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RBM3 RNA binding motif protein 3 [ Homo sapiens (human) ]

Gene ID: 5935, updated on 2-Nov-2024

Summary

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Official Symbol
RBM3provided by HGNC
Official Full Name
RNA binding motif protein 3provided by HGNC
Primary source
HGNC:HGNC:9900
See related
Ensembl:ENSG00000102317 MIM:300027; AllianceGenome:HGNC:9900
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNPL; IS1-RNPL
Summary
This gene is a member of the glycine-rich RNA-binding protein family and encodes a protein with one RNA recognition motif (RRM) domain. Expression of this gene is induced by cold shock and low oxygen tension. A pseudogene exists on chromosome 1. Multiple alternatively spliced transcript variants that are predicted to encode different isoforms have been characterized although some of these variants fit nonsense-mediated decay (NMD) criteria. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 49.3), fat (RPKM 41.3) and 25 other tissues See more
Orthologs
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Genomic context

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See RBM3 in Genome Data Viewer
Location:
Xp11.23
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48574484..48581162)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (47983492..47990170)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48432872..48439550)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20817 Neighboring gene CRISPRi-validated cis-regulatory element chrX.929 Neighboring gene EBP cholestenol delta-isomerase Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48397756-48398256 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48398257-48398757 Neighboring gene TBC1 domain family member 25 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48426332-48426532 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 4 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48436957-48437166 Neighboring gene MRPL32 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29606 Neighboring gene WD repeat domain 13 Neighboring gene Sharpr-MPRA regulatory region 1547

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 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. Cold-Inducible Protein RBM3 Protects UV Irradiation-Induced Apoptosis in Neuroblastoma Cells by Affecting p38 and JNK Pathways and Bcl2 Family Proteins. Zhuang RJ, et al. J Mol Neurosci, 2017 Oct. PMID 28831692
  2. Differential expression of the RNA-binding motif protein 3 in human astrocytoma. Zhang HT, et al. Chin Med J (Engl), 2013. PMID 23673116
  3. Low RBM3 protein expression correlates with clinical stage, prognostic classification and increased risk of treatment failure in testicular non-seminomatous germ cell cancer. Olofsson SE, et al. PLoS One, 2015. PMID 25811459, Free PMC Article
  4. Loss of RNA-binding motif protein 3 expression is associated with right-sided localization and poor prognosis in colorectal cancer. Melling N, et al. Histopathology, 2016 Jan. PMID 25922889
  5. RNA binding protein RBM3 increases β-catenin signaling to increase stem cell characteristics in colorectal cancer cells. Venugopal A, et al. Mol Carcinog, 2016 Nov. PMID 26331352, Free PMC Article

See all (125) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RBM3 Accelerates Wound Healing of Skin in Diabetes through ERK1/2 Signaling.
    Title: RBM3 Accelerates Wound Healing of Skin in Diabetes through ERK1/2 Signaling.
  2. RBM3 is associated with acute lung injury in septic mice and patients via the NF-kappaB/NLRP3 pathway.
    Title: RBM3 is associated with acute lung injury in septic mice and patients via the NF-κB/NLRP3 pathway.
  3. Influence of RRM, RGG and Potential Phosphorylated Sites in Cold-Inducible Protein RBM3 on its Subcellular Localization and Neuroprotective Effects.
    Title: Influence of RRM, RGG and Potential Phosphorylated Sites in Cold-Inducible Protein RBM3 on its Subcellular Localization and Neuroprotective Effects.
  4. RBM3 interacts with Raptor to regulate autophagy and protect cardiomyocytes from ischemia-reperfusion-induced injury.
    Title: RBM3 interacts with Raptor to regulate autophagy and protect cardiomyocytes from ischemia-reperfusion-induced injury.
  5. Mild hypothermia ameliorates hepatic ischemia reperfusion injury by inducing RBM3 expression.
    Title: Mild hypothermia ameliorates hepatic ischemia reperfusion injury by inducing RBM3 expression.
  6. RBM3 is an outstanding cold shock protein with multiple physiological functions beyond hypothermia.
    Title: RBM3 is an outstanding cold shock protein with multiple physiological functions beyond hypothermia.
  7. MZF1 alleviates oxidative stress and apoptosis induced by rotenone in SH-SY5Y cells by promoting RBM3 transcription.
    Title: MZF1 alleviates oxidative stress and apoptosis induced by rotenone in SH-SY5Y cells by promoting RBM3 transcription.
  8. Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.
    Title: Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.
  9. PRR11 unveiled as a top candidate biomarker within the RBM3-regulated transcriptome in pancreatic cancer.
    Title: PRR11 unveiled as a top candidate biomarker within the RBM3-regulated transcriptome in pancreatic cancer.
  10. Characterization of RNA-Binding Motif 3 (RBM3) Protein Levels and Nuclear Architecture Changes in Aggressive and Recurrent Prostate Cancer.
    Title: Characterization of RNA-Binding Motif 3 (RBM3) Protein Levels and Nuclear Architecture Changes in Aggressive and Recurrent Prostate Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (49)

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribosomal large subunit binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in RNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of large ribosomal subunit ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
RNA-binding protein 3
Names
RNA binding motif (RNP1, RRM) protein 3

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_006743.5 → NP_006734.1  RNA-binding protein 3

    See identical proteins and their annotated locations for NP_006734.1

    Status: REVIEWED

    Source sequence(s)
    AC115618, BC006825
    Consensus CDS
    CCDS14301.1
    UniProtKB/Swiss-Prot
    P98179
    Related
    ENSP00000365950.3, ENST00000376759.8
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    48574484..48581162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    47983492..47990170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001017430.1: Suppressed sequence

    Description
    NM_001017430.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_001017431.1: Suppressed sequence

    Description
    NM_001017431.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P98179.1 GenPept UniProtKB/Swiss-Prot:P98179

Gene LinkOut

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