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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
A de novo paradigm for male infertility.
Title: A de novo paradigm for male infertility.
Circular circPSMC3 inhibits hepatocellular carcinoma migration and invasion by upregulating RBM5.
Title: Circular circPSMC3 inhibits hepatocellular carcinoma migration and invasion by upregulating RBM5.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC22669P19 (e-PCR)
- UniSTS:272131

D10S275 (e-PCR)
- UniSTS:147992

STS-AA037589 (e-PCR)
- UniSTS:3379

RH24950 (e-PCR)
- UniSTS:90462

D10S16 (e-PCR)
- UniSTS:155756

D3S3165 (e-PCR)
- UniSTS:153490

D3S3180 (e-PCR)
- UniSTS:153505

D3S3479E (e-PCR)
- UniSTS:154048

IB431 (e-PCR)
- UniSTS:72908

G16543 (e-PCR)
- UniSTS:25816

STS-AA001762 (e-PCR)
- UniSTS:53740

RH77698 (e-PCR)
- UniSTS:34804

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables RNA binding	HDA more info	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

NG_030403.1 RefSeqGene

Range

5012..35114

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

50088919..50119021

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
XM_047447138.1 → XP_047303094.1 RNA-binding protein 5 isoform X4
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
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
XM_047447140.1 → XP_047303096.1 RNA-binding protein 5 isoform X7
XM_047447139.1 → XP_047303095.1 RNA-binding protein 5 isoform X6