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Q9JJW6

- ALRF2_MOUSE

UniProt

Q9JJW6 - ALRF2_MOUSE

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Protein
Aly/REF export factor 2
Gene
Alyref2, Ref2, Refbp2
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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. RNA binding Source: MGI
  2. nucleotide binding Source: InterPro
  3. single-stranded DNA binding Source: MGI
Complete GO annotation...

GO - Biological processi

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

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
Complete GO annotation...

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 2
PRO_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.

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.4 Publications

Protein-protein interaction databases

IntActiQ9JJW6. 2 interactions.
MINTiMINT-4132115.

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiQ9JJW6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini75 – 15278RRM
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni16 – 3722Sufficient for RNA-binding, interaction with NXF1-NXT1
Add
BLAST
Regioni54 – 155102Interaction with HHV-8 ORF57 protein and with ICP27 from HHV-1
Add
BLAST

Domaini

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

Sequence similaritiesi

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei198 – 1981Missing in isoform 2.
VSP_008598

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti151 – 1511A → T in BAC33282. 1 Publication
Sequence conflicti200 – 2001S → F in BAC33282. 1 Publication
Sequence conflicti215 – 2151M → R in BAC33282. 1 Publication

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...

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 99 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

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