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

Gene ID: 5936, updated on 10-Mar-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, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 17.5), ovary (RPKM 17.2) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66638703..66668380)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66634947..66664627)
105.20220307 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. 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
  2. Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Foroushani AK, et al. Proc Natl Acad Sci U S A, 2020 Oct 20. PMID 33020268, Free PMC Article
  3. RBM4 modulates the proliferation and expression of inflammatory factors via the alternative splicing of regulatory factors in HeLa cells. Wang WY, et al. Mol Genet Genomics, 2020 Jan. PMID 31489484
  4. 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
  5. Prognostic value of decreased expression of RBM4 in human gastric cancer. Yong H, et al. Sci Rep, 2016 Jun 21. PMID 27324405, Free PMC Article

See all (130) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. RBM4 regulates cellular senescence via miR1244/SERPINE1 axis.
    Title: RBM4 regulates cellular senescence via miR1244/SERPINE1 axis.
  5. 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.
  6. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4.
    Title: G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4.
  7. 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.
  8. 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.
  9. 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.
  10. The SRSF1 and RBM4 constitute an antagonistic mechanism on regulating the splicing profiles of HIF-1alpha gene, which is relevant to the oncogenic signatures of lung cancer cells.
    Title: SRSF1 and RBM4 differentially modulate the oncogenic effect of HIF-1α in lung cancer cells through alternative splicing mechanism.
Submit: New GeneRIF Correction See all GeneRIFs (34)

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)

Genotypes

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 mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
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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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_2023_10

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
Miscellaneous