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Q8C7Q4 (RBM4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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:
RNA-binding protein 4
Alternative name(s):
Lark homolog
Short name=mLark
RNA-binding motif protein 4
RNA-binding motif protein 4a
Gene names
Name:Rbm4
Synonyms:Rbm4a
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length361 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of AGO2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro. Ref.4

Subunit structure

Interacts with TNPO3; the interaction mediates nuclear import of the protein and is disrupted by nuclear Ran bound to GTP. Interacts with EIF4G1 and WT1. Interacts with EIF4A1; the interaction is modulated under stress-induced conditions. Interacts with AGO1. Interacts with AGO2; the interaction occurs under both cell proliferation and differentiation conditions and in an RNA- and phosphorylation-independent manner. Interacts with DDX5; the interaction occurs in an RNA-independent manner By similarity.

Subcellular location

Nucleus By similarity. Nucleusnucleolus By similarity. Nucleus speckle By similarity. Cytoplasm By similarity. Cytoplasmic granule By similarity. Note: Undergoes continuous nucleocytoplasmic shuttling. Upon nuclear import colocalizes with SR proteins in nuclear speckles. Arsenite stress-induced phosphorylation increases its subcellular relocalization from the nucleus to the cytoplasm and to cytoplasmic stress granules (SG) via a p38 MAPK signaling pathway. Primarily localized in nucleus and nucleoli under cell growth conditions and accumulated in the cytoplasm and cytoplasm perinuclear granules upon muscle cell differentiation By similarity. Ref.5

Tissue specificity

Expressed in the suprachiasmatic nucleus (SCN). Expressed in myocytes; expression gradually increases during muscle cell differentiation (at protein level). Expressed in the suprachiasmatic nucleus (SCN). Ref.4 Ref.5 Ref.6

Induction

Accumulates according to a circadian rhythm in the SCN. Ref.4

Post-translational modification

Phosphorylated. Phosphorylated in vitro on Ser-306 by SRPK1. Phosphorylation on Ser-306 is induced upon cell stress signaling, which alters its subcellular localization and may modulate its activity on IRES-mediated mRNA translation By similarity. Phosphorylated. Phosphorylation on Ser-306 is induced upon cell muscle differentiation. Ref.5

Sequence similarities

Contains 1 CCHC-type zinc finger.

Contains 2 RRM (RNA recognition motif) domains.

Sequence caution

The sequence AAC53171.1 differs from that shown. Reason: Frameshift at position 239.

Ontologies

Keywords
   Biological processDifferentiation
mRNA processing
mRNA splicing
RNA-mediated gene silencing
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
Zinc-finger
   LigandMetal-binding
RNA-binding
Zinc
   Molecular functionActivator
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processIRES-dependent translational initiation

Inferred from sequence or structural similarity. Source: UniProtKB

RNA splicing

Inferred from electronic annotation. Source: UniProtKB-KW

cap-independent translational initiation

Inferred from sequence or structural similarity. Source: UniProtKB

cell differentiation

Inferred from electronic annotation. Source: UniProtKB-KW

circadian regulation of translation

Inferred from direct assay Ref.4. Source: UniProtKB

entrainment of circadian clock by photoperiod

Inferred from direct assay Ref.4. Source: UniProtKB

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

negative regulation of translation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of translation in response to stress

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of translation involved in gene silencing by miRNA

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of translational initiation

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of muscle cell differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of alternative mRNA splicing, via spliceosome

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of nucleocytoplasmic transport

Inferred from direct assay Ref.5. Source: UniProtKB

response to arsenic-containing substance

Inferred from sequence or structural similarity. Source: UniProtKB

stress-activated MAPK cascade

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from direct assay Ref.5. Source: UniProtKB

cytoplasmic stress granule

Inferred from sequence or structural similarity. Source: UniProtKB

nuclear speck

Inferred from sequence or structural similarity. Source: UniProtKB

nucleolus

Inferred from direct assay Ref.5. Source: UniProtKB

nucleoplasm

Inferred from sequence or structural similarity. Source: UniProtKB

nucleus

Inferred from direct assay Ref.5. Source: UniProtKB

perinuclear region of cytoplasm

Inferred from direct assay Ref.5. Source: UniProtKB

   Molecular_functionRNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

mRNA 3'-UTR binding

Inferred from direct assay Ref.4. Source: UniProtKB

miRNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

nucleotide binding

Inferred from electronic annotation. Source: InterPro

pre-mRNA binding

Inferred from direct assay Ref.3. Source: UniProtKB

pre-mRNA intronic binding

Inferred from sequence or structural similarity. Source: UniProtKB

pre-mRNA intronic pyrimidine-rich binding

Inferred from sequence or structural similarity. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8C7Q4-1)

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: Q8C7Q4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     139-168: KRMHVQLSTSRLRTAPGMGDQSGCYRCGKE → ESLFWSAQYKAVRNELVEKRKALGWKDFAG
     169-361: Missing.
Note: May be due to an intron retention. No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 361361RNA-binding protein 4
PRO_0000081755

Regions

Domain2 – 7271RRM 1
Domain78 – 14871RRM 2
Zinc finger160 – 17718CCHC-type
Region196 – 361166Interaction with TNPO3 By similarity
Compositional bias233 – 2419Poly-Ala
Compositional bias283 – 29210Poly-Ala

Amino acid modifications

Modified residue3061Phosphoserine By similarity

Natural variations

Alternative sequence139 – 16830KRMHV…RCGKE → ESLFWSAQYKAVRNELVEKR KALGWKDFAG in isoform 2.
VSP_013417
Alternative sequence169 – 361193Missing in isoform 2.
VSP_013418

Experimental info

Sequence conflict2431S → N in AAC53171. Ref.1
Sequence conflict2921A → AAAAA in AAC53171. Ref.1
Sequence conflict2991S → P in AAC53171. Ref.1
Sequence conflict3161L → P in AAC53171. Ref.1

Sequences

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

Last modified March 1, 2003. Version 1.
Checksum: D50BB51553AFA4E0

FASTA36140,046
        10         20         30         40         50         60 
MVKLFIGNLP REATEQEIRS LFEQYGKVLE CDIIKNYGFV HIEDKTAAED AIRNLHHYKL 

        70         80         90        100        110        120 
HGVNINVEAS KNKSKASTKL HVGNISPTCT NQELRAKFEE YGPVIECDIV KDYAFVHMER 

       130        140        150        160        170        180 
AEDAVEAIRG LDNTEFQGKR MHVQLSTSRL RTAPGMGDQS GCYRCGKEGH WSKECPIDRS 

       190        200        210        220        230        240 
GRVADLTEQY NEQYGAVRTP YTMSYGDSLY YNNTYGALDA YYKRCRAARS YEAVAAAAAS 

       250        260        270        280        290        300 
AYSNYAEQTL SQLPQVQNTA MASHLTSTSL DPYNRHLLPP SGAAAAAAAA AACTAASTSY 

       310        320        330        340        350        360 
YGRDRSPLRR ATGPVLTVGE GYGYGHDSEL SQASAAARNS LYDMARYERE QYADRARYSA 


F 

« Hide

Isoform 2 [UniParc].

Checksum: 5E2CD35CB4E4FEFB
Show »

FASTA16819,206

References

« Hide 'large scale' references
[1]"A novel zinc finger-containing RNA-binding protein conserved from fruitflies to humans."
Jackson F.R., Banfi S., Guffanti A., Rossi E.
Genomics 41:444-452(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[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] (ISOFORMS 1 AND 2).
Strain: C57BL/6J.
Tissue: Eye and Spinal cord.
[3]"Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB."
Lin J.C., Tarn W.Y.
Mol. Cell. Biol. 25:10111-10121(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: RNA-BINDING.
[4]"LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1."
Kojima S., Matsumoto K., Hirose M., Shimada M., Nagano M., Shigeyoshi Y., Hoshino S., Ui-Tei K., Saigo K., Green C.B., Sakaki Y., Tei H.
Proc. Natl. Acad. Sci. U.S.A. 104:1859-1864(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INDUCTION, TISSUE SPECIFICITY.
[5]"RNA-binding motif protein 4 translocates to cytoplasmic granules and suppresses translation via argonaute2 during muscle cell differentiation."
Lin J.C., Tarn W.Y.
J. Biol. Chem. 284:34658-34665(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[6]"RBM4 down-regulates PTB and antagonizes its activity in muscle cell-specific alternative splicing."
Lin J.C., Tarn W.Y.
J. Cell Biol. 193:509-520(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U89506 mRNA. Translation: AAC53171.1. Frameshift.
AK049659 mRNA. Translation: BAC33862.1.
AK087488 mRNA. Translation: BAC39895.1.
CCDSCCDS29436.1. [Q8C7Q4-1]
RefSeqNP_001277051.1. NM_001290122.1. [Q8C7Q4-1]
NP_001277052.1. NM_001290123.1. [Q8C7Q4-1]
NP_001277053.1. NM_001290124.1.
NP_001277054.1. NM_001290125.1.
NP_033058.2. NM_009032.3. [Q8C7Q4-1]
XP_006531863.1. XM_006531800.1. [Q8C7Q4-1]
XP_006531864.1. XM_006531801.1. [Q8C7Q4-1]
UniGeneMm.276338.
Mm.426069.

3D structure databases

ProteinModelPortalQ8C7Q4.
SMRQ8C7Q4. Positions 1-155.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid202822. 1 interaction.

PTM databases

PhosphoSiteQ8C7Q4.

Proteomic databases

MaxQBQ8C7Q4.
PaxDbQ8C7Q4.
PRIDEQ8C7Q4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000180248; ENSMUSP00000137345; ENSMUSG00000094936. [Q8C7Q4-1]
GeneID19653.
56275.
KEGGmmu:19653.
mmu:56275.
UCSCuc008gau.1. mouse. [Q8C7Q4-1]

Organism-specific databases

CTD10432.
5936.
MGIMGI:1100865. Rbm4.

Phylogenomic databases

eggNOGNOG294108.
GeneTreeENSGT00390000020883.
HOGENOMHOG000026790.
HOVERGENHBG062217.
InParanoidQ8C7Q4.
KOK13187.
K13189.
TreeFamTF320661.

Gene expression databases

BgeeQ8C7Q4.
CleanExMM_RBM4.
GenevestigatorQ8C7Q4.

Family and domain databases

Gene3D3.30.70.330. 2 hits.
4.10.60.10. 1 hit.
InterProIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF00076. RRM_1. 2 hits.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTSM00360. RRM. 2 hits.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view]
PROSITEPS50102. RRM. 2 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio296920.
PROQ8C7Q4.
SOURCESearch...

Entry information

Entry nameRBM4_MOUSE
AccessionPrimary (citable) accession number: Q8C7Q4
Secondary accession number(s): O08752, Q8BN66
Entry history
Integrated into UniProtKB/Swiss-Prot: April 12, 2005
Last sequence update: March 1, 2003
Last modified: July 9, 2014
This is version 99 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

MGD cross-references

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