UniProtKB - Q9H1J1 (REN3A_HUMAN)
Protein
Regulator of nonsense transcripts 3A
Gene
UPF3A
Organism
Homo sapiens (Human)
Status
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. However, UPF3A is shown to be only marginally active in NMD as compared to UPF3B. Binds spliced mRNA upstream of exon-exon junctions. In vitro, weakly stimulates translation.2 Publications
GO - Molecular functioni
- RNA binding Source: UniProtKB-KW
- structural constituent of nuclear pore Source: UniProtKB
- telomeric DNA binding Source: BHF-UCL
GO - Biological processi
- mRNA transport Source: UniProtKB-KW
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: Reactome
- positive regulation of translation Source: UniProtKB
Keywordsi
Molecular function | RNA-binding |
Biological process | mRNA transport, Nonsense-mediated mRNA decay, Transport |
Enzyme and pathway databases
PathwayCommonsi | Q9H1J1 |
Reactomei | R-HSA-9010553, Regulation of expression of SLITs and ROBOs R-HSA-975957, Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) [Q9H1J1-2] |
Names & Taxonomyi
Protein namesi | Recommended name: Regulator of nonsense transcripts 3AAlternative name(s): Nonsense mRNA reducing factor 3A Up-frameshift suppressor 3 homolog A Short name: hUpf3 |
Gene namesi | Name:UPF3A Synonyms:RENT3A, UPF3 |
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:20332, UPF3A |
MIMi | 605530, gene |
neXtProti | NX_Q9H1J1 |
VEuPathDBi | HostDB:ENSG00000169062.14 |
Subcellular locationi
Cytosol
- cytosol Source: HPA
Nucleus
- exon-exon junction complex Source: GO_Central
- nucleolus Source: GO_Central
- nucleoplasm Source: HPA
- nucleus Source: UniProtKB
Other locations
- cytoplasm Source: GO_Central
- intracellular membrane-bounded organelle Source: HPA
Keywords - Cellular componenti
Cytoplasm, NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 432 | A → R: Increases NMD activity and translation stimulation. 1 Publication | 1 |
Organism-specific databases
DisGeNETi | 65110 |
OpenTargetsi | ENSG00000169062 |
PharmGKBi | PA134961553 |
Miscellaneous databases
Pharosi | Q9H1J1, Tbio |
Genetic variation databases
BioMutai | UPF3A |
DMDMi | 60390646 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000215296 | 1 – 476 | Regulator of nonsense transcripts 3AAdd BLAST | 476 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 341 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
EPDi | Q9H1J1 |
jPOSTi | Q9H1J1 |
MassIVEi | Q9H1J1 |
MaxQBi | Q9H1J1 |
PaxDbi | Q9H1J1 |
PeptideAtlasi | Q9H1J1 |
PRIDEi | Q9H1J1 |
ProteomicsDBi | 80415 [Q9H1J1-1] 80416 [Q9H1J1-2] 80417 [Q9H1J1-3] |
TopDownProteomicsi | Q9H1J1-2 [Q9H1J1-2] |
PTM databases
iPTMneti | Q9H1J1 |
PhosphoSitePlusi | Q9H1J1 |
Expressioni
Tissue specificityi
Isoform 1 is strongly expressed in testis, uterus, muscle, fetal brain and spinal cord. Isoform 2 is strongly expressed in fetal brain and spinal cord.1 Publication
Gene expression databases
Bgeei | ENSG00000169062, Expressed in testis and 164 other tissues |
ExpressionAtlasi | Q9H1J1, baseline and differential |
Genevisiblei | Q9H1J1, HS |
Organism-specific databases
HPAi | ENSG00000169062, Low tissue specificity |
Interactioni
Subunit structurei
Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC).
Interacts with UPF2 and RBM8A.
4 PublicationsBinary interactionsi
Hide detailsQ9H1J1
With | #Exp. | IntAct |
---|---|---|
RBM8A [Q9Y5S9] | 4 | EBI-521530,EBI-447231 |
UPF1 [Q92900] | 4 | EBI-521530,EBI-373471 |
UPF2 [Q9HAU5] | 5 | EBI-521530,EBI-372073 |
UPF3B - isoform 2 [Q9BZI7-2] | 2 | EBI-521530,EBI-15674130 |
Protein-protein interaction databases
BioGRIDi | 122397, 42 interactors |
CORUMi | Q9H1J1 |
DIPi | DIP-31146N |
IntActi | Q9H1J1, 36 interactors |
MINTi | Q9H1J1 |
STRINGi | 9606.ENSP00000364448 |
Miscellaneous databases
RNActi | Q9H1J1, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
BMRBi | Q9H1J1 |
SMRi | Q9H1J1 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9H1J1 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 66 – 140 | Required for interaction with UPF2Add BLAST | 75 | |
Regioni | 421 – 434 | Required for association with EIF4A3 and ECJ core components CASC3, MAGOH and RBM8AAdd BLAST | 14 |
Sequence similaritiesi
Belongs to the RENT3 family.Curated
Phylogenomic databases
eggNOGi | KOG1295, Eukaryota |
GeneTreei | ENSGT00390000017146 |
HOGENOMi | CLU_041202_1_0_1 |
InParanoidi | Q9H1J1 |
OMAi | ELIWRFV |
OrthoDBi | 737663at2759 |
PhylomeDBi | Q9H1J1 |
TreeFami | TF316034 |
Family and domain databases
Gene3Di | 3.30.70.330, 1 hit |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR039722, Upf3 IPR005120, UPF3_dom IPR034978, UPF3A |
PANTHERi | PTHR13112, PTHR13112, 1 hit PTHR13112:SF2, PTHR13112:SF2, 1 hit |
Pfami | View protein in Pfam PF03467, Smg4_UPF3, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
s (3+)i Sequence
Sequence statusi: Complete.
This entry describes 3 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All
Isoform 1 (identifier: Q9H1J1-1) [UniParc]FASTAAdd to basket
Also known as: hUpf3p, hUPF3L
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
MRSEKEGAGG LRAAVAARGP SGREKLSALE VQFHRDSQQQ EAETPPTSSS
60 70 80 90 100
GCGGGAGKPR EEKRTALSKV VIRRLPPGLT KEQLEEQLRP LPAHDYFEFF
110 120 130 140 150
AADLSLYPHL YSRAYINFRN PDDILLFRDR FDGYIFLDSK GLEYPAVVEF
160 170 180 190 200
APFQKIAKKK LRKKDAKTGS IEDDPEYKKF LETYCVEEEK TSANPETLLG
210 220 230 240 250
EMEAKTRELI ARRTTPLLEY IKNRKLEKQR IREEKREERR RRELEKKRLR
260 270 280 290 300
EEEKRRRREE ERCKKKETDK QKKIAEKEVR IKLLKKPEKG EEPTTEKPKE
310 320 330 340 350
RGEEIDTGGG KQESCAPGAV VKARPMEGSL EEPQETSHSG SDKEHRDVER
360 370 380 390 400
SQEQESEAQR YHVDDGRRHR AHHEPERLSR RSEDEQRWGK GPGQDRGKKG
410 420 430 440 450
SQDSGAPGEA MERLGRAQRC DDSPAPRKER LANKDRPALQ LYDPGARFRA
460 470
RECGGNRRIC KAEGSGTGPE KREEAE
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketA0A087WZ33 | A0A087WZ33_HUMAN | Regulator of nonsense transcripts 3... | UPF3A | 105 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 25 | K → M in AAG60690 (PubMed:11113196).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_062143 | 64 | R → K. Corresponds to variant dbSNP:rs3752105Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_012961 | 1 – 325 | Missing in isoform 3. 1 PublicationAdd BLAST | 325 | |
Alternative sequenceiVSP_012962 | 141 – 173 | Missing in isoform 2. 1 PublicationAdd BLAST | 33 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY013250 mRNA Translation: AAG48510.1 AL160396 Genomic DNA No translation available. CH471085 Genomic DNA Translation: EAX09252.1 BC008694 mRNA Translation: AAH08694.1 BC023569 mRNA Translation: AAH23569.1 AF318575 mRNA Translation: AAG60690.1 |
CCDSi | CCDS9543.1 [Q9H1J1-1] CCDS9544.1 [Q9H1J1-2] |
RefSeqi | NP_075387.1, NM_023011.3 [Q9H1J1-1] NP_542418.1, NM_080687.2 [Q9H1J1-2] |
Genome annotation databases
Ensembli | ENST00000351487; ENSP00000329592; ENSG00000169062 [Q9H1J1-2] ENST00000375299; ENSP00000364448; ENSG00000169062 [Q9H1J1-1] |
GeneIDi | 65110 |
KEGGi | hsa:65110 |
UCSCi | uc001vup.4, human [Q9H1J1-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY013250 mRNA Translation: AAG48510.1 AL160396 Genomic DNA No translation available. CH471085 Genomic DNA Translation: EAX09252.1 BC008694 mRNA Translation: AAH08694.1 BC023569 mRNA Translation: AAH23569.1 AF318575 mRNA Translation: AAG60690.1 |
CCDSi | CCDS9543.1 [Q9H1J1-1] CCDS9544.1 [Q9H1J1-2] |
RefSeqi | NP_075387.1, NM_023011.3 [Q9H1J1-1] NP_542418.1, NM_080687.2 [Q9H1J1-2] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2L08 | NMR | - | A | 70-155 | [»] | |
BMRBi | Q9H1J1 | |||||
SMRi | Q9H1J1 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 122397, 42 interactors |
CORUMi | Q9H1J1 |
DIPi | DIP-31146N |
IntActi | Q9H1J1, 36 interactors |
MINTi | Q9H1J1 |
STRINGi | 9606.ENSP00000364448 |
PTM databases
iPTMneti | Q9H1J1 |
PhosphoSitePlusi | Q9H1J1 |
Genetic variation databases
BioMutai | UPF3A |
DMDMi | 60390646 |
Proteomic databases
EPDi | Q9H1J1 |
jPOSTi | Q9H1J1 |
MassIVEi | Q9H1J1 |
MaxQBi | Q9H1J1 |
PaxDbi | Q9H1J1 |
PeptideAtlasi | Q9H1J1 |
PRIDEi | Q9H1J1 |
ProteomicsDBi | 80415 [Q9H1J1-1] 80416 [Q9H1J1-2] 80417 [Q9H1J1-3] |
TopDownProteomicsi | Q9H1J1-2 [Q9H1J1-2] |
Protocols and materials databases
Antibodypediai | 11926, 79 antibodies |
Genome annotation databases
Ensembli | ENST00000351487; ENSP00000329592; ENSG00000169062 [Q9H1J1-2] ENST00000375299; ENSP00000364448; ENSG00000169062 [Q9H1J1-1] |
GeneIDi | 65110 |
KEGGi | hsa:65110 |
UCSCi | uc001vup.4, human [Q9H1J1-1] |
Organism-specific databases
CTDi | 65110 |
DisGeNETi | 65110 |
GeneCardsi | UPF3A |
HGNCi | HGNC:20332, UPF3A |
HPAi | ENSG00000169062, Low tissue specificity |
MIMi | 605530, gene |
neXtProti | NX_Q9H1J1 |
OpenTargetsi | ENSG00000169062 |
PharmGKBi | PA134961553 |
VEuPathDBi | HostDB:ENSG00000169062.14 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1295, Eukaryota |
GeneTreei | ENSGT00390000017146 |
HOGENOMi | CLU_041202_1_0_1 |
InParanoidi | Q9H1J1 |
OMAi | ELIWRFV |
OrthoDBi | 737663at2759 |
PhylomeDBi | Q9H1J1 |
TreeFami | TF316034 |
Enzyme and pathway databases
PathwayCommonsi | Q9H1J1 |
Reactomei | R-HSA-9010553, Regulation of expression of SLITs and ROBOs R-HSA-975957, Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) [Q9H1J1-2] |
Miscellaneous databases
BioGRID-ORCSi | 65110, 92 hits in 860 CRISPR screens |
ChiTaRSi | UPF3A, human |
EvolutionaryTracei | Q9H1J1 |
GeneWikii | UPF3A |
GenomeRNAii | 65110 |
Pharosi | Q9H1J1, Tbio |
PROi | PR:Q9H1J1 |
RNActi | Q9H1J1, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000169062, Expressed in testis and 164 other tissues |
ExpressionAtlasi | Q9H1J1, baseline and differential |
Genevisiblei | Q9H1J1, HS |
Family and domain databases
Gene3Di | 3.30.70.330, 1 hit |
InterProi | View protein in InterPro IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR039722, Upf3 IPR005120, UPF3_dom IPR034978, UPF3A |
PANTHERi | PTHR13112, PTHR13112, 1 hit PTHR13112:SF2, PTHR13112:SF2, 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 | REN3A_HUMAN | |
Accessioni | Q9H1J1Primary (citable) accession number: Q9H1J1 Secondary accession number(s): A2A366 Q9BZI8 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 1, 2005 |
Last sequence update: | March 1, 2001 | |
Last modified: | February 10, 2021 | |
This is version 164 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 13
Human chromosome 13: 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