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Protein

Regulator of nonsense transcripts 3B

Gene

UPF3B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core.5 Publications

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • structural constituent of nuclear pore Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processmRNA transport, Nonsense-mediated mRNA decay, Transport

Enzyme and pathway databases

ReactomeiR-HSA-109688 Cleavage of Growing Transcript in the Termination Region
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-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
SIGNORiQ9BZI7

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 3B
Alternative 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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000125351.10
HGNCiHGNC:20439 UPF3B
MIMi300298 gene
neXtProtiNX_Q9BZI7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked, syndromic, 14 (MRXS14)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXS14 patients manifest mental retardation associated with other variable signs such as autistic features, slender build, poor musculature, long, thin face, high-arched palate, high nasal bridge, and pectus deformities.
See also OMIM:300676
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037666160Y → D in MRXS14. 1 PublicationCorresponds to variant dbSNP:rs122468182EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52K → E: Abolishes interaction with UPF2. 1 Publication1
Mutagenesisi53 – 58VVIRRL → AVARRA: Abolishes interaction with UPF2. 1 Publication6
Mutagenesisi56R → E: Does not abolish interaction with UPF2. 1 Publication1
Mutagenesisi117 – 119YVF → DVD: Abolishes interaction with UPF2. 1 Publication3
Mutagenesisi430R → A: Reduces NMD. 1 Publication1
Mutagenesisi432R → A: Reduces NMD. 2 Publications1
Mutagenesisi434 – 447Missing : Abolishes NMD. 1 PublicationAdd BLAST14
Mutagenesisi434K → A: Reduces NMD. 1 Publication1
Mutagenesisi435D → A: Reduces NMD. 1 Publication1
Mutagenesisi436R → A: Impairs association with EJC. 2 Publications1
Mutagenesisi436R → A: Reduces NMD. 2 Publications1
Mutagenesisi441L → F: Reduces NMD. 1 Publication1
Mutagenesisi442Y → A: Impairs association with EJC. 1 Publication1
Mutagenesisi447R → E: Abolishes NMD; when associated with E-449 and E-451. 1 Publication1
Mutagenesisi449R → E: Abolishes NMD; when associated with E-447 and E-451. 1 Publication1
Mutagenesisi451R → E: Abolishes NMD; when associated with E-447 and E-449. 1 Publication1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi65109
MalaCardsiUPF3B
MIMi300676 phenotype
OpenTargetsiENSG00000125351
Orphaneti323 FG syndrome
776 X-linked intellectual disability with marfanoid habitus
777 X-linked non-syndromic intellectual disability
PharmGKBiPA128394708

Polymorphism and mutation databases

BioMutaiUPF3B
DMDMi60390643

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002152971 – 483Regulator of nonsense transcripts 3BAdd BLAST483

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei169PhosphothreonineCombined sources1
Modified residuei198PhosphothreonineCombined sources1
Modified residuei310PhosphoserineCombined sources1
Modified residuei447Omega-N-methylarginineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ9BZI7
MaxQBiQ9BZI7
PaxDbiQ9BZI7
PeptideAtlasiQ9BZI7
PRIDEiQ9BZI7

PTM databases

iPTMnetiQ9BZI7
PhosphoSitePlusiQ9BZI7

Expressioni

Tissue specificityi

Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta.1 Publication

Gene expression databases

BgeeiENSG00000125351
CleanExiHS_UPF3B
ExpressionAtlasiQ9BZI7 baseline and differential
GenevisibleiQ9BZI7 HS

Organism-specific databases

HPAiHPA001592
HPA001800
HPA001882

Interactioni

Subunit structurei

Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC); 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. Interacts with EST1A, UPF2 and RBM8A. Interacts with CPSF6 (PubMed:19864460).10 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi122396, 44 interactors
CORUMiQ9BZI7
DIPiDIP-31143N
IntActiQ9BZI7, 24 interactors
MINTiQ9BZI7
STRINGi9606.ENSP00000276201

Structurei

Secondary structure

1483
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi52 – 58Combined sources7
Helixi64 – 71Combined sources8
Beta strandi77 – 85Combined sources9
Beta strandi95 – 104Combined sources10
Helixi105 – 114Combined sources10
Beta strandi118 – 120Combined sources3
Beta strandi126 – 128Combined sources3
Beta strandi130 – 133Combined sources4
Turni433 – 435Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UW4X-ray1.95A/C50-140[»]
2XB2X-ray3.40G/U424-483[»]
ProteinModelPortaliQ9BZI7
SMRiQ9BZI7
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BZI7

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 255Necessary for interaction with UPF2Add BLAST226
Regioni52 – 57Binds to UPF26
Regioni94 – 483Sufficient for association with EJC coreAdd BLAST390
Regioni430 – 447Necessary for interaction with RBM8A and for activating NMDAdd BLAST18

Sequence similaritiesi

Belongs to the RENT3 family.Curated

Phylogenomic databases

eggNOGiKOG1295 Eukaryota
ENOG41122XD LUCA
GeneTreeiENSGT00390000017146
HOGENOMiHOG000230909
HOVERGENiHBG059714
InParanoidiQ9BZI7
KOiK14328
OMAiQDPEFMA
OrthoDBiEOG091G0JKF
PhylomeDBiQ9BZI7
TreeFamiTF316034

Family and domain databases

CDDicd12728 RRM_like_Smg4_UPF3B, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR005120 UPF3_dom
IPR034979 UPF3B_RRM-like
PfamiView protein in Pfam
PF03467 Smg4_UPF3, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BZI7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        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
Length:483
Mass (Da):57,762
Last modified:June 1, 2001 - v1
Checksum:iF5A8A395783D1A69
GO
Isoform 2 (identifier: Q9BZI7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     270-282: Missing.

Show »
Length:470
Mass (Da):56,213
Checksum:iC012044D45D9957F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti358R → H in AAI21018 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037666160Y → D in MRXS14. 1 PublicationCorresponds to variant dbSNP:rs122468182EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_012963270 – 282Missing in isoform 2. 2 PublicationsAdd BLAST13

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
CCDSiCCDS14587.1 [Q9BZI7-2]
CCDS14588.1 [Q9BZI7-1]
RefSeqiNP_075386.1, NM_023010.3 [Q9BZI7-2]
NP_542199.1, NM_080632.2 [Q9BZI7-1]
UniGeneiHs.103832

Genome annotation databases

EnsembliENST00000276201; ENSP00000276201; ENSG00000125351 [Q9BZI7-1]
ENST00000345865; ENSP00000245418; ENSG00000125351 [Q9BZI7-2]
GeneIDi65109
KEGGihsa:65109
UCSCiuc004erz.3 human [Q9BZI7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiREN3B_HUMAN
AccessioniPrimary (citable) accession number: Q9BZI7
Secondary accession number(s): D3DWI3
, D3DWI4, Q0VAK8, Q9H1J0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: June 1, 2001
Last modified: May 23, 2018
This is version 154 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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, Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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