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Q9H1J1

- REN3A_HUMAN

UniProt

Q9H1J1 - REN3A_HUMAN

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Protein

Regulator of nonsense transcripts 3A

Gene

UPF3A

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- 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

  1. nucleocytoplasmic transporter activity Source: UniProtKB
  2. nucleotide binding Source: InterPro
  3. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA metabolic process Source: Reactome
  3. mRNA transport Source: UniProtKB-KW
  4. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB
  5. nucleocytoplasmic transport Source: GOC
  6. positive regulation of translation Source: UniProtKB
  7. RNA metabolic process Source: Reactome
Complete GO annotation...

Keywords - Biological processi

mRNA transport, Nonsense-mediated mRNA decay, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_75822. 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
ProteomesiUP000005640: Chromosome 13

Organism-specific databases

HGNCiHGNC:20332. UPF3A.

Subcellular locationi

Nucleus. Cytoplasm
Note: Shuttling between the nucleus and the cytoplasm.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. cytosol Source: Reactome
  3. nucleus Source: UniProtKB
  4. plasma membrane Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi432 – 4321A → R: Increases NMD activity and translation stimulation. 1 Publication

Organism-specific databases

PharmGKBiPA134961553.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 476476Regulator of nonsense transcripts 3APRO_0000215296Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei341 – 3411Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9H1J1.
PaxDbiQ9H1J1.
PRIDEiQ9H1J1.

PTM databases

PhosphoSiteiQ9H1J1.

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

BgeeiQ9H1J1.
CleanExiHS_UPF3A.
ExpressionAtlasiQ9H1J1. baseline.
GenevestigatoriQ9H1J1.

Organism-specific databases

HPAiHPA018325.

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

WithEntry#Exp.IntActNotes
RBM8AQ9Y5S94EBI-521530,EBI-447231
UPF1Q929004EBI-521530,EBI-373471

Protein-protein interaction databases

BioGridi122397. 20 interactions.
DIPiDIP-31146N.
IntActiQ9H1J1. 19 interactions.
MINTiMINT-1417517.
STRINGi9606.ENSP00000364448.

Structurei

Secondary structure

1
476
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi70 – 734Combined sources
Helixi81 – 844Combined sources
Turni85 – 884Combined sources
Beta strandi92 – 965Combined sources
Beta strandi104 – 1063Combined sources
Beta strandi115 – 1195Combined sources
Helixi121 – 13010Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi143 – 1508Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L08NMR-A70-155[»]
ProteinModelPortaliQ9H1J1.
SMRiQ9H1J1. Positions 70-155.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H1J1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni66 – 14075Required for interaction with UPF2Add
BLAST
Regioni421 – 43414Required for association with EIF4A3 and ECJ core components CASC3, MAGOH and RBM8AAdd
BLAST

Sequence similaritiesi

Belongs to the RENT3 family.Curated

Phylogenomic databases

eggNOGiNOG251520.
GeneTreeiENSGT00390000017146.
HOVERGENiHBG059714.
InParanoidiQ9H1J1.
KOiK14328.
OMAiTHYEFDK.
OrthoDBiEOG7M6D9K.
PhylomeDBiQ9H1J1.
TreeFamiTF316034.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR005120. Nonsense_mediated_decay_UPF3.
IPR012677. Nucleotide-bd_a/b_plait.
[Graphical view]
PfamiPF03467. Smg4_UPF3. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti25 – 251K → M in AAG60690. (PubMed:11113196)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti64 – 641R → K.
Corresponds to variant rs3752105 [ dbSNP | Ensembl ].
VAR_062143

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 325325Missing in isoform 3. 1 PublicationVSP_012961Add
BLAST
Alternative sequencei141 – 17333Missing in isoform 2. 1 PublicationVSP_012962Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
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.3. human. [Q9H1J1-1]
uc001vuq.3. human. [Q9H1J1-2]

Polymorphism databases

DMDMi60390646.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
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 ]
UniGenei Hs.533855.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2L08 NMR - A 70-155 [» ]
ProteinModelPortali Q9H1J1.
SMRi Q9H1J1. Positions 70-155.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 122397. 20 interactions.
DIPi DIP-31146N.
IntActi Q9H1J1. 19 interactions.
MINTi MINT-1417517.
STRINGi 9606.ENSP00000364448.

PTM databases

PhosphoSitei Q9H1J1.

Polymorphism databases

DMDMi 60390646.

Proteomic databases

MaxQBi Q9H1J1.
PaxDbi Q9H1J1.
PRIDEi Q9H1J1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000351487 ; ENSP00000329592 ; ENSG00000169062 . [Q9H1J1-2 ]
ENST00000375299 ; ENSP00000364448 ; ENSG00000169062 . [Q9H1J1-1 ]
GeneIDi 65110.
KEGGi hsa:65110.
UCSCi uc001vup.3. human. [Q9H1J1-1 ]
uc001vuq.3. human. [Q9H1J1-2 ]

Organism-specific databases

CTDi 65110.
GeneCardsi GC13P115047.
HGNCi HGNC:20332. UPF3A.
HPAi HPA018325.
MIMi 605530. gene.
neXtProti NX_Q9H1J1.
PharmGKBi PA134961553.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG251520.
GeneTreei ENSGT00390000017146.
HOVERGENi HBG059714.
InParanoidi Q9H1J1.
KOi K14328.
OMAi THYEFDK.
OrthoDBi EOG7M6D9K.
PhylomeDBi Q9H1J1.
TreeFami TF316034.

Enzyme and pathway databases

Reactomei REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

ChiTaRSi UPF3A. human.
EvolutionaryTracei Q9H1J1.
GeneWikii UPF3A.
GenomeRNAii 65110.
NextBioi 67308.
PROi Q9H1J1.
SOURCEi Search...

Gene expression databases

Bgeei Q9H1J1.
CleanExi HS_UPF3A.
ExpressionAtlasi Q9H1J1. baseline.
Genevestigatori Q9H1J1.

Family and domain databases

Gene3Di 3.30.70.330. 1 hit.
InterProi IPR005120. Nonsense_mediated_decay_UPF3.
IPR012677. Nucleotide-bd_a/b_plait.
[Graphical view ]
Pfami PF03467. Smg4_UPF3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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.

Entry informationi

Entry nameiREN3A_HUMAN
AccessioniPrimary (citable) accession number: Q9H1J1
Secondary accession number(s): A2A366
, Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2001
Last modified: November 26, 2014
This is version 114 of the entry and version 1 of the sequence. [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 13
    Human chromosome 13: 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

External Data

Dasty 3