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Q9JJW6 (ALRF2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Aly/REF export factor 2
Alternative name(s):
RNA and export factor-binding protein 2
Gene names
Name:Alyref2
Synonyms:Ref2, Refbp2
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length218 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.3 Ref.4

Subunit structure

Interacts (via N-terminus and RRM domain) with DDX39B and th NXF1-NXT1 heterodimer. Interacts with HHV-1 ICP27 and HVS ORF57 proteins. Ref.1 Ref.4 Ref.6 Ref.7

Subcellular location

Nucleus. Cytoplasm.

Domain

The RRM domain and the N-terminal region (15-58) seem to be involved in RNA binding. Ref.6

Post-translational modification

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

Sequence similarities

Contains 1 RRM (RNA recognition motif) domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
mRNA transport
Transport
   Cellular componentCytoplasm
Nucleus
Spliceosome
   Coding sequence diversityAlternative splicing
   LigandRNA-binding
   Molecular functionChaperone
   PTMMethylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA splicing

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA transport

Inferred from direct assay Ref.4. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

spliceosomal complex

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionRNA binding

Inferred from direct assay Ref.1. Source: MGI

nucleotide binding

Inferred from electronic annotation. Source: InterPro

single-stranded DNA binding

Inferred from direct assay Ref.1. Source: MGI

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9JJW6-1)

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.
Isoform 2 (identifier: Q9JJW6-2)

Also known as: Refbp2-II;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 218218Aly/REF export factor 2
PRO_0000081976

Regions

Domain75 – 15278RRM
Region16 – 3722Sufficient for RNA-binding, interaction with NXF1-NXT1

Amino acid modifications

Modified residue321Asymmetric dimethylarginine; by PRMT1; in vitro Ref.5
Modified residue371Asymmetric dimethylarginine; alternate; by PRMT1; in vitro Ref.5
Modified residue371Omega-N-methylated arginine; alternate; by PRMT1; in vitro Ref.5
Modified residue1661Asymmetric dimethylarginine; alternate; by PRMT1; in vitro Ref.5
Modified residue1661Omega-N-methylated arginine; alternate; by PRMT1; in vitro Ref.5
Modified residue1731Omega-N-methylated arginine; by PRMT1; in vitro Ref.5
Modified residue1811Omega-N-methylated arginine; by PRMT1; in vitro
Modified residue1861Omega-N-methylated arginine; by PRMT1; in vitro Ref.5
Modified residue1921Omega-N-methylated arginine; by PRMT1; in vitro Ref.5

Natural variations

Alternative sequence1981Missing in isoform 2.
VSP_008598

Experimental info

Mutagenesis241R → E: Impairs interaction with NXF1. Ref.4
Mutagenesis291R → E: Abolishes interaction with NXF1; when associated with E-30. Ref.4
Mutagenesis301R → E: Abolishes interaction with NXF1; when associated with E-29. Ref.4
Mutagenesis321R → E: Impairs interaction with NXF1. Ref.4
Sequence conflict1511A → T in BAC33282. Ref.2
Sequence conflict2001S → F in BAC33282. Ref.2
Sequence conflict2151M → R in BAC33282. Ref.2

Secondary structure

.................................. 218
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Refbp2-I) [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 977901CECDCF18FC

FASTA21823,730
        10         20         30         40         50         60 
MADKMDMSLD DIIKLNRNQR RVNRGGGPRR NRPAIARGGR NRPAPYSRPK PLPDKWQHDL 

        70         80         90        100        110        120 
FDSGCGGGEG VETGAKLLVS NLDFGVSDAD IQELFAEFGT LKKAAVDYDR SGRSLGTADV 

       130        140        150        160        170        180 
HFERRADALK AMKQYKGVPL DGRPMDIQLV ASQIDPQRRP AQSGNRGGMT RSRGSGGFGG 

       190        200        210 
RGSQGRGRGT GRNSKQQQLS AEELDAQLDA YNARMDTS 

« Hide

Isoform 2 (Refbp2-II) [UniParc].

Checksum: 4622274B18AA50C2
Show »

FASTA21723,602

References

« Hide 'large scale' references
[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. expand/collapse author list , 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-32; ARG-37; ARG-166; ARG-173; ARG-186 AND ARG-192.
[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 COMPLEX WITH HHV-1 ICP27 PEPTIDE, INTERACTION WITH HHV-1 ICP27 AND HVS ORF57.
[8]"Interactions of Orf57 with Ref and RNA."
Tunnicliffe R.B., Hautbergue G.M., Kalra P., Jackson B.R., Whitehouse A., Wilson S.A., Golovanov A.P.
Submitted (MAY-2011) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 53-155 IN COMPLEX WITH HVS ORF57 PEPTIDE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ252141 mRNA. Translation: CAB76384.1.
AK048243 mRNA. Translation: BAC33282.1.
RefSeqNP_062357.3. NM_019484.4.
UniGeneMm.389208.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2F3JNMR-A1-155[»]
2KT5NMR-A53-155[»]
2YKANMR-A53-155[»]
ProteinModelPortalQ9JJW6.
SMRQ9JJW6. Positions 1-155.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9JJW6. 2 interactions.
MINTMINT-4132115.

PTM databases

PhosphoSiteQ9JJW6.

Proteomic databases

PaxDbQ9JJW6.
PRIDEQ9JJW6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID56009.
KEGGmmu:56009.

Organism-specific databases

CTD56009.
MGIMGI:1913144. Alyref2.

Phylogenomic databases

eggNOGNOG316507.
HOGENOMHOG000239962.
HOVERGENHBG054806.
InParanoidQ9JJW6.
KOK12881.
PhylomeDBQ9JJW6.

Gene expression databases

CleanExMM_REFBP2.
GenevestigatorQ9JJW6.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
InterProIPR025715. FoP_duplication.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamPF13865. FoP_duplication. 1 hit.
[Graphical view]
SMARTSM00360. RRM. 1 hit.
[Graphical view]
PROSITEPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9JJW6.
NextBio311734.
PROQ9JJW6.
SOURCESearch...

Entry information

Entry nameALRF2_MOUSE
AccessionPrimary (citable) accession number: Q9JJW6
Secondary accession number(s): Q8C869
Entry history
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot