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RBM5 RNA binding motif protein 5 [ Homo sapiens (human) ]

Gene ID: 10181, updated on 7-Apr-2024

Summary

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Official Symbol
RBM5provided by HGNC
Official Full Name
RNA binding motif protein 5provided by HGNC
Primary source
HGNC:HGNC:9902
See related
Ensembl:ENSG00000003756 MIM:606884; AllianceGenome:HGNC:9902
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
G15; H37; RMB5; LUCA15; LUCA-15
Summary
This gene is a candidate tumor suppressor gene which encodes a nuclear RNA binding protein that is a component of the spliceosome A complex. The encoded protein plays a role in the induction of cell cycle arrest and apoptosis through pre-mRNA splicing of multiple target genes including the tumor suppressor protein p53. This gene is located within the tumor suppressor region 3p21.3, and may play a role in the inhibition of tumor transformation and progression of several malignancies including lung cancer. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in skin (RPKM 32.9), endometrium (RPKM 30.9) and 25 other tissues See more
Orthologs
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Genomic context

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See RBM5 in Genome Data Viewer
Location:
3p21.31
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50088919..50119021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50118235..50148343)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50126352..50156454)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49949147-49949724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14377 Neighboring gene MON1 homolog A, secretory trafficking associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977213-49977735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977736-49978257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14379 Neighboring gene RNA binding motif protein 6 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50050258-50050926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50119658-50120158 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:50120996-50121560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126209-50126800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126801-50127391 Neighboring gene MPRA-validated peak4650 silencer Neighboring gene RBM5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50157731-50158609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50158610-50159487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50160473-50160973 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50162997-50163986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50170449-50170950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50172709-50173300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50177671-50178232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50178233-50178794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50188081-50188752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14381 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene Sharpr-MPRA regulatory region 10077 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:50207171-50207381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50207797-50208770 Neighboring gene semaphorin 3F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50230799-50231315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231316-50231832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231833-50232348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50232401-50232932 Neighboring gene G protein subunit alpha transducin 1

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. A bacterial virulence factor interacts with the splicing factor RBM5 and stimulates formation of nuclear RBM5 granules. Pourpre R, et al. Sci Rep, 2022 Dec 19. PMID 36535993, Free PMC Article
  2. A de novo paradigm for male infertility. Oud MS, et al. Nat Commun, 2022 Jan 10. PMID 35013161, Free PMC Article
  3. RBM5 Acts as Tumor Suppressor in Medulloblastoma through Regulating Wnt/β-Catenin Signaling. Yu J, et al. Eur Neurol, 2020. PMID 32610314
  4. Down-regulated RBM5 inhibits bladder cancer cell apoptosis by initiating an miR-432-5p/β-catenin feedback loop. Zhang YP, et al. FASEB J, 2019 Oct. PMID 31318608
  5. RBM5 inhibits tumorigenesis of gliomas through inhibition of Wnt/β-catenin signaling and induction of apoptosis. Jiang Y, et al. World J Surg Oncol, 2017 Jan 6. PMID 28061901, Free PMC Article

See all (120) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CHIP suppresses the proliferation and migration of A549 cells by mediating the ubiquitination of eIF2alpha and upregulation of tumor suppressor RBM5.
    Title: CHIP suppresses the proliferation and migration of A549 cells by mediating the ubiquitination of eIF2α and upregulation of tumor suppressor RBM5.
  2. RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9.
    Title: RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9.
  3. Elucidating the role of RBM5 in osteoclastogenesis: a novel potential therapeutic target for osteoporosis.
    Title: Elucidating the role of RBM5 in osteoclastogenesis: a novel potential therapeutic target for osteoporosis.
  4. RNA-binding protein PUM2 promotes T-cell acute lymphoblastic leukemia via competitively binding to RBM5 3'UTR with miR-28-5p.
    Title: RNA-binding protein PUM2 promotes T-cell acute lymphoblastic leukemia via competitively binding to RBM5 3'UTR with miR-28-5p.
  5. A bacterial virulence factor interacts with the splicing factor RBM5 and stimulates formation of nuclear RBM5 granules.
    Title: A bacterial virulence factor interacts with the splicing factor RBM5 and stimulates formation of nuclear RBM5 granules.
  6. A de novo paradigm for male infertility.
    Title: A de novo paradigm for male infertility.
  7. Circular circPSMC3 inhibits hepatocellular carcinoma migration and invasion by upregulating RBM5.
    Title: Circular circPSMC3 inhibits hepatocellular carcinoma migration and invasion by upregulating RBM5.
  8. RBM5 Acts as Tumor Suppressor in Medulloblastoma through Regulating Wnt/beta-Catenin Signaling.
    Title: RBM5 Acts as Tumor Suppressor in Medulloblastoma through Regulating Wnt/β-Catenin Signaling.
  9. Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5.
    Title: Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5.
  10. RBM5 expression was significantly down-regulated in bladder cancer tissues. Downrergulated RBM5 inhibits bladder cancer cell apoptosis via miR-432-5p/beta-catenin signaling.
    Title: Down-regulated RBM5 inhibits bladder cancer cell apoptosis by initiating an miR-432-5p/β-catenin feedback loop.
Submit: New GeneRIF Correction See all GeneRIFs (42)

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
Discovery and refinement of loci associated with lipid levels.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of RNA binding motif protein 5 (RBM5) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

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

  • FLJ39876

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of apoptotic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of alternative mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spliceosomal complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding protein 5
Names
putative tumor suppressor LUCA15
renal carcinoma antigen NY-REN-9

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.

Genomic

  1. NG_030403.1 RefSeqGene

    Range
    5012..35114
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005778.4 → NP_005769.1  RNA-binding protein 5

    See identical proteins and their annotated locations for NP_005769.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and is protein coding.
    Source sequence(s)
    AC104450, AF091263, BM985111, CN293007, DA776815, DB080737
    Consensus CDS
    CCDS2810.1
    UniProtKB/Swiss-Prot
    B2RA45, B4DM16, B4DMF9, B4DZ63, P52756, Q93021, Q9BU14, Q9HDA6, Q9UKY8, Q9UL24
    Related
    ENSP00000343054.3, ENST00000347869.8
    Conserved Domains (7) summary
    COG0724
    Location:40 → 181
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12752
    Location:93 → 179
    RRM1_RBM5; RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)
    cd12755
    Location:229 → 314
    RRM2_RBM5; RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)
    sd00025
    Location:185 → 204
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00641
    Location:181 → 210
    zf-RanBP; Zn-finger in Ran binding protein and others
    pfam01585
    Location:743 → 787
    G-patch; G-patch domain
    cd16168
    Location:455 → 510
    OCRE_RBM5; OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins

RNA

  1. NR_036627.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC104450, AK297249, AU129811, BM985111, BX441555, DB080737, DR762951

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    50088919..50119021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533262.3 → XP_011531564.1  RNA-binding protein 5 isoform X3

    Conserved Domains (7) summary
    COG0724
    Location:40 → 181
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12752
    Location:93 → 179
    RRM1_RBM5; RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)
    cd12755
    Location:229 → 314
    RRM2_RBM5; RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)
    sd00025
    Location:185 → 204
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00641
    Location:181 → 210
    zf-RanBP; Zn-finger in Ran binding protein and others
    pfam01585
    Location:669 → 713
    G-patch; G-patch domain
    cd16168
    Location:455 → 510
    OCRE_RBM5; OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins

  2. XM_006712917.3 → XP_006712980.1  RNA-binding protein 5 isoform X1

    Conserved Domains (8) summary
    COG0724
    Location:40 → 181
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12752
    Location:93 → 179
    RRM1_RBM5; RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)
    cd12755
    Location:229 → 314
    RRM2_RBM5; RNA recognition motif 2 in vertebrate RNA-binding protein 5 (RBM5)
    sd00025
    Location:185 → 204
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam00641
    Location:181 → 210
    zf-RanBP; Zn-finger in Ran binding protein and others
    pfam01585
    Location:684 → 728
    G-patch; G-patch domain
    cd16074
    Location:425 → 431
    OCRE; OCRE repeat 4 [structural motif]
    cl23757
    Location:423 → 451
    OCRE; OCRE domain

  3. XM_047447138.1 → XP_047303094.1  RNA-binding protein 5 isoform X4

  4. XM_011533261.3 → XP_011531563.1  RNA-binding protein 5 isoform X2

    Conserved Domains (4) summary
    COG0724
    Location:40 → 181
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12752
    Location:93 → 179
    RRM1_RBM5; RNA recognition motif 1 in vertebrate RNA-binding protein 5 (RBM5)
    pfam01585
    Location:669 → 713
    G-patch; G-patch domain
    cd16168
    Location:381 → 436
    OCRE_RBM5; OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins

  5. XM_017005504.3 → XP_016860993.1  RNA-binding protein 5 isoform X5

    Conserved Domains (4) summary
    smart00443
    Location:608 → 654
    G_patch; glycine rich nucleic binding domain
    smart00360
    Location:99 → 171
    RRM; RNA recognition motif
    cd16074
    Location:351 → 357
    OCRE; OCRE repeat 4 [structural motif]
    cl23757
    Location:349 → 377
    OCRE; OCRE domain

  6. XM_047447140.1 → XP_047303096.1  RNA-binding protein 5 isoform X7

  7. XM_047447139.1 → XP_047303095.1  RNA-binding protein 5 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50118235..50148343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344846.1 → XP_054200821.1  RNA-binding protein 5 isoform X3

  2. XM_054344844.1 → XP_054200819.1  RNA-binding protein 5 isoform X1

  3. XM_054344847.1 → XP_054200822.1  RNA-binding protein 5 isoform X4

  4. XM_054344845.1 → XP_054200820.1  RNA-binding protein 5 isoform X2

  5. XM_054344848.1 → XP_054200823.1  RNA-binding protein 5 isoform X5

  6. XM_054344850.1 → XP_054200825.1  RNA-binding protein 5 isoform X7

  7. XM_054344849.1 → XP_054200824.1  RNA-binding protein 5 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52756.2 GenPept UniProtKB/Swiss-Prot:P52756

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