Q9JJW6 (REFP2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA and export factor-binding protein 2

Gene names

Name:	Refbp2
Synonyms:	Ref2

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	218 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as chaperone and promotes the dimerization of transcription factors containing basic leucine zipper (bZIP) domains and thereby promotes transcriptional activation. Plays a role in mRNA processing and export. May function as scaffold that mediates interactions between proteins and/or RNA. Integral part of the THO/TREX complex that is recruited to transcribed genes and travels with the RNA polymerase during elongation By similarity. Is part of the exon junction complex that remains associated with spliced mRNA and plays an important role in mRNA export and nonsense-mediated RNA decay. Ref.1
Subunit structure	Homomultimer. Binds LEF1 and RUNX1. Is part of several complexes involved in mRNA processing and export. Part of the heteromultimeric THO/TREX complex containing THOC1, THOC2, THOC3, ALYREF/THOC4 and DDX39B. Associates with the spliceosome Binds NXF1 and RBM8A directly and is part of the exon junction complex (EJC) containing NCBP1, NCBP2, RNPS1, RBM8A, SRRM1, NXF1, UPF3B, UPF2, ALYREF/THOC4 and/or REFBP2 By similarity.
Subcellular location	Nucleus. Cytoplasm. Note: Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA.
Sequence similarities	Contains 1 RRM (RNA recognition motif) domain.

Ontologies

Keywords
Biological process	Transport mRNA processing mRNA splicing mRNA transport
Cellular component	Cytoplasm Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Ligand	RNA-binding
Molecular function	Chaperone
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW mRNA transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell spliceosomal complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	RNA 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 218

218

RNA and export factor-binding protein 2

PRO_0000081976

Regions

Domain

75 – 152

78

RRM

Natural variations

Alternative sequence

198

1

Missing in isoform 2.

VSP_008598

Experimental info

Sequence conflict

151

1

A → T in BAC33282. Ref.2

Sequence conflict

200

1

S → F in BAC33282. Ref.2

Sequence conflict

215

1

M → R in BAC33282. Ref.2

Secondary structure

1

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218

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Helix

9 – 17

9

Beta strand

23 – 25

3

Beta strand

28 – 32

5

Turn

36 – 38

3

Turn

41 – 43

3

Beta strand

46 – 48

3

Beta strand

59 – 61

3

Beta strand

75 – 80

6

Helix

88 – 97

10

Beta strand

102 – 106

5

Beta strand

110 – 113

4

Beta strand

118 – 123

6

Helix

125 – 134

10

Beta strand

141 – 144

4

Beta strand

146 – 152

7

Helix

153 – 155

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Refbp2-I) [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 977901CECDCF18FC	FASTA	218	23,730
	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
	Isoform 2 (Refbp2-II) [UniParc]. Checksum: 4622274B18AA50C2	FASTA	217	23,602
	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 GRNSKQQLSA EELDAQLDAY NARMDTS

References

	« Hide 'large scale' referencesShow '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. , 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ252141 mRNA. Translation: CAB76384.1.
AK048243 mRNA. Translation: BAC33282.1.

IPI

IPI00311103.
IPI00377350.

RefSeq

NP_062357.3. NM_019484.4.

UniGene

Mm.389208.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2F3J	NMR	-	A	1-155	[»]
2KT5	NMR	-	A	53-155	[»]
2YKA	NMR	-	A	53-155	[»]

ProteinModelPortal

Q9JJW6.

SMR

Q9JJW6. Positions 1-155.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9JJW6. 1 interaction.

PTM databases

PhosphoSite

Q9JJW6.

Proteomic databases

PaxDb

Q9JJW6.

PRIDE

Q9JJW6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

56009.

KEGG

mmu:56009.

Organism-specific databases

CTD

56009.

MGI

MGI:1913144. Refbp2.

Phylogenomic databases

eggNOG

NOG316507.

HOGENOM

HOG000239962.

HOVERGEN

HBG054806.

InParanoid

Q9JJW6.

KO

K12881.

OrthoDB

EOG4MW87F.

Gene expression databases

CleanEx

MM_REFBP2.

Genevestigator

Q9JJW6.

GermOnline

ENSMUSG00000060244. Mus musculus.

Family and domain databases

Gene3D

3.30.70.330. 1 hit.

InterPro

IPR025715. FoP_duplication.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]

Pfam

PF13865. FoP_duplication. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]

SMART

SM00360. RRM. 1 hit.
[Graphical view]

PROSITE

PS50102. RRM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9JJW6.

NextBio

311734.

SOURCE

Search...

Entry information

Entry name

REFP2_MOUSE

Accession

Primary (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 3, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program