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RBM25 Gene(Protein Coding)

RNA Binding Motif Protein 25

GCID:
GC14P073058
GIFtS:
50
Genes Participants
UDN Logo

Aliases for RBM25 Gene

Aliases for RBM25 Gene

  • RNA Binding Motif Protein 25 2 3 5
  • Functional Spliceosome-Associated Protein 94 2 3
  • RNA-Binding Region (RNP1, RRM) Containing 7 2 3
  • RNA-Binding Region-Containing Protein 7 3 4
  • Arg/Glu/Asp-Rich Protein Of 120 KDa 3 4
  • RED120 3 4
  • RNPC7 3 4
  • U1 Small Nuclear Ribonucleoprotein 1SNRP Homolog 3
  • Arg/Glu/Asp-Rich Protein, 120 KDa 3
  • RNA-Binding Motif Protein 25 4
  • RNA-Binding Protein 25 3
  • Protein S164 4
  • FSAP94 3
  • NET52 3
  • Snu71 3
  • S164 3

External Ids for RBM25 Gene

Previous HGNC Symbols for RBM25 Gene

  • RNPC7

Previous GeneCards Identifiers for RBM25 Gene

  • GC14P071517
  • GC14P072594
  • GC14P073525
  • GC14P053691

Summaries for RBM25 Gene

GeneCards Summary for RBM25 Gene

RBM25 (RNA Binding Motif Protein 25) is a Protein Coding gene. Diseases associated with RBM25 include Kabuki Syndrome 1. Among its related pathways are mRNA Splicing - Major Pathway. GO annotations related to this gene include nucleic acid binding and nucleotide binding.

UniProtKB/Swiss-Prot for RBM25 Gene

  • RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5-splice site (5-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5-ss usage through the 5-CGGGCA-3 RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5 ss in a 5-CGGGCA-3-dependent manner. Binds to the exonic splicing enhancer 5-CGGGCA-3 RNA sequence located within exon 2 of the BCL2L1 pre-mRNA. Also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure.

Gene Wiki entry for RBM25 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RBM25 Gene

Genomics for RBM25 Gene

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  1. Regulatory Element

Regulatory Elements for RBM25 Gene

Enhancers for RBM25 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14G073226 1.6 FANTOM5 Ensembl ENCODE 67.7 +169.4 169375 3.3 HDGF FOXA2 ZNF493 ZFP64 SIN3A ZNF121 GLIS2 KLF7 FOS ZNF202 RBM25 ELMSAN1 ENSG00000258891 PNMA1 LIN52 ENSG00000258443 PSEN1 LOC100420966 ENSG00000258695 LOC101928123
GH14G073767 1.9 FANTOM5 Ensembl ENCODE dbSUPER 33.5 +713.1 713104 7.9 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 SLC30A9 ENSG00000258559 RBM25 PTGR2 LOC100506476 PNMA1 ENSG00000223300 ELMSAN1 LINC02274 ACOT1 ENTPD5
GH14G073717 1.3 Ensembl ENCODE dbSUPER 43.2 +660.3 660311 2.9 MXI1 NFIB ZNF195 RBBP5 ZNF121 ZFHX2 ZNF776 POLR2A ZNF350 HNF4G RBM25 ENSG00000258559 DNAL1 PNMA1 ELMSAN1 LOC100506476 ACOT1 NT5CP2 GC14P073756
GH14G072960 1.3 Ensembl ENCODE 26.7 -96.3 -96259 2.4 FOXA2 ATF1 ZNF133 ARID4B DMAP1 GLI4 ZNF2 ZNF48 YY1 ZNF302 RBM25 ELMSAN1 LOC101928123 DCAF4 LOC100420966 ZFYVE1 GC14P072963
GH14G073885 1.4 ENCODE dbSUPER 15.1 +829.0 829039 4.3 HDGF HNRNPUL1 PKNOX1 MLX CREB3L1 AGO1 WRNIP1 ARID4B SIN3A DMAP1 PTGR2 LOC100506476 LOC100420966 ELMSAN1 RBM25 ENSG00000223300 FCF1 PNMA1 FAM161B LIN52
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RBM25 on UCSC Golden Path with GeneCards custom track

Promoters for RBM25 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000070600 464 2201 PKNOX1 FOXA2 MLX CREB3L1 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF766

Transcription factor binding sites by QIAGEN in the RBM25 gene promoter:

Genomic Location for RBM25 Gene

Chromosome:
14
Start:
73,058,436 bp from pter
End:
73,123,898 bp from pter
Size:
65,463 bases
Orientation:
Plus strand

Genomic View for RBM25 Gene

Genes around RBM25 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM25 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM25 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RBM25 Gene

Proteins for RBM25 Gene

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  • Protein details for RBM25 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49756-RBM25_HUMAN
    Recommended name:
    RNA-binding protein 25
    Protein Accession:
    P49756
    Secondary Accessions:
    • A0PJL9
    • B2RNA8
    • B3KT03
    • Q2TA72
    • Q5XJ17
    • Q6P665
    • Q9H6A1
    • Q9UEQ5
    • Q9UIE9

    Protein attributes for RBM25 Gene

    Size:
    843 amino acids
    Molecular mass:
    100185 Da
    Quaternary structure:
    • Interacts with LUC7L3 and SRRM1. Specifically associates with functional splicing complexes, including Sm proteins and U1, U2, U4, U5 and U6 snRNAs. Associates with exon junction complex (EJC) proteins, including APEX1, BAT1, NCBP1, RBM8A and RNPS1. Interaction with NCBP1 is RNA-dependent.
    SequenceCaution:
    • Sequence=AAH62440.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH62440.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH83496.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAG52915.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RBM25 Gene

    Alternative splice isoforms for RBM25 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBM25 Gene

Protein Expression for RBM25 Gene

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

Post-translational modifications for RBM25 Gene

Other Protein References for RBM25 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RBM25 Gene

Domains & Families for RBM25 Gene

Gene Families for RBM25 Gene

HGNC:

Protein Domains for RBM25 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RBM25 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P49756

UniProtKB/Swiss-Prot:

RBM25_HUMAN :
  • The PWI domain binds nucleic acids with significant help from its N-terminal flanking basic region. It has an equal preference for binding to single- or double-stranded species, and it contributes to RBM25 role in modulation of alternative splicing, maybe by mediating RNA-dependent association with LUC7L3.
Domain:
  • The PWI domain binds nucleic acids with significant help from its N-terminal flanking basic region. It has an equal preference for binding to single- or double-stranded species, and it contributes to RBM25 role in modulation of alternative splicing, maybe by mediating RNA-dependent association with LUC7L3.
genes like me logo Genes that share domains with RBM25: view

Function for RBM25 Gene

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Molecular function for RBM25 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5-splice site (5-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5-ss usage through the 5-CGGGCA-3 RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5 ss in a 5-CGGGCA-3-dependent manner. Binds to the exonic splicing enhancer 5-CGGGCA-3 RNA sequence located within exon 2 of the BCL2L1 pre-mRNA. Also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure.

Gene Ontology (GO) - Molecular Function for RBM25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IDA,IEA 22658674
GO:0003729 mRNA binding IDA 18663000
GO:0005515 protein binding IPI 18663000
genes like me logo Genes that share ontologies with RBM25: view
genes like me logo Genes that share phenotypes with RBM25: view

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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBM25 Gene

Localization for RBM25 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM25 Gene

Nucleus speckle. Cytoplasm. Note=Colocalizes predominantly, with SFRS2 and LUC7L3 splicing factors, in nuclear speckles. Cytoplasmic localization is faint.

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 RBM25 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RBM25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005681 spliceosomal complex IBA --
GO:0005737 cytoplasm IEA --
GO:0016607 nuclear speck IDA,IEA 18663000
genes like me logo Genes that share ontologies with RBM25: view

Pathways & Interactions for RBM25 Gene

SuperPathways for RBM25 Gene

PathCards logo More details on SuperPathways for RBM25
SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
Spliceosome
.50
genes like me logo Genes that share pathways with RBM25: view

Pathways by source for RBM25 Gene

1 KEGG pathway for RBM25 Gene

Gene Ontology (GO) - Biological Process for RBM25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IDA 18663000
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0042981 regulation of apoptotic process IDA 18663000
genes like me logo Genes that share ontologies with RBM25: view

No data available for SIGNOR curated interactions for RBM25 Gene

Drugs & Compounds for RBM25 Gene

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No Compound Related Data Available

Transcripts for RBM25 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for RBM25 Gene

(3) REFSEQ mRNAs :
(16) Additional mRNA sequences :
(418) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RBM25 Gene

RNA binding motif protein 25:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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Alternative Splicing Database (ASD) splice patterns (SP) for RBM25 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b · 17c ^ 18 ^
SP1: - - -
SP2: -
SP3:
SP4:
SP5:
SP6: -
SP7:
SP8: -
SP9:

ExUns: 19a · 19b ^ 20 ^ 21 ^ 22a · 22b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for RBM25 Gene

GeneLoc Exon Structure for
RBM25
ECgene alternative splicing isoforms for
RBM25

Expression for RBM25 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RBM25 Gene

mRNA expression in normal human tissues for RBM25 Gene
mRNA expression by BioGPS for RBM25 GenemRNA expression by GTEx for RBM25 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RBM25 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RBM25 Gene



Protein tissue co-expression partners for RBM25 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RBM25 Gene:

RBM25

SOURCE GeneReport for Unigene cluster for RBM25 Gene:

Hs.531106

Evidence on tissue expression from TISSUES for RBM25 Gene

  • Nervous system(4.6)
  • Blood(4.4)
  • Kidney(4.4)
  • Liver(4.3)
  • Bone marrow(2.2)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with RBM25: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBM25 Gene

Orthologs for RBM25 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBM25 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
 Mammalia Rbm25 35
  • 100 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia RBM25 34 35
  • 99.92 (n)
dog
(Canis familiaris)
 Mammalia RBM25 35
  • 98 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia RBM25 35
  • 98 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia RBM25 35
  • 95 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia RBM25 34 35
  • 93.44 (n)
chicken
(Gallus gallus)
 Aves RBM25 34 35
  • 83.7 (n)
lizard
(Anolis carolinensis)
 Reptilia RBM25 35
  • 96 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.8931 34
African clawed frog
(Xenopus laevis)
 Amphibia Xl.1918 34
zebrafish
(Danio rerio)
 Actinopterygii rbm25 35
  • 71 (a)
 OneToMany
RBM25 (2 of 2) 35
  • 70 (a)
 OneToMany
-- 34
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.2941 34
fruit fly
(Drosophila melanogaster)
 Insecta CG4119 35
  • 34 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea W04D2.6 35
  • 35 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 40 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4527 34
Species where no ortholog for RBM25 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 RBM25 Gene

ENSEMBL:
Gene Tree for RBM25 (if available)
TreeFam:
Gene Tree for RBM25 (if available)

Paralogs for RBM25 Gene

No data available for Paralogs for RBM25 Gene

Variants for RBM25 Gene

Sequence variations from dbSNP and Humsavar for RBM25 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000014961 -- 73,105,348(+) TTTGA(C/G)AACTT intron-variant
rs1000040566 -- 73,097,957(+) AGGAA(A/G)TGTTC intron-variant
rs1000072095 -- 73,112,517(+) TGGTC(A/G)AGGAG intron-variant
rs1000076325 -- 73,073,031(+) CCATC(C/T)CAGCC intron-variant
rs1000080886 -- 73,063,302(+) CTGCC(A/G)CTATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RBM25 Gene

Variant ID Type Subtype PubMed ID
dgv133e215 CNV deletion 23714750
dgv3752n54 CNV loss 21841781
dgv3753n54 CNV loss 21841781
dgv3754n54 CNV loss 21841781
dgv3755n54 CNV loss 21841781
dgv3756n54 CNV loss 21841781
dgv3757n54 CNV loss 21841781
dgv3758n54 CNV loss 21841781
dgv3759n54 CNV loss 21841781
esv2658707 CNV deletion 23128226
esv2669446 CNV deletion 23128226
esv2677511 CNV deletion 23128226
esv2748862 CNV deletion 23290073
esv2748864 CNV deletion 23290073
esv27604 CNV loss 19812545
esv27860 CNV loss 19812545
esv33255 CNV loss 17666407
esv3551761 CNV deletion 23714750
esv3634899 CNV loss 21293372
esv3634900 CNV loss 21293372
nsv1035460 CNV gain 25217958
nsv1036282 CNV gain 25217958
nsv1048734 CNV gain 25217958
nsv1049819 CNV gain 25217958
nsv565050 CNV gain 21841781
nsv565051 CNV loss 21841781
nsv565052 CNV loss 21841781

Variation tolerance for RBM25 Gene

Residual Variation Intolerance Score: 5.95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.68; 14.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RBM25 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM25

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM25 Gene

Disorders for RBM25 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RBM25 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
kabuki syndrome 1
  • kabuki syndrome
- elite association - COSMIC cancer census association via MalaCards
Search RBM25 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RBM25

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RBM25
genes like me logo Genes that share disorders with RBM25: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBM25 Gene

Publications for RBM25 Gene

  1. Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. (PMID: 7596406) Sherrington R. … St George-Hyslop P.H. (Nature 1995) 2 3 4 64
  2. Crystal structure and functional characterization of the human RBM25 PWI domain and its flanking basic region. (PMID: 23190262) Gong D. … Shi Y. (Biochem. J. 2013) 3 4 64
  3. Role of RBM25/LUC7L3 in abnormal cardiac sodium channel splicing regulation in human heart failure. (PMID: 21859973) Gao G. … Dudley S.C. (Circulation 2011) 3 4 64
  4. Novel splicing factor RBM25 modulates Bcl-x pre-mRNA 5' splice site selection. (PMID: 18663000) Zhou A. … Huang S.C. (Mol. Cell. Biol. 2008) 3 4 64
  5. Identification and characterization of RED120: a conserved PWI domain protein with links to splicing and 3'-end formation. (PMID: 17560998) Fortes P. … Blencowe B.J. (FEBS Lett. 2007) 3 4 64

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