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Q8C7Q4

- RBM4_MOUSE

UniProt

Q8C7Q4 - RBM4_MOUSE

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Protein

RNA-binding protein 4

Gene

Rbm4

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri160 – 17718CCHC-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. miRNA binding Source: UniProtKB
  2. mRNA 3'-UTR binding Source: UniProtKB
  3. nucleotide binding Source: InterPro
  4. pre-mRNA binding Source: UniProtKB
  5. pre-mRNA intronic binding Source: UniProtKB
  6. pre-mRNA intronic pyrimidine-rich binding Source: UniProtKB
  7. RNA binding Source: UniProtKB
  8. zinc ion binding Source: InterPro

GO - Biological processi

  1. cap-independent translational initiation Source: UniProtKB
  2. cell differentiation Source: UniProtKB-KW
  3. circadian regulation of translation Source: UniProtKB
  4. entrainment of circadian clock by photoperiod Source: UniProtKB
  5. IRES-dependent translational initiation Source: UniProtKB
  6. mRNA processing Source: UniProtKB-KW
  7. negative regulation of translation Source: UniProtKB
  8. negative regulation of translational initiation Source: UniProtKB
  9. negative regulation of translation in response to stress Source: UniProtKB
  10. negative regulation of translation involved in gene silencing by miRNA Source: UniProtKB
  11. positive regulation of muscle cell differentiation Source: UniProtKB
  12. regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
  13. regulation of nucleocytoplasmic transport Source: UniProtKB
  14. response to arsenic-containing substance Source: UniProtKB
  15. RNA splicing Source: UniProtKB-KW
  16. stress-activated MAPK cascade Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Differentiation, mRNA processing, mRNA splicing, RNA-mediated gene silencing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein 4
Alternative name(s):
Lark homolog
Short name:
mLark
RNA-binding motif protein 4
RNA-binding motif protein 4a
Gene namesi
Name:Rbm4
Synonyms:Rbm4a
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 19

Organism-specific databases

MGIiMGI:1100865. Rbm4.

Subcellular locationi

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).By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. cytoplasmic stress granule Source: UniProtKB
  3. nuclear speck Source: UniProtKB
  4. nucleolus Source: UniProtKB
  5. nucleoplasm Source: UniProtKB
  6. nucleus Source: UniProtKB
  7. perinuclear region of cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 361361RNA-binding protein 4PRO_0000081755Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei306 – 3061PhosphoserineBy similarity

Post-translational modificationi

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.By similarity1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ8C7Q4.
PaxDbiQ8C7Q4.
PRIDEiQ8C7Q4.

PTM databases

PhosphoSiteiQ8C7Q4.

Expressioni

Tissue specificityi

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).3 Publications

Inductioni

Accumulates according to a circadian rhythm in the SCN.1 Publication

Gene expression databases

BgeeiQ8C7Q4.
CleanExiMM_RBM4.
ExpressionAtlasiQ8C7Q4. baseline and differential.
GenevestigatoriQ8C7Q4.

Interactioni

Subunit structurei

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).By similarity

Protein-protein interaction databases

BioGridi202822. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ8C7Q4.
SMRiQ8C7Q4. Positions 1-155.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 7271RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini78 – 14871RRM 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni196 – 361166Interaction with TNPO3By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi233 – 2419Poly-Ala
Compositional biasi283 – 29210Poly-Ala

Sequence similaritiesi

Contains 1 CCHC-type zinc finger.PROSITE-ProRule annotation
Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri160 – 17718CCHC-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG294108.
GeneTreeiENSGT00390000020883.
HOGENOMiHOG000026790.
HOVERGENiHBG062217.
InParanoidiQ8C7Q4.
KOiK13187.
K13189.
TreeFamiTF320661.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q8C7Q4-1) [UniParc]FASTAAdd to Basket

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

        10         20         30         40         50
MVKLFIGNLP REATEQEIRS LFEQYGKVLE CDIIKNYGFV HIEDKTAAED
60 70 80 90 100
AIRNLHHYKL HGVNINVEAS KNKSKASTKL HVGNISPTCT NQELRAKFEE
110 120 130 140 150
YGPVIECDIV KDYAFVHMER AEDAVEAIRG LDNTEFQGKR MHVQLSTSRL
160 170 180 190 200
RTAPGMGDQS GCYRCGKEGH WSKECPIDRS GRVADLTEQY NEQYGAVRTP
210 220 230 240 250
YTMSYGDSLY YNNTYGALDA YYKRCRAARS YEAVAAAAAS AYSNYAEQTL
260 270 280 290 300
SQLPQVQNTA MASHLTSTSL DPYNRHLLPP SGAAAAAAAA AACTAASTSY
310 320 330 340 350
YGRDRSPLRR ATGPVLTVGE GYGYGHDSEL SQASAAARNS LYDMARYERE
360
QYADRARYSA F
Length:361
Mass (Da):40,046
Last modified:March 1, 2003 - v1
Checksum:iD50BB51553AFA4E0
GO
Isoform 2 (identifier: Q8C7Q4-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:168
Mass (Da):19,206
Checksum:i5E2CD35CB4E4FEFB
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti243 – 2431S → N in AAC53171. (PubMed:9169144)Curated
Sequence conflicti292 – 2921A → AAAAA in AAC53171. (PubMed:9169144)Curated
Sequence conflicti299 – 2991S → P in AAC53171. (PubMed:9169144)Curated
Sequence conflicti316 – 3161L → P in AAC53171. (PubMed:9169144)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei139 – 16830KRMHV…RCGKE → ESLFWSAQYKAVRNELVEKR KALGWKDFAG in isoform 2. 1 PublicationVSP_013417Add
BLAST
Alternative sequencei169 – 361193Missing in isoform 2. 1 PublicationVSP_013418Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89506 mRNA. Translation: AAC53171.1. Frameshift.
AK049659 mRNA. Translation: BAC33862.1.
AK087488 mRNA. Translation: BAC39895.1.
CCDSiCCDS29436.1. [Q8C7Q4-1]
RefSeqiNP_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]
UniGeneiMm.276338.
Mm.426069.

Genome annotation databases

EnsembliENSMUST00000180248; ENSMUSP00000137345; ENSMUSG00000094936. [Q8C7Q4-1]
GeneIDi19653.
56275.
KEGGimmu:19653.
mmu:56275.
UCSCiuc008gau.1. mouse. [Q8C7Q4-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89506 mRNA. Translation: AAC53171.1 . Frameshift.
AK049659 mRNA. Translation: BAC33862.1 .
AK087488 mRNA. Translation: BAC39895.1 .
CCDSi CCDS29436.1. [Q8C7Q4-1 ]
RefSeqi NP_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 ]
UniGenei Mm.276338.
Mm.426069.

3D structure databases

ProteinModelPortali Q8C7Q4.
SMRi Q8C7Q4. Positions 1-155.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 202822. 1 interaction.

PTM databases

PhosphoSitei Q8C7Q4.

Proteomic databases

MaxQBi Q8C7Q4.
PaxDbi Q8C7Q4.
PRIDEi Q8C7Q4.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000180248 ; ENSMUSP00000137345 ; ENSMUSG00000094936 . [Q8C7Q4-1 ]
GeneIDi 19653.
56275.
KEGGi mmu:19653.
mmu:56275.
UCSCi uc008gau.1. mouse. [Q8C7Q4-1 ]

Organism-specific databases

CTDi 10432.
5936.
MGIi MGI:1100865. Rbm4.

Phylogenomic databases

eggNOGi NOG294108.
GeneTreei ENSGT00390000020883.
HOGENOMi HOG000026790.
HOVERGENi HBG062217.
InParanoidi Q8C7Q4.
KOi K13187.
K13189.
TreeFami TF320661.

Miscellaneous databases

NextBioi 296920.
PROi Q8C7Q4.
SOURCEi Search...

Gene expression databases

Bgeei Q8C7Q4.
CleanExi MM_RBM4.
ExpressionAtlasi Q8C7Q4. baseline and differential.
Genevestigatori Q8C7Q4.

Family and domain databases

Gene3Di 3.30.70.330. 2 hits.
4.10.60.10. 1 hit.
InterProi IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR001878. Znf_CCHC.
[Graphical view ]
Pfami PF00076. RRM_1. 2 hits.
PF00098. zf-CCHC. 1 hit.
[Graphical view ]
SMARTi SM00360. RRM. 2 hits.
SM00343. ZnF_C2HC. 1 hit.
[Graphical view ]
PROSITEi PS50102. RRM. 2 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiRBM4_MOUSE
AccessioniPrimary (citable) accession number: Q8C7Q4
Secondary accession number(s): O08752, Q8BN66
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 12, 2005
Last sequence update: March 1, 2003
Last modified: October 29, 2014
This is version 101 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

Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3