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Aliases for RBM4 Gene

Aliases for RBM4 Gene

  • RNA Binding Motif Protein 4 2 3 5
  • RNA-Binding Motif Protein 4a 3 4
  • Lark Homolog 3 4
  • RBM4A 3 4
  • Zinc Finger CCHC-Type And RNA Binding Motif 3A 3
  • Transcriptional Coactivator CoAZ 3
  • RNA-Binding Motif Protein 4 4
  • RNA-Binding Protein 4 3
  • ZCCHC21 3
  • ZCRB3A 3
  • HLark 4
  • LARK 3

External Ids for RBM4 Gene

Previous GeneCards Identifiers for RBM4 Gene

  • GC11P068940
  • GC11P068087
  • GC11P066181
  • GC11P066162
  • GC11P066142
  • GC11P066385
  • GC11P066406
  • GC11P062734
  • GC11P066394
  • GC11P066397

Summaries for RBM4 Gene

GeneCards Summary for RBM4 Gene

RBM4 (RNA Binding Motif Protein 4) is a Protein Coding gene. Among its related pathways are Circadian rythm related genes and BMAL1-CLOCK,NPAS2 activates circadian gene expression. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is RBM4B.

UniProtKB/Swiss-Prot for RBM4 Gene

  • 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 3UTR 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.

Gene Wiki entry for RBM4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RBM4 Gene

Genomics for RBM4 Gene

Regulatory Elements for RBM4 Gene

Enhancers for RBM4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G066615 1.4 ENCODE dbSUPER 13.2 -20.7 -20683 4.8 HNRNPUL1 HDGF FOXA2 PKNOX1 CREB3L1 AGO1 WRNIP1 ARID4B SIN3A DMAP1 ACTN3 RBM4 RAD9A RBM4B LOC105369352 MRPL11 EIF1AD RIN1 PIR51437 PIR40941
GH11G066606 1.3 Ensembl ENCODE dbSUPER 11.9 -30.8 -30777 1.9 RAD21 YY1 POLR3A ZNF548 IKZF2 SP5 CEBPB NR2F2 TGIF2 CEBPA ACTN3 ENSG00000258297 MUS81 RBM14 RBM4 ZDHHC24 EIF1AD LOC105369352 MRPL11 PC
GH11G066601 0.8 ENCODE 11.5 -36.4 -36417 1.2 HDGF PKNOX1 FEZF1 YY1 ZEB1 ZNF121 GLIS2 ZNF350 ZNF362 ZNF398 ACTN3 ENSG00000258297 KAT5 RBM14 MUS81 ENSG00000255320 PCNX3 RBM4 ZDHHC24 RBM4B
GH11G066609 0.7 ENCODE dbSUPER 11.9 -28.3 -28336 1.1 ZNF146 CREB1 HNF4A RBM4 ACTN3 ZDHHC24 PC RNU4-39P GC11P066598
GH11G066600 0.7 dbSUPER 11.5 -37.9 -37889 1.2 PAF1 MAX ZNF664 JUND GLIS2 GLIS1 U2AF1 ZNF24 HNF4A SPI1 ZDHHC24 ACTN3 RBM4 RBM4B ENSG00000201733 GC11P066598 RNU4-39P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RBM4 on UCSC Golden Path with GeneCards custom track

Promoters for RBM4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040992 283 1401 HDGF PKNOX1 CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B

Genomic Location for RBM4 Gene

Chromosome:
11
Start:
66,638,617 bp from pter
End:
66,668,385 bp from pter
Size:
29,769 bases
Orientation:
Plus strand

Genomic View for RBM4 Gene

Genes around RBM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBM4 Gene

Proteins for RBM4 Gene

  • Protein details for RBM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BWF3-RBM4_HUMAN
    Recommended name:
    RNA-binding protein 4
    Protein Accession:
    Q9BWF3
    Secondary Accessions:
    • B3KUN0
    • B4E1U0
    • E7EQS3
    • O02916
    • Q4VC48
    • Q6P1P2
    • Q8WU85

    Protein attributes for RBM4 Gene

    Size:
    364 amino acids
    Molecular mass:
    40314 Da
    Quaternary 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.
    SequenceCaution:
    • Sequence=AAC51293.1; Type=Frameshift; Positions=234; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RBM4 Gene

    Alternative splice isoforms for RBM4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBM4 Gene

Post-translational modifications for RBM4 Gene

  • Phosphorylation on Ser-309 is induced upon cell muscle differentiation (By similarity). Phosphorylated. Phosphorylated in vitro on Ser-309 by SRPK1. Phosphorylation on Ser-309 is induced upon cell stress signaling, which alters its subcellular localization and may modulate its activity on IRES-mediated mRNA translation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RBM4 Gene

Domains & Families for RBM4 Gene

Suggested Antigen Peptide Sequences for RBM4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RBM4: view

No data available for UniProtKB/Swiss-Prot for RBM4 Gene

Function for RBM4 Gene

Molecular function for RBM4 Gene

GENATLAS Biochemistry:
RNA binding protein,Drosophila lark homolog,ubiquitously expressed
UniProtKB/Swiss-Prot 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 3UTR 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.

Gene Ontology (GO) - Molecular Function for RBM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding TAS,IDA 19561594
GO:0003729 mRNA binding IDA 21518792
GO:0003730 mRNA 3-UTR binding ISS --
GO:0005515 protein binding IPI 12628928
genes like me logo Genes that share ontologies with RBM4: view
genes like me logo Genes that share phenotypes with RBM4: view

Animal Models for RBM4 Gene

MGI Knock Outs for RBM4:

Animal Model Products

CRISPR Products

miRNA for RBM4 Gene

miRTarBase miRNAs that target RBM4

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RBM4 Gene

Localization for RBM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM4 Gene

Nucleus. Nucleus, nucleolus. Nucleus speckle. Cytoplasm. Cytoplasmic granule. 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.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RBM4 gene
Compartment Confidence
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for RBM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 16777844
GO:0005654 nucleoplasm IDA 12628928
GO:0005730 nucleolus IEA,IDA 12628928
GO:0005737 cytoplasm IDA,IEA 12628928
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with RBM4: view

Pathways & Interactions for RBM4 Gene

genes like me logo Genes that share pathways with RBM4: view

Pathways by source for RBM4 Gene

1 BioSystems pathway for RBM4 Gene

SIGNOR curated interactions for RBM4 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for RBM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IDA 12628928
GO:0002190 cap-independent translational initiation IDA 17284590
GO:0002192 IRES-dependent translational initiation IDA 17284590
GO:0006396 RNA processing TAS 9169144
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with RBM4: view

Drugs & Compounds for RBM4 Gene

(1) Drugs for RBM4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RBM4: view

Transcripts for RBM4 Gene

Unigene Clusters for RBM4 Gene

RNA binding motif protein 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RBM4 Gene

No ASD Table

Relevant External Links for RBM4 Gene

GeneLoc Exon Structure for
RBM4
ECgene alternative splicing isoforms for
RBM4

Expression for RBM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RBM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RBM4 Gene

This gene is overexpressed in Fetal Brain (7.9) and Fetal ovary (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RBM4 Gene



Protein tissue co-expression partners for RBM4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RBM4 Gene:

RBM4

SOURCE GeneReport for Unigene cluster for RBM4 Gene:

Hs.523822

mRNA Expression by UniProt/SwissProt for RBM4 Gene:

Q9BWF3-RBM4_HUMAN
Tissue specificity: Expressed in the cerebellum. Expressed in neurons and glial cells, including layers II neurons in the frontal cortex and CA1 pyramidal neurons in the hippocampus. Expressed in heart, liver, pancreas, skeletal muscle, placenta, primary fibroblasts and peripheral blood monocytes (at protein level). Ubiquitously expressed. Highly expressed in heart, placenta and skeletal muscle. Weakly expressed in pancreas, kidney, liver, lung and brain.

Evidence on tissue expression from TISSUES for RBM4 Gene

  • Nervous system(4.2)
  • Lung(4)
  • Pancreas(4)
  • Skin(4)
genes like me logo Genes that share expression patterns with RBM4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBM4 Gene

Orthologs for RBM4 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RBM4 34 35
  • 99.91 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 99 (a)
OneToMany
RBM4 34
  • 96.34 (n)
cow
(Bos Taurus)
Mammalia RBM4 34 35
  • 94.11 (n)
mouse
(Mus musculus)
Mammalia Rbm4 34 16 35
  • 93.98 (n)
Gm21992 35
  • 73 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Rbm4 34
  • 93.41 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 92 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 92 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 35
  • 88 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 76 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii rbm4.2 35
  • 46 (a)
ManyToMany
rbm4.1 35
  • 45 (a)
ManyToMany
rbm4.3 35
  • 43 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta lark 36 35
  • 49 (a)
worm
(Caenorhabditis elegans)
Secernentea rnp-1 35
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 22 (a)
OneToMany
Species where no ortholog for RBM4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for RBM4 Gene

ENSEMBL:
Gene Tree for RBM4 (if available)
TreeFam:
Gene Tree for RBM4 (if available)

Paralogs for RBM4 Gene

Paralogs for RBM4 Gene

(9) SIMAP similar genes for RBM4 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for RBM4 Gene

genes like me logo Genes that share paralogs with RBM4: view

Variants for RBM4 Gene

Sequence variations from dbSNP and Humsavar for RBM4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000086987 -- 66,638,683(+) GCGGC(C/T)GCCGC intron-variant, utr-variant-5-prime
rs1000177182 -- 66,640,753(+) TGGTT(A/T)GGGGG intron-variant
rs1000341221 -- 66,646,975(+) AAATC(C/T)AAAGA intron-variant
rs1000426657 -- 66,657,867(+) CACTG(A/G)CGCAT intron-variant
rs1000670481 -- 66,666,498(+) CCTGG(A/C)AGGTA intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for RBM4 Gene

Variant ID Type Subtype PubMed ID
esv990794 OTHER inversion 20482838
nsv518919 CNV loss 19592680
nsv522277 CNV loss 19592680
nsv975943 CNV duplication 23825009

Variation tolerance for RBM4 Gene

Residual Variation Intolerance Score: 12.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.03; 0.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RBM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM4 Gene

Disorders for RBM4 Gene

Relevant External Links for RBM4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RBM4

No disorders were found for RBM4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RBM4 Gene

Publications for RBM4 Gene

  1. Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB. (PMID: 16260624) Lin J.C. … Tarn W.Y. (Mol. Cell. Biol. 2005) 2 3 4 22 64
  2. Cell stress modulates the function of splicing regulatory protein RBM4 in translation control. (PMID: 17284590) Lin J.C. … Tarn W.Y. (Proc. Natl. Acad. Sci. U.S.A. 2007) 3 4 22 64
  3. RBM4 interacts with an intronic element and stimulates tau exon 10 inclusion. (PMID: 16777844) Kar A. … Wu J.Y. (J. Biol. Chem. 2006) 3 4 22 64
  4. Lark is the splicing factor RBM4 and exhibits unique subnuclear localization properties. (PMID: 16907643) Markus M.A. … Morris B.J. (DNA Cell Biol. 2006) 3 4 22 64
  5. A novel splicing regulator shares a nuclear import pathway with SR proteins. (PMID: 12628928) Lai M.-C. … Tarn W.-Y. (EMBO J. 2003) 3 4 22 64

Products for RBM4 Gene

Sources for RBM4 Gene

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