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Q9JJW6

- ALRF2_MOUSE

UniProt

Q9JJW6 - ALRF2_MOUSE

Protein

Aly/REF export factor 2

Gene

Alyref2

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Export adapter involved in spliced and unspliced mRNA nuclear export. Binds mRNA which is transferred to the NXF1-NXT1 heterodimer for export (TAP/NFX1 pathway); enhances NXF1-NXT1 RNA-binding activity.3 Publications

    GO - Molecular functioni

    1. nucleotide binding Source: InterPro
    2. RNA binding Source: MGI
    3. single-stranded DNA binding Source: MGI

    GO - Biological processi

    1. mRNA processing Source: UniProtKB-KW
    2. mRNA transport Source: UniProtKB
    3. RNA splicing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chaperone

    Keywords - Biological processi

    mRNA processing, mRNA splicing, mRNA transport, Transport

    Keywords - Ligandi

    RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Aly/REF export factor 2
    Alternative name(s):
    Alyref
    RNA and export factor-binding protein 2
    Gene namesi
    Name:Alyref2
    Synonyms:Ref2, Refbp2
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Unplaced

    Organism-specific databases

    MGIiMGI:1913144. Alyref2.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. spliceosomal complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Spliceosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi24 – 241R → E: Impairs interaction with NXF1. 1 Publication
    Mutagenesisi29 – 291R → E: Abolishes interaction with NXF1; when associated with E-30. 1 Publication
    Mutagenesisi30 – 301R → E: Abolishes interaction with NXF1; when associated with E-29. 1 Publication
    Mutagenesisi32 – 321R → E: Impairs interaction with NXF1. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 218218Aly/REF export factor 2PRO_0000081976Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei24 – 241Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei24 – 241Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei32 – 321Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei32 – 321Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei37 – 371Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei37 – 371Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei40 – 401Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei40 – 401Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei166 – 1661Asymmetric dimethylarginine; by PRMT1; in vitro1 Publication
    Modified residuei171 – 1711Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei171 – 1711Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei173 – 1731Asymmetric dimethylarginine; by PRMT1; in vitro1 Publication
    Modified residuei181 – 1811Asymmetric dimethylarginine; by PRMT1; in vitro1 Publication
    Modified residuei186 – 1861Asymmetric dimethylarginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei186 – 1861Omega-N-methylated arginine; alternate; by PRMT1; in vitro1 Publication
    Modified residuei188 – 1881Asymmetric dimethylarginine; by PRMT1; in vitro1 Publication

    Post-translational modificationi

    Arginine methylation reduces RNA binding and enhances mRNA transfer to the NXF1-NXT1 heterodimer for nuclear export.1 Publication

    Keywords - PTMi

    Methylation

    Proteomic databases

    PaxDbiQ9JJW6.
    PRIDEiQ9JJW6.

    PTM databases

    PhosphoSiteiQ9JJW6.

    Expressioni

    Gene expression databases

    CleanExiMM_REFBP2.
    GenevestigatoriQ9JJW6.

    Interactioni

    Subunit structurei

    Interacts (via N-terminus and RRM domain) with DDX39B and th NXF1-NXT1 heterodimer. Interacts with HHV-1 ICP27 and HVS ORF57 proteins.5 Publications

    Protein-protein interaction databases

    IntActiQ9JJW6. 2 interactions.
    MINTiMINT-4132115.

    Structurei

    Secondary structure

    1
    218
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 63
    Helixi9 – 179
    Beta strandi23 – 253
    Beta strandi28 – 325
    Turni36 – 383
    Turni41 – 433
    Beta strandi46 – 483
    Beta strandi59 – 613
    Beta strandi75 – 806
    Helixi88 – 9710
    Beta strandi102 – 1065
    Beta strandi110 – 1134
    Beta strandi118 – 1236
    Helixi125 – 13410
    Beta strandi141 – 1444
    Beta strandi146 – 1527
    Helixi153 – 1553

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2F3JNMR-A1-155[»]
    2KT5NMR-A53-155[»]
    2YKANMR-A53-155[»]
    ProteinModelPortaliQ9JJW6.
    SMRiQ9JJW6. Positions 1-155.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9JJW6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini75 – 15278RRMPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni16 – 3722Sufficient for RNA-binding, interaction with NXF1-NXT1Add
    BLAST
    Regioni54 – 155102Interaction with HHV-8 ORF57 protein and with ICP27 from HHV-1Add
    BLAST

    Domaini

    The RRM domain and the N-terminal region (15-58) seem to be involved in RNA binding.1 Publication

    Sequence similaritiesi

    Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG316507.
    HOGENOMiHOG000239962.
    HOVERGENiHBG054806.
    InParanoidiQ9JJW6.
    KOiK12881.
    PhylomeDBiQ9JJW6.

    Family and domain databases

    Gene3Di3.30.70.330. 1 hit.
    InterProiIPR025715. FoP_duplication.
    IPR012677. Nucleotide-bd_a/b_plait.
    IPR000504. RRM_dom.
    [Graphical view]
    PfamiPF13865. FoP_duplication. 1 hit.
    [Graphical view]
    SMARTiSM00360. RRM. 1 hit.
    [Graphical view]
    PROSITEiPS50102. RRM. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9JJW6-1) [UniParc]FASTAAdd to Basket

    Also known as: Refbp2-I

    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

    MADKMDMSLD DIIKLNRNQR RVNRGGGPRR NRPAIARGGR NRPAPYSRPK    50
    PLPDKWQHDL FDSGCGGGEG VETGAKLLVS NLDFGVSDAD IQELFAEFGT 100
    LKKAAVDYDR SGRSLGTADV HFERRADALK AMKQYKGVPL DGRPMDIQLV 150
    ASQIDPQRRP AQSGNRGGMT RSRGSGGFGG RGSQGRGRGT GRNSKQQQLS 200
    AEELDAQLDA YNARMDTS 218
    Length:218
    Mass (Da):23,730
    Last modified:October 1, 2000 - v1
    Checksum:i977901CECDCF18FC
    GO
    Isoform 2 (identifier: Q9JJW6-2) [UniParc]FASTAAdd to Basket

    Also known as: Refbp2-II

    The sequence of this isoform differs from the canonical sequence as follows:
         198-198: Missing.

    Show »
    Length:217
    Mass (Da):23,602
    Checksum:i4622274B18AA50C2
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti151 – 1511A → T in BAC33282. (PubMed:16141072)Curated
    Sequence conflicti200 – 2001S → F in BAC33282. (PubMed:16141072)Curated
    Sequence conflicti215 – 2151M → R in BAC33282. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei198 – 1981Missing in isoform 2. 1 PublicationVSP_008598

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ252141 mRNA. Translation: CAB76384.1.
    AK048243 mRNA. Translation: BAC33282.1.
    CCDSiCCDS15497.1. [Q9JJW6-1]
    RefSeqiNP_062357.3. NM_019484.4.
    UniGeneiMm.389208.

    Genome annotation databases

    GeneIDi56009.
    KEGGimmu:56009.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ252141 mRNA. Translation: CAB76384.1 .
    AK048243 mRNA. Translation: BAC33282.1 .
    CCDSi CCDS15497.1. [Q9JJW6-1 ]
    RefSeqi NP_062357.3. NM_019484.4.
    UniGenei Mm.389208.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2F3J NMR - A 1-155 [» ]
    2KT5 NMR - A 53-155 [» ]
    2YKA NMR - A 53-155 [» ]
    ProteinModelPortali Q9JJW6.
    SMRi Q9JJW6. Positions 1-155.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9JJW6. 2 interactions.
    MINTi MINT-4132115.

    PTM databases

    PhosphoSitei Q9JJW6.

    Proteomic databases

    PaxDbi Q9JJW6.
    PRIDEi Q9JJW6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 56009.
    KEGGi mmu:56009.

    Organism-specific databases

    CTDi 56009.
    MGIi MGI:1913144. Alyref2.

    Phylogenomic databases

    eggNOGi NOG316507.
    HOGENOMi HOG000239962.
    HOVERGENi HBG054806.
    InParanoidi Q9JJW6.
    KOi K12881.
    PhylomeDBi Q9JJW6.

    Miscellaneous databases

    EvolutionaryTracei Q9JJW6.
    NextBioi 311734.
    PROi Q9JJW6.
    SOURCEi Search...

    Gene expression databases

    CleanExi MM_REFBP2.
    Genevestigatori Q9JJW6.

    Family and domain databases

    Gene3Di 3.30.70.330. 1 hit.
    InterProi IPR025715. FoP_duplication.
    IPR012677. Nucleotide-bd_a/b_plait.
    IPR000504. RRM_dom.
    [Graphical view ]
    Pfami PF13865. FoP_duplication. 1 hit.
    [Graphical view ]
    SMARTi SM00360. RRM. 1 hit.
    [Graphical view ]
    PROSITEi PS50102. RRM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "REF, an evolutionarily conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export."
      Stutz F., Bachi A., Doerks T., Braun I.C., Seraphin B., Wilm M., Bork P., Izaurralde E.
      RNA 6:638-650(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION, INTERACTION WITH NXF1.
      Tissue: Embryo.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Strain: C57BL/6J.
      Tissue: Head.
    3. "REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus."
      Rodrigues J.P., Rode M., Gatfield D., Blencowe B.J., Carmo-Fonseca M., Izaurralde E.
      Proc. Natl. Acad. Sci. U.S.A. 98:1030-1035(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    4. "Mutually exclusive interactions drive handover of mRNA from export adaptors to TAP."
      Hautbergue G.M., Hung M.L., Golovanov A.P., Lian L.Y., Wilson S.A.
      Proc. Natl. Acad. Sci. U.S.A. 105:5154-5159(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH NXF1, MUTAGENESIS OF ARG-24; ARG-29; ARG-30 AND ARG-32.
    5. "Arginine methylation of REF/ALY promotes efficient handover of mRNA to TAP/NXF1."
      Hung M.L., Hautbergue G.M., Snijders A.P., Dickman M.J., Wilson S.A.
      Nucleic Acids Res. 38:3351-3361(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT ARG-24; ARG-32; ARG-37; ARG-40; ARG-166; ARG-171; ARG-173; ARG-181; ARG-186 AND ARG-188.
    6. "The solution structure of REF2-I reveals interdomain interactions and regions involved in binding mRNA export factors and RNA."
      Golovanov A.P., Hautbergue G.M., Tintaru A.M., Lian L.Y., Wilson S.A.
      RNA 12:1933-1948(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-155, INTERACTION WITH DDX39B AND NXF1/NXT1 HETERODIMER, DOMAIN, RNA BINDING.
    7. "Structural basis for the recognition of cellular mRNA export factor REF by herpes viral proteins HSV-1 ICP27 and HVS ORF57."
      Tunnicliffe R.B., Hautbergue G.M., Kalra P., Jackson B.R., Whitehouse A., Wilson S.A., Golovanov A.P.
      PLoS Pathog. 7:E1001244-E1001244(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 53-155 IN COMPLEXES WITH HHV-1 ICP27 PEPTIDE AND WITH HVS ORF57 PEPTIDE, INTERACTION WITH HHV-1 ICP27 AND HVS ORF57, REGION.
    8. "Competitive and cooperative interactions mediate RNA transfer from herpesvirus saimiri ORF57 to the mammalian export adaptor ALYREF."
      Tunnicliffe R.B., Hautbergue G.M., Wilson S.A., Kalra P., Golovanov A.P.
      PLoS Pathog. 10:E1003907-E1003907(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 53-155 IN COMPLEX WITH HHV-1 ICP27 PEPTIDE, RNA-BINDING, REGION, INTERACTION WITH HHV-1 ICP27 PEPTIDE.

    Entry informationi

    Entry nameiALRF2_MOUSE
    AccessioniPrimary (citable) accession number: Q9JJW6
    Secondary accession number(s): Q8C869
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 10, 2003
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 100 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3