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    RBM4 RNA binding motif protein 4 [ Homo sapiens (human) ]

    Gene ID: 5936, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RBM4provided by HGNC
    Official Full Name
    RNA binding motif protein 4provided by HGNC
    Primary source
    HGNC:HGNC:9901
    See related
    Ensembl:ENSG00000173933 MIM:602571; AllianceGenome:HGNC:9901
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LARK; RBM4A; ZCRB3A; ZCCHC21
    Summary
    Enables RNA binding activity and cyclin binding activity. Involved in several processes, including IRES-dependent translational initiation of linear mRNA; negative regulation of translation; and regulation of alternative mRNA splicing, via spliceosome. Located in cytoplasmic stress granule; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 17.5), ovary (RPKM 17.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM4 in Genome Data Viewer
    Location:
    11q13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66638703..66668380)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66634947..66664627)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66406174..66435851)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5053 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66384051-66384984 Neighboring gene RBM14-RBM4 readthrough Neighboring gene RNA, U4 small nuclear 39, pseudogene Neighboring gene hESC enhancers GRCh37_chr11:66405625-66406338 and GRCh37_chr11:66406339-66407050 Neighboring gene RNA binding motif protein 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66410755-66411278 Neighboring gene MPRA-validated peak1306 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66453249-66453749 Neighboring gene RNA binding motif protein 4B Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66462288-66462788 Neighboring gene spectrin beta, non-erythrocytic 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66487347-66488304 Neighboring gene RNA, 7SL, cytoplasmic 12, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66511467-66511967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5057 Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene fragile site, folic acid type, rare, fra(11)(q13.3) Neighboring gene complement C1q binding protein pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Alanine repeats influence protein localization in splicing speckles and paraspeckles. Chang SH, et al. Nucleic Acids Res, 2014 Dec 16. PMID 25414336, Free PMC Article
    2. The impact of the RBM4-initiated splicing cascade on modulating the carcinogenic signature of colorectal cancer cells. Lin JC, et al. Sci Rep, 2017 Mar 9. PMID 28276498, Free PMC Article
    3. A Comprehensive Prognostic and Immune Infiltration Analysis of RBM4 in Pan-Cancer. Ding JJ, et al. Front Biosci (Landmark Ed), 2024 Feb 23. PMID 38420804
    4. The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Wang Y, et al. Cancer Cell, 2014 Sep 8. PMID 25203323, Free PMC Article
    5. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4. Niu K, et al. Int J Mol Sci, 2022 Jan 11. PMID 35054929, Free PMC Article

    See all (155) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Overexpression of RBM4 promotes acute myeloid leukemia cell differentiation by regulating alternative splicing of TFEB.
      Title: Overexpression of RBM4 promotes acute myeloid leukemia cell differentiation by regulating alternative splicing of TFEB.
    2. A Comprehensive Prognostic and Immune Infiltration Analysis of RBM4 in Pan-Cancer.
      Title: A Comprehensive Prognostic and Immune Infiltration Analysis of RBM4 in Pan-Cancer.
    3. RBM4 dictates ESCC cell fate switch from cellular senescence to glutamine-addiction survival through inhibiting LKB1-AMPK-axis.
      Title: RBM4 dictates ESCC cell fate switch from cellular senescence to glutamine-addiction survival through inhibiting LKB1-AMPK-axis.
    4. RBM4 inhibits the growth of clear cell renal cell carcinoma by enhancing the stability of p53 mRNA.
      Title: RBM4 inhibits the growth of clear cell renal cell carcinoma by enhancing the stability of p53 mRNA.
    5. RBM4 regulates cellular senescence via miR1244/SERPINE1 axis.
      Title: RBM4 regulates cellular senescence via miR1244/SERPINE1 axis.
    6. RNA-binding motif 4 promotes angiogenesis in HCC by selectively activating VEGF-A expression.
      Title: RNA-binding motif 4 promotes angiogenesis in HCC by selectively activating VEGF-A expression.
    7. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4.
      Title: G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4.
    8. Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination.
      Title: Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination.
    9. USP3 promotes proliferation of non-small cell lung cancer through regulating RBM4.
      Title: USP3 promotes proliferation of non-small cell lung cancer through regulating RBM4.
    10. Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4.
      Title: Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4.
    Submit: New GeneRIF Correction See all GeneRIFs (35)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ36727, MGC75138, DKFZp547K0918

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cyclin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables mRNA 3'-UTR binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables miRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pre-mRNA intronic binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pre-mRNA intronic pyrimidine-rich binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in IRES-dependent translational initiation of linear mRNA IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cap-independent translational initiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in circadian regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in enteroendocrine cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in entrainment of circadian clock by photoperiod ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in insulin secretion involved in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in miRNA-mediated gene silencing by inhibition of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of translation in response to stress IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of translational initiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pancreas development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of insulin receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of nucleocytoplasmic transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to arsenic-containing substance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding protein 4
    Names
    RNA-binding motif protein 4a
    lark homolog
    transcriptional coactivator CoAZ
    zinc finger CCHC-type and RNA binding motif 3A

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001198843.2 → NP_001185772.1  RNA-binding protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001185772.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      BC064960, DC366746
      Consensus CDS
      CCDS55776.1
      UniProtKB/TrEMBL
      E9PM61
      Related
      ENSP00000381680.4, ENST00000398692.8
      Conserved Domains (1) summary
      cl17169
      Location:78 → 138
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001198844.2 → NP_001185773.1  RNA-binding protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001185773.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AK303984, AP001157, CB242056
      Consensus CDS
      CCDS55777.1
      UniProtKB/TrEMBL
      U3KQD5
      Related
      ENSP00000413497.3, ENST00000396053.9
      Conserved Domains (2) summary
      cd12606
      Location:2 → 68
      RRM1_RBM4; RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)
      cl17169
      Location:78 → 143
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_002896.4 → NP_002887.2  RNA-binding protein 4 isoform 1

      See identical proteins and their annotated locations for NP_002887.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC032735, DC366746
      Consensus CDS
      CCDS41676.1
      UniProtKB/Swiss-Prot
      B3KUN0, B4E1U0, E7EQS3, O02916, Q4VC48, Q6P1P2, Q8WU85, Q9BWF3
      UniProtKB/TrEMBL
      A8K9U0
      Related
      ENSP00000309166.8, ENST00000310092.12
      Conserved Domains (4) summary
      PTZ00368
      Location:145 → 181
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
      smart00343
      Location:161 → 176
      ZnF_C2HC; zinc finger
      cd12606
      Location:2 → 68
      RRM1_RBM4; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4)
      cd12607
      Location:78 → 144
      RRM2_RBM4; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      66638703..66668380
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      66634947..66664627
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BWF3.1 GenPept UniProtKB/Swiss-Prot:Q9BWF3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools