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Q9H1J1

- REN3A_HUMAN

UniProt

Q9H1J1 - REN3A_HUMAN

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
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    • History
      Entry version 112 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    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. protein binding Source: IntAct
    4. 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

    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

    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.
    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 – 734
    Helixi81 – 844
    Turni85 – 884
    Beta strandi92 – 965
    Beta strandi104 – 1063
    Beta strandi115 – 1195
    Helixi121 – 13010
    Beta strandi134 – 1374
    Beta strandi143 – 1508

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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

    MRSEKEGAGG LRAAVAARGP SGREKLSALE VQFHRDSQQQ EAETPPTSSS    50
    GCGGGAGKPR EEKRTALSKV VIRRLPPGLT KEQLEEQLRP LPAHDYFEFF 100
    AADLSLYPHL YSRAYINFRN PDDILLFRDR FDGYIFLDSK GLEYPAVVEF 150
    APFQKIAKKK LRKKDAKTGS IEDDPEYKKF LETYCVEEEK TSANPETLLG 200
    EMEAKTRELI ARRTTPLLEY IKNRKLEKQR IREEKREERR RRELEKKRLR 250
    EEEKRRRREE ERCKKKETDK QKKIAEKEVR IKLLKKPEKG EEPTTEKPKE 300
    RGEEIDTGGG KQESCAPGAV VKARPMEGSL EEPQETSHSG SDKEHRDVER 350
    SQEQESEAQR YHVDDGRRHR AHHEPERLSR RSEDEQRWGK GPGQDRGKKG 400
    SQDSGAPGEA MERLGRAQRC DDSPAPRKER LANKDRPALQ LYDPGARFRA 450
    RECGGNRRIC KAEGSGTGPE KREEAE 476
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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.
    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.
    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

    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: October 1, 2014
    This is version 112 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