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Q9H1J1 (REN3A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Regulator of nonsense transcripts 3A
Alternative name(s):
Nonsense mRNA reducing factor 3A
Up-frameshift suppressor 3 homolog A
Short name=hUpf3
Gene names
Name:UPF3A
Synonyms:RENT3A, UPF3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length476 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.9

Subunit structure

Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with UPF2 and RBM8A. Ref.1 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9

Subcellular location

Nucleus. Cytoplasm. Note: Shuttling between the nucleus and the cytoplasm. Ref.1 Ref.5

Tissue specificity

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. Ref.5

Sequence similarities

Belongs to the RENT3 family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RBM8AQ9Y5S94EBI-521530,EBI-447231
UPF1Q929004EBI-521530,EBI-373471

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H1J1-1)

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.
Isoform 2 (identifier: Q9H1J1-2)

Also known as: hUpf3pdelta; hUPF3S;

The sequence of this isoform differs from the canonical sequence as follows:
     141-173: Missing.
Isoform 3 (identifier: Q9H1J1-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-325: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 476476Regulator of nonsense transcripts 3A
PRO_0000215296

Regions

Region66 – 14075Required for interaction with UPF2
Region421 – 43414Required for association with EIF4A3 and ECJ core components CASC3, MAGOH and RBM8A

Amino acid modifications

Modified residue3411Phosphoserine Ref.10

Natural variations

Alternative sequence1 – 325325Missing in isoform 3.
VSP_012961
Alternative sequence141 – 17333Missing in isoform 2.
VSP_012962
Natural variant641R → K.
Corresponds to variant rs3752105 [ dbSNP | Ensembl ].
VAR_062143

Experimental info

Mutagenesis4321A → R: Increases NMD activity and translation stimulation. Ref.9
Sequence conflict251K → M in AAG60690. Ref.5

Secondary structure

.................. 476
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (hUpf3p) (hUPF3L) [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 023031890E47C4EB

FASTA47654,696
        10         20         30         40         50         60 
MRSEKEGAGG LRAAVAARGP SGREKLSALE VQFHRDSQQQ EAETPPTSSS GCGGGAGKPR 

        70         80         90        100        110        120 
EEKRTALSKV VIRRLPPGLT KEQLEEQLRP LPAHDYFEFF AADLSLYPHL YSRAYINFRN 

       130        140        150        160        170        180 
PDDILLFRDR FDGYIFLDSK GLEYPAVVEF APFQKIAKKK LRKKDAKTGS IEDDPEYKKF 

       190        200        210        220        230        240 
LETYCVEEEK TSANPETLLG EMEAKTRELI ARRTTPLLEY IKNRKLEKQR IREEKREERR 

       250        260        270        280        290        300 
RRELEKKRLR EEEKRRRREE ERCKKKETDK QKKIAEKEVR IKLLKKPEKG EEPTTEKPKE 

       310        320        330        340        350        360 
RGEEIDTGGG KQESCAPGAV VKARPMEGSL EEPQETSHSG SDKEHRDVER SQEQESEAQR 

       370        380        390        400        410        420 
YHVDDGRRHR AHHEPERLSR RSEDEQRWGK GPGQDRGKKG SQDSGAPGEA MERLGRAQRC 

       430        440        450        460        470 
DDSPAPRKER LANKDRPALQ LYDPGARFRA RECGGNRRIC KAEGSGTGPE KREEAE 

« Hide

Isoform 2 (hUpf3pdelta) (hUPF3S) [UniParc].

Checksum: D2810FFFB457C889
Show »

FASTA44351,008
Isoform 3 [UniParc].

Checksum: A1CD017051B33DEA
Show »

FASTA15117,112

References

« Hide 'large scale' references
[1]"Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon."
Lykke-Andersen J., Shu M.-D., Steitz J.A.
Cell 103:1121-1131(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION IN NONSENSE-MEDIATED MRNA DECAY, INTERACTION WITH UPF1 AND UPF2, SUBCELLULAR LOCATION.
[2]"The DNA sequence and analysis of human chromosome 13."
Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
Tissue: Brain and Eye.
[5]"Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)."
Serin G., Gersappe A., Black J.D., Aronoff R., Maquat L.E.
Mol. Cell. Biol. 21:209-223(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 25-476 (ISOFORM 1), INTERACTION WITH UPF2, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Tissue: Cervix carcinoma.
[6]"Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex."
Kim V.N., Kataoka N., Dreyfuss G.
Science 293:1832-1836(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RBM8A, IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX, ASSOCIATION WITH THE EJC COMPLEX, RNA-BINDING.
[7]"Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1."
Lykke-Andersen J., Shu M.-D., Steitz J.A.
Science 293:1836-1839(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A POST-SPLICING MRNP COMPLEX, ASSOCIATION WITH THE EJC COMPLEX.
[8]"Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1."
Chiu S.-Y., Serin G., Ohara O., Maquat L.E.
RNA 9:77-87(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROBABLE INTERACTION WITH SMG1.
[9]"Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation."
Kunz J.B., Neu-Yilik G., Hentze M.W., Kulozik A.E., Gehring N.H.
RNA 12:1015-1022(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: LACK OF ACTIVITY IN NMD, FUNCTION IN TRANSLATION STIMULATION, PROTEIN INTERACTION, MUTAGENESIS OF ALA-432.
[10]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-341, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Solution NMR structure of nonsense mRNA reducing factor 3A from H. sapiens, northeast structural genomics consortium target HR4714B."
Northeast structural genomics consortium (NESG)
Submitted (AUG-2010) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 70-155.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY013250 mRNA. Translation: AAG48510.1.
AL160396 Genomic DNA. Translation: CAM22288.1.
CH471085 Genomic DNA. Translation: EAX09252.1.
BC008694 mRNA. Translation: AAH08694.1.
BC023569 mRNA. Translation: AAH23569.1.
AF318575 mRNA. Translation: AAG60690.1.
RefSeqNP_075387.1. NM_023011.3.
NP_542418.1. NM_080687.2.
UniGeneHs.533855.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2L08NMR-A70-155[»]
ProteinModelPortalQ9H1J1.
SMRQ9H1J1. Positions 70-155.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122397. 20 interactions.
DIPDIP-31146N.
IntActQ9H1J1. 19 interactions.
MINTMINT-1417517.
STRING9606.ENSP00000364448.

PTM databases

PhosphoSiteQ9H1J1.

Polymorphism databases

DMDM60390646.

Proteomic databases

PaxDbQ9H1J1.
PRIDEQ9H1J1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000351487; ENSP00000329592; ENSG00000169062. [Q9H1J1-2]
ENST00000375299; ENSP00000364448; ENSG00000169062. [Q9H1J1-1]
GeneID65110.
KEGGhsa:65110.
UCSCuc001vup.3. human. [Q9H1J1-1]
uc001vuq.3. human. [Q9H1J1-2]

Organism-specific databases

CTD65110.
GeneCardsGC13P115047.
HGNCHGNC:20332. UPF3A.
HPAHPA018325.
MIM605530. gene.
neXtProtNX_Q9H1J1.
PharmGKBPA134961553.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG251520.
HOVERGENHBG059714.
InParanoidQ9H1J1.
KOK14328.
OMAEDKCDDM.
OrthoDBEOG7M6D9K.
PhylomeDBQ9H1J1.
TreeFamTF316034.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

BgeeQ9H1J1.
CleanExHS_UPF3A.
GenevestigatorQ9H1J1.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
InterProIPR005120. Nonsense_mediated_decay_UPF3.
IPR012677. Nucleotide-bd_a/b_plait.
[Graphical view]
PfamPF03467. Smg4_UPF3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSUPF3A. human.
EvolutionaryTraceQ9H1J1.
GeneWikiUPF3A.
GenomeRNAi65110.
NextBio67308.
PROQ9H1J1.
SOURCESearch...

Entry information

Entry nameREN3A_HUMAN
AccessionPrimary (citable) accession number: Q9H1J1
Secondary accession number(s): A2A366 expand/collapse secondary AC list , Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2001
Last modified: April 16, 2014
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 13

Human chromosome 13: entries, gene names and cross-references to MIM