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Protein

Regulator of nonsense transcripts 3A

Gene

UPF3A

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. 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

Keywordsi

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

Enzyme and pathway databases

ReactomeiR-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Names & Taxonomyi

Protein namesi
Recommended name:
Regulator of nonsense transcripts 3A
Alternative name(s):
Nonsense mRNA reducing factor 3A
Up-frameshift suppressor 3 homolog A
Short name:
hUpf3
Gene namesi
Name:UPF3A
Synonyms:RENT3A, UPF3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

EuPathDBiHostDB:ENSG00000169062.14
HGNCiHGNC:20332 UPF3A
MIMi605530 gene
neXtProtiNX_Q9H1J1

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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi432A → R: Increases NMD activity and translation stimulation. 1 Publication1

Organism-specific databases

DisGeNETi65110
OpenTargetsiENSG00000169062
PharmGKBiPA134961553

Polymorphism and mutation databases

BioMutaiUPF3A
DMDMi60390646

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002152961 – 476Regulator of nonsense transcripts 3AAdd BLAST476

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei341PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H1J1
MaxQBiQ9H1J1
PaxDbiQ9H1J1
PeptideAtlasiQ9H1J1
PRIDEiQ9H1J1
TopDownProteomicsiQ9H1J1-2 [Q9H1J1-2]

PTM databases

iPTMnetiQ9H1J1
PhosphoSitePlusiQ9H1J1

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

BgeeiENSG00000169062
CleanExiHS_UPF3A
ExpressionAtlasiQ9H1J1 baseline and differential
GenevisibleiQ9H1J1 HS

Organism-specific databases

HPAiHPA018325
HPA061316

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 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi122397, 39 interactors
CORUMiQ9H1J1
DIPiDIP-31146N
IntActiQ9H1J1, 26 interactors
MINTiQ9H1J1
STRINGi9606.ENSP00000364448

Structurei

Secondary structure

1476
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi70 – 73Combined sources4
Helixi81 – 84Combined sources4
Turni85 – 88Combined sources4
Beta strandi92 – 96Combined sources5
Beta strandi104 – 106Combined sources3
Beta strandi115 – 119Combined sources5
Helixi121 – 130Combined sources10
Beta strandi134 – 137Combined sources4
Beta strandi143 – 150Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L08NMR-A70-155[»]
ProteinModelPortaliQ9H1J1
SMRiQ9H1J1
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H1J1

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni66 – 140Required for interaction with UPF2Add BLAST75
Regioni421 – 434Required for association with EIF4A3 and ECJ core components CASC3, MAGOH and RBM8AAdd BLAST14

Sequence similaritiesi

Belongs to the RENT3 family.Curated

Phylogenomic databases

eggNOGiKOG1295 Eukaryota
ENOG41122XD LUCA
GeneTreeiENSGT00390000017146
HOVERGENiHBG059714
InParanoidiQ9H1J1
KOiK14328
OMAiELETQRY
OrthoDBiEOG091G0JKF
PhylomeDBiQ9H1J1
TreeFamiTF316034

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR005120 UPF3_dom
IPR034978 UPF3A
PANTHERiPTHR13112:SF2 PTHR13112:SF2, 1 hit
PfamiView protein in Pfam
PF03467 Smg4_UPF3, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H1J1-1) [UniParc]FASTAAdd to basket
Also known as: hUpf3p, hUPF3L

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
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
Length:476
Mass (Da):54,696
Last modified:March 1, 2001 - v1
Checksum:i023031890E47C4EB
GO
Isoform 2 (identifier: Q9H1J1-2) [UniParc]FASTAAdd to basket
Also known as: hUpf3pdelta, hUPF3S

The sequence of this isoform differs from the canonical sequence as follows:
     141-173: Missing.

Show »
Length:443
Mass (Da):51,008
Checksum:iD2810FFFB457C889
GO
Isoform 3 (identifier: Q9H1J1-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-325: Missing.

Note: No experimental confirmation available.
Show »
Length:151
Mass (Da):17,112
Checksum:iA1CD017051B33DEA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25K → M in AAG60690 (PubMed:11113196).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06214364R → K. Corresponds to variant dbSNP:rs3752105Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0129611 – 325Missing in isoform 3. 1 PublicationAdd BLAST325
Alternative sequenceiVSP_012962141 – 173Missing in isoform 2. 1 PublicationAdd BLAST33

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
CCDSiCCDS9543.1 [Q9H1J1-1]
CCDS9544.1 [Q9H1J1-2]
RefSeqiNP_075387.1, NM_023011.3 [Q9H1J1-1]
NP_542418.1, NM_080687.2 [Q9H1J1-2]
UniGeneiHs.533855

Genome annotation databases

EnsembliENST00000351487; ENSP00000329592; ENSG00000169062 [Q9H1J1-2]
ENST00000375299; ENSP00000364448; ENSG00000169062 [Q9H1J1-1]
GeneIDi65110
KEGGihsa:65110
UCSCiuc001vup.4 human [Q9H1J1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiREN3A_HUMAN
AccessioniPrimary (citable) accession number: Q9H1J1
Secondary accession number(s): A2A366
, Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2001
Last modified: March 28, 2018
This is version 145 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

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