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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. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for RBM4 Gene

Promoters and enhancers for RBM4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I066636 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 577 -0.3 -281 3.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 RBM4 ACTN3 EIF1AD RBM14 KDM2A SART1 ENSG00000255320 ENSG00000258297 CORO1B RELA
GH11I065851 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 67 -781.1 -781133 12.2 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MUS81 CFL1 EIF1AD POLA2 PCNX3 SART1 ENSG00000258297 ZFPL1 RBM14 RBM4
GH11I067116 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 64.5 +481.1 481086 5.7 PKNOX1 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF766 ZNF207 SP3 KDM2A ENSG00000258297 RBM14 ENSG00000254461 LOC105369352 RBM4 RCE1 RAD9A ENSG00000245156 ENSG00000255320
GH11I065886 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 43.5 -743.2 -743159 18.4 CLOCK ZFP64 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 FOSL1 FIBP CCDC85B SNX32 ENSG00000258297 EIF1AD RBM14 MUS81 SART1 POLA2
GH11I066000 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 53.1 -636.3 -636334 3 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 EIF1AD BANF1 ENSG00000258297 ZFPL1 PCNX3 POLA2 SART1 RBM14 RBM4 SF3B2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RBM4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RBM4 gene promoter:

Genomic Locations for RBM4 Gene

Genomic Locations for RBM4 Gene
chr11:66,638,617-66,668,385
(GRCh38/hg38)
Size:
29,769 bases
Orientation:
Plus strand
chr11:66,384,097-66,435,856
(GRCh37/hg19)

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.

No data available for DME Specific Peptides for RBM4 Gene

Domains & Families for RBM4 Gene

Gene 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.

Phenotypes From GWAS Catalog for RBM4 Gene

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 16777844
GO:0005654 nucleoplasm IDA 12628928
GO:0005730 nucleolus IDA,IEA 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 of linear mRNA 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)
  • Skin(4.1)
  • Lung(4)
  • Pancreas(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 33 34
  • 99.91 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 99 (a)
OneToMany
RBM4 33
  • 96.34 (n)
cow
(Bos Taurus)
Mammalia RBM4 33 34
  • 94.11 (n)
mouse
(Mus musculus)
Mammalia Rbm4 33 16 34
  • 93.98 (n)
Gm21992 34
  • 73 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Rbm4 33
  • 93.41 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 92 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 88 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 76 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii rbm4.2 34
  • 46 (a)
ManyToMany
rbm4.1 34
  • 45 (a)
ManyToMany
rbm4.3 34
  • 43 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta lark 35 34
  • 49 (a)
worm
(Caenorhabditis elegans)
Secernentea rnp-1 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs1000086987 -- 66,638,683(+) C/T 5_prime_UTR_variant
rs1000177182 -- 66,640,753(+) T/A intron_variant
rs1000341221 -- 66,646,975(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000426657 -- 66,657,867(+) G/A/T genic_downstream_transcript_variant, intron_variant
rs1000670481 -- 66,666,498(+) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant

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)

Additional Variant Information 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

Additional Disease Information for 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 JC … Tarn WY (Molecular and cellular biology 2005) 2 3 4 22 58
  2. Cell stress modulates the function of splicing regulatory protein RBM4 in translation control. (PMID: 17284590) Lin JC … Tarn WY (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4 22 58
  3. RBM4 interacts with an intronic element and stimulates tau exon 10 inclusion. (PMID: 16777844) Kar A … Wu JY (The Journal of biological chemistry 2006) 3 4 22 58
  4. Lark is the splicing factor RBM4 and exhibits unique subnuclear localization properties. (PMID: 16907643) Markus MA … Morris BJ (DNA and cell biology 2006) 3 4 22 58
  5. A novel splicing regulator shares a nuclear import pathway with SR proteins. (PMID: 12628928) Lai MC … Tarn WY (The EMBO journal 2003) 3 4 22 58

Products for RBM4 Gene

Sources for RBM4 Gene

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