
RT stimulate its RNA helicase activity.";
RL Nat. Struct. Mol. Biol. 15:85-93(2008).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-169, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [13]
RP INTERACTION WITH CPSF6.
RX PubMed=19864460; DOI=10.1091/mbc.e09-05-0389;
RA Ruepp M.D., Aringhieri C., Vivarelli S., Cardinale S., Paro S.,
RA Schuemperli D., Barabino S.M.;
RT "Mammalian pre-mRNA 3' end processing factor CF I m 68 functions in mRNA
RT export.";
RL Mol. Biol. Cell 20:5211-5223(2009).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-169, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-198, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [16]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-169 AND SER-310, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [18]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-169 AND SER-310, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [19]
RP IDENTIFICATION IN THE EXON JUNCTION COMPLEX.
RX PubMed=23917022; DOI=10.4161/rna.25827;
RA Singh K.K., Wachsmuth L., Kulozik A.E., Gehring N.H.;
RT "Two mammalian MAGOH genes contribute to exon junction complex composition
RT and nonsense-mediated decay.";
RL RNA Biol. 10:1291-1298(2013).
RN [20]
RP INTERACTION WITH DHX34.
RX PubMed=25220460; DOI=10.1016/j.celrep.2014.08.020;
RA Hug N., Caceres J.F.;
RT "The RNA helicase DHX34 activates NMD by promoting a transition from the
RT surveillance to the decay-inducing complex.";
RL Cell Rep. 8:1845-1856(2014).
RN [21]
RP METHYLATION [LARGE SCALE ANALYSIS] AT ARG-447, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Colon carcinoma;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
RN [22]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 50-140 IN COMPLEX WITH UPF2,
RP RNA-BINDING, AND MUTAGENESIS OF LYS-52 AND ARG-56.
RX PubMed=15004547; DOI=10.1038/nsmb741;
RA Kadlec J., Izaurralde E., Cusack S.;
RT "The structural basis for the interaction between nonsense-mediated mRNA
RT decay factors UPF2 and UPF3.";
RL Nat. Struct. Mol. Biol. 11:330-337(2004).
RN [23]
RP X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF 424-483 IN COMPLEX WITH EIF4A3;
RP MAGOH; RBM8A AND CASC3, AND MUTAGENESIS OF ARG-436; TYR-442; ARG-447;
RP ARG-449 AND ARG-451.
RX PubMed=20479275; DOI=10.1073/pnas.1000993107;
RA Buchwald G., Ebert J., Basquin C., Sauliere J., Jayachandran U., Bono F.,
RA Le Hir H., Conti E.;
RT "Insights into the recruitment of the NMD machinery from the crystal
RT structure of a core EJC-UPF3b complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:10050-10055(2010).
RN [24]
RP VARIANT MRXS14 ASP-160.
RX PubMed=17704778; DOI=10.1038/ng2100;
RA Tarpey P.S., Raymond F.L., Nguyen L.S., Rodriguez J., Hackett A.,
RA Vandeleur L., Smith R., Shoubridge C., Edkins S., Stevens C., O'Meara S.,
RA Tofts C., Barthorpe S., Buck G., Cole J., Halliday K., Hills K., Jones D.,
RA Mironenko T., Perry J., Varian J., West S., Widaa S., Teague J., Dicks E.,
RA Butler A., Menzies A., Richardson D., Jenkinson A., Shepherd R., Raine K.,
RA Moon J., Luo Y., Parnau J., Bhat S.S., Gardner A., Corbett M., Brooks D.,
RA Thomas P., Parkinson-Lawrence E., Porteous M.E., Warner J.P., Sanderson T.,
RA Pearson P., Simensen R.J., Skinner C., Hoganson G., Superneau D.,
RA Wooster R., Bobrow M., Turner G., Stevenson R.E., Schwartz C.E.,
RA Futreal P.A., Srivastava A.K., Stratton M.R., Gecz J.;
RT "Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex,
RT cause syndromic and nonsyndromic mental retardation.";
RL Nat. Genet. 39:1127-1133(2007).
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. In vitro, stimulates
CC translation; the function is independent of association with UPF2 and
CC components of the EJC core. {ECO:0000269|PubMed:11163187,
CC ECO:0000269|PubMed:12718880, ECO:0000269|PubMed:16209946,
CC ECO:0000269|PubMed:16601204, ECO:0000269|PubMed:18066079}.
CC -!- SUBUNIT: Found in a post-splicing messenger ribonucleoprotein (mRNP)
CC complex. Core component of the mRNA splicing-dependent exon junction
CC complex (EJC); the core complex contains CASC3, EIF4A3, MAGOH or
CC MAGOHB, and RBM8A. The EJC core components EIF4A3 and the MAGOH-RBM8A
CC dimer form a composite binding site for UPF3B which overlaps with the
CC EJC binding site for WIBG (PubMed:16601204, PubMed:18066079,
CC PubMed:23917022, PubMed:20479275). Interacts with EST1A, UPF2 and RBM8A
CC (PubMed:12554878, PubMed:18066079, PubMed:15004547). Interacts with
CC CPSF6 (PubMed:19864460). Interacts with DHX34; the interaction is RNA-
CC independent. {ECO:0000269|PubMed:11113196, ECO:0000269|PubMed:11163187,
CC ECO:0000269|PubMed:11546873, ECO:0000269|PubMed:11546874,
CC ECO:0000269|PubMed:12554878, ECO:0000269|PubMed:12718880,
CC ECO:0000269|PubMed:15004547, ECO:0000269|PubMed:16209946,
CC ECO:0000269|PubMed:16601204, ECO:0000269|PubMed:18066079,
CC ECO:0000269|PubMed:19864460, ECO:0000269|PubMed:20479275,
CC ECO:0000269|PubMed:23917022}.
CC -!- INTERACTION:
CC Q9BZI7; P38919: EIF4A3; NbExp=9; IntAct=EBI-372780, EBI-299104;
CC Q9BZI7; P61326: MAGOH; NbExp=7; IntAct=EBI-372780, EBI-299134;
CC Q9BZI7; Q9Y5S9: RBM8A; NbExp=9; IntAct=EBI-372780, EBI-447231;
CC Q9BZI7; Q92900: UPF1; NbExp=10; IntAct=EBI-372780, EBI-373471;
CC Q9BZI7; Q9HAU5: UPF2; NbExp=8; IntAct=EBI-372780, EBI-372073;
CC Q9BZI7-2; P61326: MAGOH; NbExp=2; IntAct=EBI-15674130, EBI-299134;
CC Q9BZI7-2; Q9HAU5: UPF2; NbExp=7; IntAct=EBI-15674130, EBI-372073;
CC Q9BZI7-2; Q9H1J1: UPF3A; NbExp=2; IntAct=EBI-15674130, EBI-521530;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11113196,
CC ECO:0000269|PubMed:11163187}. Cytoplasm {ECO:0000269|PubMed:11163187}.
CC Note=Shuttling between the nucleus and the cytoplasm.
CC {ECO:0000269|PubMed:11163187}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9BZI7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9BZI7-2; Sequence=VSP_012963;
CC -!- TISSUE SPECIFICITY: Expressed in testis, uterus, prostate, heart,
CC muscle, brain, spinal cord and placenta. {ECO:0000269|PubMed:11113196}.
CC -!- DISEASE: Intellectual developmental disorder, X-linked, syndromic 14
CC (MRXS14) [MIM:300676]: A disorder characterized by significantly below
CC average general intellectual functioning associated with impairments in
CC adaptive behavior and manifested during the developmental period.
CC MRXS14 patients manifest intellectual disability associated with other
CC variable signs such as autistic features, slender build, poor
CC musculature, long, thin face, high-arched palate, high nasal bridge,
CC and pectus deformities. {ECO:0000269|PubMed:17704778}. Note=The disease
CC is caused by variants affecting the gene represented in this entry.
CC -!- SIMILARITY: Belongs to the RENT3 family. {ECO:0000305}.
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DR EMBL; AY013251; AAG48511.1; -; mRNA.
DR EMBL; AF318576; AAG60691.1; -; mRNA.
DR EMBL; CH471161; EAW89842.1; -; Genomic_DNA.
DR EMBL; CH471161; EAW89844.1; -; Genomic_DNA.
DR EMBL; CH471161; EAW89845.1; -; Genomic_DNA.
DR EMBL; CH471161; EAW89846.1; -; Genomic_DNA.
DR EMBL; BC121017; AAI21018.1; -; mRNA.
DR CCDS; CCDS14587.1; -. [Q9BZI7-2]
DR CCDS; CCDS14588.1; -. [Q9BZI7-1]
DR RefSeq; NP_075386.1; NM_023010.3. [Q9BZI7-2]
DR RefSeq; NP_542199.1; NM_080632.2. [Q9BZI7-1]
DR PDB; 1UW4; X-ray; 1.95 A; A/C=50-140.
DR PDB; 2XB2; X-ray; 3.40 A; G/U=424-483.
DR PDBsum; 1UW4; -.
DR PDBsum; 2XB2; -.
DR AlphaFoldDB; Q9BZI7; -.
DR SMR; Q9BZI7; -.
DR BioGRID; 122396; 113.
DR CORUM; Q9BZI7; -.
DR DIP; DIP-31143N; -.
DR IntAct; Q9BZI7; 36.
DR MINT; Q9BZI7; -.
DR STRING; 9606.ENSP00000276201; -.
DR iPTMnet; Q9BZI7; -.
DR PhosphoSitePlus; Q9BZI7; -.
DR BioMuta; UPF3B; -.
DR DMDM; 60390643; -.
DR EPD; Q9BZI7; -.
DR jPOST; Q9BZI7; -.
DR MassIVE; Q9BZI7; -.
DR MaxQB; Q9BZI7; -.
DR PaxDb; Q9BZI7; -.
DR PeptideAtlas; Q9BZI7; -.
DR PRIDE; Q9BZI7; -.
DR ProteomicsDB; 79849; -. [Q9BZI7-1]
DR ProteomicsDB; 79850; -. [Q9BZI7-2]
DR Antibodypedia; 464; 106 antibodies from 24 providers.
DR DNASU; 65109; -.
DR Ensembl; ENST00000276201.7; ENSP00000276201.3; ENSG00000125351.13. [Q9BZI7-1]
DR Ensembl; ENST00000345865.6; ENSP00000245418.2; ENSG00000125351.13. [Q9BZI7-2]
DR GeneID; 65109; -.
DR KEGG; hsa:65109; -.
DR MANE-Select; ENST00000276201.7; ENSP00000276201.3; NM_080632.3; NP_542199.1.
DR UCSC; uc004erz.3; human. [Q9BZI7-1]
DR CTD; 65109; -.
DR DisGeNET; 65109; -.
DR GeneCards; UPF3B; -.
DR HGNC; HGNC:20439; UPF3B.
DR HPA; ENSG00000125351; Low tissue specificity.
DR MalaCards; UPF3B; -.
DR MIM; 300298; gene.
DR MIM; 300676; phenotype.
DR neXtProt; NX_Q9BZI7; -.
DR OpenTargets; ENSG00000125351; -.
DR Orphanet; 776; Lujan-Fryns syndrome.
DR Orphanet; 323; NON RARE IN EUROPE: FG syndrome phenotypic spectrum.
DR Orphanet; 777; X-linked non-syndromic intellectual disability.
DR PharmGKB; PA128394708; -.
DR VEuPathDB; HostDB:ENSG00000125351; -.
DR eggNOG; KOG1295; Eukaryota.
DR GeneTree; ENSGT00390000017146; -.
DR HOGENOM; CLU_041202_1_0_1; -.
DR InParanoid; Q9BZI7; -.
DR OMA; PPTLEYA; -.
DR OrthoDB; 737663at2759; -.
DR PhylomeDB; Q9BZI7; -.
DR TreeFam; TF316034; -.
DR PathwayCommons; Q9BZI7; -.
DR Reactome; R-HSA-159236; Transport of Mature mRNA derived from an Intron-Containing Transcript.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-HSA-72187; mRNA 3'-end processing.
DR Reactome; R-HSA-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-HSA-9010553; Regulation of expression of SLITs and ROBOs.
DR Reactome; R-HSA-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR SignaLink; Q9BZI7; -.
DR SIGNOR; Q9BZI7; -.
DR BioGRID-ORCS; 65109; 26 hits in 720 CRISPR screens.
DR EvolutionaryTrace; Q9BZI7; -.
DR GeneWiki; UPF3B; -.
DR GenomeRNAi; 65109; -.
DR Pharos; Q9BZI7; Tbio.
DR PRO; PR:Q9BZI7; -.
DR Proteomes; UP000005640; Chromosome X.
DR RNAct; Q9BZI7; protein.
DR Bgee; ENSG00000125351; Expressed in sural nerve and 186 other tissues.
DR ExpressionAtlas; Q9BZI7; baseline and differential.
DR Genevisible; Q9BZI7; HS.
DR GO; GO:0034451; C:centriolar satellite; IDA:HPA.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0035145; C:exon-exon junction complex; IDA:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; NAS:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0017056; F:structural constituent of nuclear pore; NAS:UniProtKB.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IDA:UniProtKB.
DR GO; GO:0045727; P:positive regulation of translation; IDA:UniProtKB.
DR CDD; cd12728; RRM_like_Smg4_UPF3B; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR IDEAL; IID00251; -.
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; IPR034979; UPF3B_RRM-like.
DR PANTHER; PTHR13112; PTHR13112; 1.
DR Pfam; PF03467; Smg4_UPF3; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Disease variant;
KW Intellectual disability; Methylation; mRNA transport;
KW Nonsense-mediated mRNA decay; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; Transport.
FT CHAIN 1..483
FT /note="Regulator of nonsense transcripts 3B"
FT /id="PRO_0000215297"
FT REGION 1..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 30..255
FT /note="Necessary for interaction with UPF2"
FT REGION 52..57
FT /note="Binds to UPF2"
FT REGION 206..483
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 424..483
FT /note="Sufficient for association with EJC core"
FT /evidence="ECO:0000269|PubMed:20479275"
FT REGION 430..447
FT /note="Necessary for interaction with RBM8A and for
FT activating NMD"
FT COMPBIAS 34..51
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 206..271
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 284..312
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 324..436
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 453..483
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 169
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 198
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:20068231"
FT MOD_RES 310
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21406692,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 447
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0007744|PubMed:24129315"
FT VAR_SEQ 270..282
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11163187,
FT ECO:0000303|PubMed:15489334"
FT /id="VSP_012963"
FT VARIANT 160
FT /note="Y -> D (in MRXS14; dbSNP:rs122468182)"
FT /evidence="ECO:0000269|PubMed:17704778"
FT /id="VAR_037666"
FT MUTAGEN 52
FT /note="K->E: Abolishes interaction with UPF2."
FT /evidence="ECO:0000269|PubMed:15004547"
FT MUTAGEN 53..58
FT /note="VVIRRL->AVARRA: Abolishes interaction with UPF2."
FT /evidence="ECO:0000269|PubMed:11113196"
FT MUTAGEN 56
FT /note="R->E: Does not abolish interaction with UPF2."
FT /evidence="ECO:0000269|PubMed:15004547"
FT MUTAGEN 117..119
FT /note="YVF->DVD: Abolishes interaction with UPF2."
FT /evidence="ECO:0000269|PubMed:11113196"
FT MUTAGEN 430
FT /note="R->A: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880"
FT MUTAGEN 432
FT /note="R->A: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880,
FT ECO:0000269|PubMed:16601204"
FT MUTAGEN 434..447
FT /note="Missing: Abolishes NMD."
FT /evidence="ECO:0000269|PubMed:12718880"
FT MUTAGEN 434
FT /note="K->A: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880"
FT MUTAGEN 435
FT /note="D->A: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880"
FT MUTAGEN 436
FT /note="R->A: Impairs association with EJC."
FT /evidence="ECO:0000269|PubMed:12718880,
FT ECO:0000269|PubMed:20479275"
FT MUTAGEN 436
FT /note="R->A: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880,
FT ECO:0000269|PubMed:20479275"
FT MUTAGEN 441
FT /note="L->F: Reduces NMD."
FT /evidence="ECO:0000269|PubMed:12718880"
FT MUTAGEN 442
FT /note="Y->A: Impairs association with EJC."
FT /evidence="ECO:0000269|PubMed:20479275"
FT MUTAGEN 447
FT /note="R->E: Abolishes NMD; when associated with E-449 and
FT E-451."
FT /evidence="ECO:0000269|PubMed:20479275"
FT MUTAGEN 449
FT /note="R->E: Abolishes NMD; when associated with E-447 and
FT E-451."
FT /evidence="ECO:0000269|PubMed:20479275"
FT MUTAGEN 451
FT /note="R->E: Abolishes NMD; when associated with E-447 and
FT E-449."
FT /evidence="ECO:0000269|PubMed:20479275"
FT CONFLICT 358
FT /note="R -> H (in Ref. 4; AAI21018)"
FT /evidence="ECO:0000305"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:1UW4"
FT HELIX 64..71
FT /evidence="ECO:0007829|PDB:1UW4"
FT STRAND 77..85
FT /evidence="ECO:0007829|PDB:1UW4"
FT STRAND 95..104
FT /evidence="ECO:0007829|PDB:1UW4"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:1UW4"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:1UW4"
FT STRAND 126..128
FT /evidence="ECO:0007829|PDB:1UW4"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:1UW4"
FT TURN 433..435
FT /evidence="ECO:0007829|PDB:2XB2"
SQ SEQUENCE 483 AA; 57762 MW; F5A8A395783D1A69 CRC64;
MKEEKEHRPK EKRVTLLTPA GATGSGGGTS GDSSKGEDKQ DRNKEKKEAL SKVVIRRLPP
TLTKEQLQEH LQPMPEHDYF EFFSNDTSLY PHMYARAYIN FKNQEDIILF RDRFDGYVFL
DNKGQEYPAI VEFAPFQKAA KKKTKKRDTK VGTIDDDPEY RKFLESYATD NEKMTSTPET
LLEEIEAKNR ELIAKKTTPL LSFLKNKQRM REEKREERRR REIERKRQRE EERRKWKEEE
KRKRKDIEKL KKIDRIPERD KLKDEPKIKV HRFLLQAVNQ KNLLKKPEKG DEKELDKREK
AKKLDKENLS DERASGQSCT LPKRSDSELK DEKPKRPEDE SGRDYRERER EYERDQERIL
RERERLKRQE EERRRQKERY EKEKTFKRKE EEMKKEKDTL RDKGKKAEST ESIGSSEKTE
KKEEVVKRDR IRNKDRPAMQ LYQPGARSRN RLCPPDDSTK SGDSAAERKQ ESGISHRKEG
GEE
