UniProtKB - Q9BZI7 (REN3B_HUMAN)
Regulator of nonsense transcripts 3B
UPF3B
Functioni
GO - Molecular functioni
- mRNA binding Source: UniProtKB
- RNA binding Source: UniProtKB
- structural constituent of nuclear pore Source: UniProtKB
GO - Biological processi
- mRNA 3'-end processing Source: Reactome
- mRNA export from nucleus Source: Reactome
- mRNA splicing, via spliceosome Source: Reactome
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
- positive regulation of translation Source: UniProtKB
- RNA export from nucleus Source: Reactome
Keywordsi
Molecular function | RNA-binding |
Biological process | mRNA transport, Nonsense-mediated mRNA decay, Transport |
Enzyme and pathway databases
PathwayCommonsi | Q9BZI7 |
Reactomei | R-HSA-159236, Transport of Mature mRNA derived from an Intron-Containing Transcript R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72187, mRNA 3'-end processing R-HSA-73856, RNA Polymerase II Transcription Termination R-HSA-9010553, Regulation of expression of SLITs and ROBOs R-HSA-975957, Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) |
SIGNORi | Q9BZI7 |
Names & Taxonomyi
Protein namesi | Recommended name: Regulator of nonsense transcripts 3BAlternative name(s): Nonsense mRNA reducing factor 3B Up-frameshift suppressor 3 homolog B Short name: hUpf3B Up-frameshift suppressor 3 homolog on chromosome X Short name: hUpf3p-X |
Gene namesi | Name:UPF3B Synonyms:RENT3B, UPF3X |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:20439, UPF3B |
MIMi | 300298, gene |
neXtProti | NX_Q9BZI7 |
VEuPathDBi | HostDB:ENSG00000125351.10 |
Subcellular locationi
Cytoskeleton
- centriolar satellite Source: HPA
Cytosol
- cytosol Source: HPA
Nucleus
- exon-exon junction complex Source: UniProtKB
- nucleolus Source: HPA
- nucleoplasm Source: HPA
- nucleus Source: UniProtKB
Other locations
- cytoplasm Source: GO_Central
Keywords - Cellular componenti
Cytoplasm, NucleusPathology & Biotechi
Involvement in diseasei
Mental retardation, X-linked, syndromic, 14 (MRXS14)1 Publication
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_037666 | 160 | Y → D in MRXS14. 1 PublicationCorresponds to variant dbSNP:rs122468182EnsemblClinVar. | 1 |
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 52 | K → E: Abolishes interaction with UPF2. 1 Publication | 1 | |
Mutagenesisi | 53 – 58 | VVIRRL → AVARRA: Abolishes interaction with UPF2. 1 Publication | 6 | |
Mutagenesisi | 56 | R → E: Does not abolish interaction with UPF2. 1 Publication | 1 | |
Mutagenesisi | 117 – 119 | YVF → DVD: Abolishes interaction with UPF2. 1 Publication | 3 | |
Mutagenesisi | 430 | R → A: Reduces NMD. 1 Publication | 1 | |
Mutagenesisi | 432 | R → A: Reduces NMD. 2 Publications | 1 | |
Mutagenesisi | 434 – 447 | Missing : Abolishes NMD. 1 PublicationAdd BLAST | 14 | |
Mutagenesisi | 434 | K → A: Reduces NMD. 1 Publication | 1 | |
Mutagenesisi | 435 | D → A: Reduces NMD. 1 Publication | 1 | |
Mutagenesisi | 436 | R → A: Impairs association with EJC. 2 Publications | 1 | |
Mutagenesisi | 436 | R → A: Reduces NMD. 2 Publications | 1 | |
Mutagenesisi | 441 | L → F: Reduces NMD. 1 Publication | 1 | |
Mutagenesisi | 442 | Y → A: Impairs association with EJC. 1 Publication | 1 | |
Mutagenesisi | 447 | R → E: Abolishes NMD; when associated with E-449 and E-451. 1 Publication | 1 | |
Mutagenesisi | 449 | R → E: Abolishes NMD; when associated with E-447 and E-451. 1 Publication | 1 | |
Mutagenesisi | 451 | R → E: Abolishes NMD; when associated with E-447 and E-449. 1 Publication | 1 |
Keywords - Diseasei
Disease variant, Mental retardationOrganism-specific databases
DisGeNETi | 65109 |
MalaCardsi | UPF3B |
MIMi | 300676, phenotype |
OpenTargetsi | ENSG00000125351 |
Orphaneti | 323, NON RARE IN EUROPE: FG syndrome phenotypic spectrum 776, X-linked intellectual disability with marfanoid habitus 777, X-linked non-syndromic intellectual disability |
PharmGKBi | PA128394708 |
Miscellaneous databases
Pharosi | Q9BZI7, Tbio |
Genetic variation databases
BioMutai | UPF3B |
DMDMi | 60390643 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000215297 | 1 – 483 | Regulator of nonsense transcripts 3BAdd BLAST | 483 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 169 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 198 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 310 | PhosphoserineCombined sources | 1 | |
Modified residuei | 447 | Omega-N-methylarginineCombined sources | 1 |
Keywords - PTMi
Methylation, PhosphoproteinProteomic databases
EPDi | Q9BZI7 |
jPOSTi | Q9BZI7 |
MassIVEi | Q9BZI7 |
MaxQBi | Q9BZI7 |
PaxDbi | Q9BZI7 |
PeptideAtlasi | Q9BZI7 |
PRIDEi | Q9BZI7 |
ProteomicsDBi | 79849 [Q9BZI7-1] 79850 [Q9BZI7-2] |
PTM databases
iPTMneti | Q9BZI7 |
PhosphoSitePlusi | Q9BZI7 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000125351, Expressed in sural nerve and 221 other tissues |
ExpressionAtlasi | Q9BZI7, baseline and differential |
Genevisiblei | Q9BZI7, HS |
Organism-specific databases
HPAi | ENSG00000125351, Low tissue specificity |
Interactioni
Subunit structurei
Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Core component of the mRNA splicing-dependent exon junction complex (EJC); the core complex contains CASC3, EIF4A3, MAGOH or MAGOHB, and RBM8A. The EJC core components EIF4A3 and the MAGOH-RBM8A dimer form a composite binding site for UPF3B which overlaps with the EJC binding site for WIBG (PubMed:16601204, PubMed:18066079, PubMed:23917022, PubMed:20479275).
Interacts with EST1A, UPF2 and RBM8A (PubMed:12554878, PubMed:18066079, PubMed:15004547).
Interacts with CPSF6 (PubMed:19864460).
13 PublicationsBinary interactionsi
Hide detailsQ9BZI7
With | #Exp. | IntAct |
---|---|---|
EIF4A3 [P38919] | 9 | EBI-372780,EBI-299104 |
MAGOH [P61326] | 7 | EBI-372780,EBI-299134 |
RBM8A [Q9Y5S9] | 9 | EBI-372780,EBI-447231 |
UPF1 [Q92900] | 10 | EBI-372780,EBI-373471 |
UPF2 [Q9HAU5] | 8 | EBI-372780,EBI-372073 |
Isoform 2 [Q9BZI7-2]
With | #Exp. | IntAct |
---|---|---|
MAGOH [P61326] | 2 | EBI-15674130,EBI-299134 |
UPF2 [Q9HAU5] | 7 | EBI-15674130,EBI-372073 |
UPF3A [Q9H1J1] | 2 | EBI-15674130,EBI-521530 |
Protein-protein interaction databases
BioGRIDi | 122396, 63 interactors |
CORUMi | Q9BZI7 |
DIPi | DIP-31143N |
IntActi | Q9BZI7, 34 interactors |
MINTi | Q9BZI7 |
STRINGi | 9606.ENSP00000276201 |
Miscellaneous databases
RNActi | Q9BZI7, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q9BZI7 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9BZI7 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 30 – 255 | Necessary for interaction with UPF2Add BLAST | 226 | |
Regioni | 52 – 57 | Binds to UPF2 | 6 | |
Regioni | 424 – 483 | Sufficient for association with EJC core1 PublicationAdd BLAST | 60 | |
Regioni | 430 – 447 | Necessary for interaction with RBM8A and for activating NMDAdd BLAST | 18 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG1295, Eukaryota |
GeneTreei | ENSGT00390000017146 |
HOGENOMi | CLU_041202_1_0_1 |
InParanoidi | Q9BZI7 |
OMAi | DRCPEKE |
OrthoDBi | 737663at2759 |
PhylomeDBi | Q9BZI7 |
TreeFami | TF316034 |
Family and domain databases
CDDi | cd12728, RRM_like_Smg4_UPF3B, 1 hit |
Gene3Di | 3.30.70.330, 1 hit |
IDEALi | IID00251 |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR039722, Upf3 IPR005120, UPF3_dom IPR034979, UPF3B_RRM-like |
PANTHERi | PTHR13112, PTHR13112, 1 hit |
Pfami | View protein in Pfam PF03467, Smg4_UPF3, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
s (2+)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MKEEKEHRPK EKRVTLLTPA GATGSGGGTS GDSSKGEDKQ DRNKEKKEAL
60 70 80 90 100
SKVVIRRLPP TLTKEQLQEH LQPMPEHDYF EFFSNDTSLY PHMYARAYIN
110 120 130 140 150
FKNQEDIILF RDRFDGYVFL DNKGQEYPAI VEFAPFQKAA KKKTKKRDTK
160 170 180 190 200
VGTIDDDPEY RKFLESYATD NEKMTSTPET LLEEIEAKNR ELIAKKTTPL
210 220 230 240 250
LSFLKNKQRM REEKREERRR REIERKRQRE EERRKWKEEE KRKRKDIEKL
260 270 280 290 300
KKIDRIPERD KLKDEPKIKV HRFLLQAVNQ KNLLKKPEKG DEKELDKREK
310 320 330 340 350
AKKLDKENLS DERASGQSCT LPKRSDSELK DEKPKRPEDE SGRDYRERER
360 370 380 390 400
EYERDQERIL RERERLKRQE EERRRQKERY EKEKTFKRKE EEMKKEKDTL
410 420 430 440 450
RDKGKKAEST ESIGSSEKTE KKEEVVKRDR IRNKDRPAMQ LYQPGARSRN
460 470 480
RLCPPDDSTK SGDSAAERKQ ESGISHRKEG GEE
Computationally mapped potential isoform sequencesi
There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketA0A087WYC8 | A0A087WYC8_HUMAN | Regulator of nonsense transcripts 3... | UPF3B | 217 | Annotation score: | ||
A0A1B0GVA2 | A0A1B0GVA2_HUMAN | Regulator of nonsense transcripts 3... | UPF3B | 232 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 358 | R → H in AAI21018 (PubMed:15489334).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_037666 | 160 | Y → D in MRXS14. 1 PublicationCorresponds to variant dbSNP:rs122468182EnsemblClinVar. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_012963 | 270 – 282 | Missing in isoform 2. 2 PublicationsAdd BLAST | 13 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY013251 mRNA Translation: AAG48511.1 AF318576 mRNA Translation: AAG60691.1 CH471161 Genomic DNA Translation: EAW89842.1 CH471161 Genomic DNA Translation: EAW89844.1 CH471161 Genomic DNA Translation: EAW89845.1 CH471161 Genomic DNA Translation: EAW89846.1 BC121017 mRNA Translation: AAI21018.1 |
CCDSi | CCDS14587.1 [Q9BZI7-2] CCDS14588.1 [Q9BZI7-1] |
RefSeqi | NP_075386.1, NM_023010.3 [Q9BZI7-2] NP_542199.1, NM_080632.2 [Q9BZI7-1] |
Genome annotation databases
Ensembli | ENST00000276201; ENSP00000276201; ENSG00000125351 [Q9BZI7-1] ENST00000345865; ENSP00000245418; ENSG00000125351 [Q9BZI7-2] |
GeneIDi | 65109 |
KEGGi | hsa:65109 |
UCSCi | uc004erz.3, human [Q9BZI7-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY013251 mRNA Translation: AAG48511.1 AF318576 mRNA Translation: AAG60691.1 CH471161 Genomic DNA Translation: EAW89842.1 CH471161 Genomic DNA Translation: EAW89844.1 CH471161 Genomic DNA Translation: EAW89845.1 CH471161 Genomic DNA Translation: EAW89846.1 BC121017 mRNA Translation: AAI21018.1 |
CCDSi | CCDS14587.1 [Q9BZI7-2] CCDS14588.1 [Q9BZI7-1] |
RefSeqi | NP_075386.1, NM_023010.3 [Q9BZI7-2] NP_542199.1, NM_080632.2 [Q9BZI7-1] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1UW4 | X-ray | 1.95 | A/C | 50-140 | [»] | |
2XB2 | X-ray | 3.40 | G/U | 424-483 | [»] | |
SMRi | Q9BZI7 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 122396, 63 interactors |
CORUMi | Q9BZI7 |
DIPi | DIP-31143N |
IntActi | Q9BZI7, 34 interactors |
MINTi | Q9BZI7 |
STRINGi | 9606.ENSP00000276201 |
PTM databases
iPTMneti | Q9BZI7 |
PhosphoSitePlusi | Q9BZI7 |
Genetic variation databases
BioMutai | UPF3B |
DMDMi | 60390643 |
Proteomic databases
EPDi | Q9BZI7 |
jPOSTi | Q9BZI7 |
MassIVEi | Q9BZI7 |
MaxQBi | Q9BZI7 |
PaxDbi | Q9BZI7 |
PeptideAtlasi | Q9BZI7 |
PRIDEi | Q9BZI7 |
ProteomicsDBi | 79849 [Q9BZI7-1] 79850 [Q9BZI7-2] |
Protocols and materials databases
Antibodypediai | 464, 95 antibodies |
Genome annotation databases
Ensembli | ENST00000276201; ENSP00000276201; ENSG00000125351 [Q9BZI7-1] ENST00000345865; ENSP00000245418; ENSG00000125351 [Q9BZI7-2] |
GeneIDi | 65109 |
KEGGi | hsa:65109 |
UCSCi | uc004erz.3, human [Q9BZI7-1] |
Organism-specific databases
CTDi | 65109 |
DisGeNETi | 65109 |
GeneCardsi | UPF3B |
HGNCi | HGNC:20439, UPF3B |
HPAi | ENSG00000125351, Low tissue specificity |
MalaCardsi | UPF3B |
MIMi | 300298, gene 300676, phenotype |
neXtProti | NX_Q9BZI7 |
OpenTargetsi | ENSG00000125351 |
Orphaneti | 323, NON RARE IN EUROPE: FG syndrome phenotypic spectrum 776, X-linked intellectual disability with marfanoid habitus 777, X-linked non-syndromic intellectual disability |
PharmGKBi | PA128394708 |
VEuPathDBi | HostDB:ENSG00000125351.10 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1295, Eukaryota |
GeneTreei | ENSGT00390000017146 |
HOGENOMi | CLU_041202_1_0_1 |
InParanoidi | Q9BZI7 |
OMAi | DRCPEKE |
OrthoDBi | 737663at2759 |
PhylomeDBi | Q9BZI7 |
TreeFami | TF316034 |
Enzyme and pathway databases
PathwayCommonsi | Q9BZI7 |
Reactomei | R-HSA-159236, Transport of Mature mRNA derived from an Intron-Containing Transcript R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72187, mRNA 3'-end processing R-HSA-73856, RNA Polymerase II Transcription Termination R-HSA-9010553, Regulation of expression of SLITs and ROBOs R-HSA-975957, Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) |
SIGNORi | Q9BZI7 |
Miscellaneous databases
BioGRID-ORCSi | 65109, 22 hits in 640 CRISPR screens |
EvolutionaryTracei | Q9BZI7 |
GeneWikii | UPF3B |
GenomeRNAii | 65109 |
Pharosi | Q9BZI7, Tbio |
PROi | PR:Q9BZI7 |
RNActi | Q9BZI7, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000125351, Expressed in sural nerve and 221 other tissues |
ExpressionAtlasi | Q9BZI7, baseline and differential |
Genevisiblei | Q9BZI7, HS |
Family and domain databases
CDDi | cd12728, RRM_like_Smg4_UPF3B, 1 hit |
Gene3Di | 3.30.70.330, 1 hit |
IDEALi | IID00251 |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR039722, Upf3 IPR005120, UPF3_dom IPR034979, UPF3B_RRM-like |
PANTHERi | PTHR13112, PTHR13112, 1 hit |
Pfami | View protein in Pfam PF03467, Smg4_UPF3, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | REN3B_HUMAN | |
Accessioni | Q9BZI7Primary (citable) accession number: Q9BZI7 Secondary accession number(s): D3DWI3 Q9H1J0 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 1, 2005 |
Last sequence update: | June 1, 2001 | |
Last modified: | April 7, 2021 | |
This is version 175 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Human chromosome X
Human chromosome X: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families