RBM5 Gene (Protein Coding)

RNA Binding Motif Protein 5

GC03P050110
GIFtS:
39
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 3p2... See more...

Aliases for RBM5 Gene

Aliases for RBM5 Gene

  • RNA Binding Motif Protein 5 2 3 5
  • Putative Tumor Suppressor LUCA15 3 4
  • Renal Carcinoma Antigen NY-REN-9 3 4
  • RNA-Binding Protein 5 3 4
  • LUCA-15 2 3
  • LUCA15 2 3
  • H37 2 3
  • RNA-Binding Motif Protein 5 4
  • Protein G15 4
  • RMB5 3
  • RBM5 5
  • G15 3

External Ids for RBM5 Gene

Previous GeneCards Identifiers for RBM5 Gene

  • GC03M049830
  • GC03M050000
  • GC03P049980
  • GC03P050085
  • GC03P050101
  • GC03P050094
  • GC03P050103

Summaries for RBM5 Gene

Entrez Gene Summary for RBM5 Gene

  • 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]

GeneCards Summary for RBM5 Gene

RBM5 (RNA Binding Motif Protein 5) is a Protein Coding gene. Diseases associated with RBM5 include Lung Cancer and Testis Seminoma. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is RBM10.

UniProtKB/Swiss-Prot Summary for RBM5 Gene

  • Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5' and 3' splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis.

Gene Wiki entry for RBM5 Gene

Additional gene information for RBM5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RBM5 Gene

Genomics for RBM5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RBM5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBM5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RBM5

Top Transcription factor binding sites by QIAGEN in the RBM5 gene promoter:
  • AML1a
  • CREB
  • deltaCREB
  • HSF1 (long)
  • HSF1short
  • NRSF form 1
  • NRSF form 2
  • Pax-2a
  • Spz1
  • SRY

Genomic Locations for RBM5 Gene

Genomic Locations for RBM5 Gene
chr3:50,088,919-50,119,021
(GRCh38/hg38)
Size:
30,103 bases
Orientation:
Plus strand
chr3:50,126,341-50,156,454
(GRCh37/hg19)
Size:
30,114 bases
Orientation:
Plus strand

Genomic View for RBM5 Gene

Genes around RBM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM5 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RBM5 Gene

Proteins for RBM5 Gene

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  • Protein details for RBM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P52756-RBM5_HUMAN
    Recommended name:
    RNA-binding protein 5
    Protein Accession:
    P52756
    Secondary Accessions:
    • B2RA45
    • B4DM16
    • B4DMF9
    • B4DZ63
    • Q93021
    • Q9BU14
    • Q9HDA6
    • Q9UKY8
    • Q9UL24

    Protein attributes for RBM5 Gene

    Size:
    815 amino acids
    Molecular mass:
    92154 Da
    Quaternary structure:
    • Component of the spliceosome A complex (also known as the prespliceosome). Appears to dissociate from the spliceosome upon formation of the spliceosome B complex (also known as the precatalytic spliceosome), in which the heterotrimeric U4/U6.U5 snRNPs are bound. Interacts with U2AF2; this interaction is direct. Also interacts with ACIN1, PRPF8, SFRS3, SNRPB, SNRPN, SNRNP70 and SNRNP200; these interactions may be indirect.
    SequenceCaution:
    • Sequence=BAG59728.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=BAG59871.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=BAG63975.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RBM5 Gene

    Alternative splice isoforms for RBM5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBM5 Gene

Protein Expression for RBM5 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RBM5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RBM5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RBM5 Gene

Domains & Families for RBM5 Gene

Gene Families for RBM5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RBM5 Gene

InterPro:
Blocks:
  • Zn-finger, Ran-binding
  • RNA-binding region RNP-1 (RNA recognition motif)
  • D111/G-patch domain
ProtoNet:

Suggested Antigen Peptide Sequences for RBM5 Gene

GenScript: Design optimal peptide antigens:
  • Renal carcinoma antigen NY-REN-9 (RBM5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P52756

UniProtKB/Swiss-Prot:

RBM5_HUMAN :
  • Belongs to the RBM5/RBM10 family.
Family:
  • Belongs to the RBM5/RBM10 family.
genes like me logo Genes that share domains with RBM5: view

Function for RBM5 Gene

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Molecular function for RBM5 Gene

UniProtKB/Swiss-Prot Function:
Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5' and 3' splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis.
GENATLAS Biochemistry:
RNA binding protein 5 in the TSG3B region,homolog with DXS8237E,located in a region duplicated for the Xp11.3-p11.23 region containing UBE1 and DXS8237E

Phenotypes From GWAS Catalog for RBM5 Gene

Gene Ontology (GO) - Molecular Function for RBM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding TAS 10352938
GO:0003723 RNA binding TAS,IBA 21873635
GO:0003729 mRNA binding IDA 18840686
GO:0005515 protein binding IPI 18951082
genes like me logo Genes that share ontologies with RBM5: view
genes like me logo Genes that share phenotypes with RBM5: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBM5 Gene

Localization for RBM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM5 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RBM5 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 18951082
GO:0005654 nucleoplasm IDA,TAS --
GO:0005681 spliceosomal complex IEA,TAS 18951082
genes like me logo Genes that share ontologies with RBM5: view

Pathways & Interactions for RBM5 Gene

genes like me logo Genes that share pathways with RBM5: view

Pathways by source for RBM5 Gene

1 BioSystems pathway for RBM5 Gene

Gene Ontology (GO) - Biological Process for RBM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IDA 18951082
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IEA,IDA 18840686
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006396 RNA processing TAS 10352938
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with RBM5: view

No data available for SIGNOR curated interactions for RBM5 Gene

Drugs & Compounds for RBM5 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for RBM5 Gene

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  3. Inhibitory RNA
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mRNA/cDNA for RBM5 Gene

1 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
26 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM5

Alternative Splicing Database (ASD) splice patterns (SP) for RBM5 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d · 7e ^ 8 ^ 9a · 9b · 9c · 9d ^ 10 ^ 11a ·
SP1: - - - - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: -
SP5: - - - - - -
SP6:
SP7: - - - - - - - -
SP8: - - - - - - - - - -
SP9:
SP10:
SP11:
SP12: - - - - - - - - - - - - - - - - -
SP13: - - -
SP14: - - - - - -
SP15: - -
SP16: - -
SP17: - - - - - - - - - - - - - - - - - - - -
SP18: -
SP19:
SP20: - -
SP21:
SP22:
SP23:
SP24:

ExUns: 11b ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b · 25c ^ 26a · 26b ^ 27 ^ 28a ·
SP1: - - -
SP2: - -
SP3: -
SP4: -
SP5: -
SP6: - -
SP7:
SP8:
SP9: - - - -
SP10:
SP11: - - - -
SP12: - -
SP13:
SP14:
SP15:
SP16:
SP17: -
SP18:
SP19:
SP20:
SP21:
SP22: -
SP23: -
SP24:

ExUns: 28b ^ 29a · 29b · 29c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:

Relevant External Links for RBM5 Gene

GeneLoc Exon Structure for
RBM5

Expression for RBM5 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RBM5 Gene

mRNA expression in normal human tissues for RBM5 Gene
mRNA expression by BioGPS for RBM5 GenemRNA expression by GTEx for RBM5 Gene

Protein differential expression in normal tissues from HIPED for RBM5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (26.9) and CD8 Tcells (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RBM5 Gene



Protein tissue co-expression partners for RBM5 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RBM5

SOURCE GeneReport for Unigene cluster for RBM5 Gene:

Hs.439480

mRNA Expression by UniProt/SwissProt for RBM5 Gene:

P52756-RBM5_HUMAN
Tissue specificity: Isoform 5 is widely expressed in normal tissues and is expressed at increased levels in T-leukemic cell lines.

Evidence on tissue expression from TISSUES for RBM5 Gene

  • Nervous system(5)
  • Liver(4.5)
  • Lung(4)
  • Kidney(3)
  • Intestine(2.9)
  • Skin(2.9)
  • Muscle(2.7)
  • Bone marrow(2.6)
  • Heart(2.6)
  • Lymph node(2.5)
  • Blood(2.5)
  • Stomach(2.4)
  • Thyroid gland(2.3)
  • Spleen(2.1)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with RBM5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBM5 Gene

Orthologs for RBM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBM5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RBM5 30 31
  • 99.67 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RBM5 30 31
  • 94.11 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RBM5 31
  • 94 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RBM5 30 31
  • 93.29 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RBM5 31
  • 93 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rbm5 30
  • 92.27 (n)
Mouse
(Mus musculus)
 Mammalia Rbm5 30 17 31
  • 92.11 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves RBM5 31
  • 85 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RBM5 31
  • 85 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rbm5 30
  • 72.77 (n)
Str.11018 30
African clawed frog
(Xenopus laevis)
 Amphibia MGC68576 30
Zebrafish
(Danio rerio)
 Actinopterygii rbm5 30 31
  • 67.25 (n)
 OneToOne
Dr.24454 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.12407 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG4896 31 32
  • 26 (a)
 ManyToMany
CG4887 31 32
  • 26 (a)
 ManyToMany
Worm
(Caenorhabditis elegans)
 Secernentea T08B2.5 30 31
  • 41.96 (n)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 44 (a)
 OneToMany
Species where no ortholog for RBM5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for RBM5 Gene

ENSEMBL:
Gene Tree for RBM5 (if available)
TreeFam:
Gene Tree for RBM5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RBM5: view image

Paralogs for RBM5 Gene

Paralogs for RBM5 Gene

(3) SIMAP similar genes for RBM5 Gene using alignment to 7 proteins:

  • RBM5_HUMAN
  • C9J9P7_HUMAN
  • C9JFQ5_HUMAN
  • C9JR02_HUMAN
  • F8W910_HUMAN
  • F8WE23_HUMAN
  • H7BYM9_HUMAN
genes like me logo Genes that share paralogs with RBM5: view

Variants for RBM5 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RBM5 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs56783610 - p.Lys163Asn

Additional dbSNP identifiers (rs#s) for RBM5 Gene

Structural Variations from Database of Genomic Variants (DGV) for RBM5 Gene

Variant ID Type Subtype PubMed ID
dgv806n67 CNV gain 20364138
dgv8316n54 CNV loss 21841781
nsv515986 CNV loss 19592680
nsv523662 CNV loss 19592680
nsv590249 CNV loss 21841781
nsv818139 CNV loss 17921354
nsv822083 CNV loss 20364138
nsv834690 CNV loss 17160897

Variation tolerance for RBM5 Gene

Residual Variation Intolerance Score: 5.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.52; 11.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RBM5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM5 Gene

Disorders for RBM5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RBM5 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lung cancer
  • adenocarcinoma of lung
testis seminoma
  • seminoma
- elite association - COSMIC cancer census association via MalaCards
Search RBM5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RBM5

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RBM5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBM5 Gene

Publications for RBM5 Gene

  1. RBM5 is a male germ cell splicing factor and is required for spermatid differentiation and male fertility. (PMID: 23935508) O'Bryan MK … Jamsai D (PLoS genetics 2013) 2 3
  2. Identification and characterisation of a novel antisense non-coding RNA from the RBM5 gene locus. (PMID: 19559772) Rintala-Maki ND … Sutherland LC (Gene 2009) 3 23
  3. Up-regulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM5. (PMID: 18840686) Fushimi K … Wu JY (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4
  4. Promoter methylation study of the H37/RBM5 tumor suppressor gene from the 3p21.3 human lung cancer tumor suppressor locus. (PMID: 18038152) Oh JJ … Slamon DJ (Human genetics 2008) 3 23
  5. RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. (PMID: 18851835) Bonnal S … Valcárcel J (Molecular cell 2008) 3 4

ExternalLinks

View latest publications for RBM5 gene in Mastermind

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Sources for RBM5 Gene