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Q8C7Q4

- RBM4_MOUSE

UniProt

Q8C7Q4 - RBM4_MOUSE

Protein

RNA-binding protein 4

Gene

Rbm4

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (01 Mar 2003)
      Previous versions | rss
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    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

    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

    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.
    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

    MVKLFIGNLP REATEQEIRS LFEQYGKVLE CDIIKNYGFV HIEDKTAAED    50
    AIRNLHHYKL HGVNINVEAS KNKSKASTKL HVGNISPTCT NQELRAKFEE 100
    YGPVIECDIV KDYAFVHMER AEDAVEAIRG LDNTEFQGKR MHVQLSTSRL 150
    RTAPGMGDQS GCYRCGKEGH WSKECPIDRS GRVADLTEQY NEQYGAVRTP 200
    YTMSYGDSLY YNNTYGALDA YYKRCRAARS YEAVAAAAAS AYSNYAEQTL 250
    SQLPQVQNTA MASHLTSTSL DPYNRHLLPP SGAAAAAAAA AACTAASTSY 300
    YGRDRSPLRR ATGPVLTVGE GYGYGHDSEL SQASAAARNS LYDMARYERE 350
    QYADRARYSA F 361
    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.

    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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.
    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

    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 1, 2014
    This is version 100 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