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Aliases for RBM39 Gene

Aliases for RBM39 Gene

  • RNA Binding Motif Protein 39 2 3 5
  • Coactivator Of Activating Protein-1 And Estrogen Receptors 2 3
  • Functional Spliceosome-Associated Protein 59 2 3
  • RNA-Binding Region (RNP1, RRM) Containing 2 2 3
  • Hepatocellular Carcinoma Protein 1 3 4
  • RNA-Binding Motif Protein 39 3 4
  • Splicing Factor HCC1 3 4
  • CAPER Alpha 3 4
  • RNPC2 3 4
  • HCC1 3 4
  • RNA-Binding Region-Containing Protein 2 4
  • RNA-Binding Protein 39 3
  • CAPERalpha 3
  • FSAP59 3
  • CAPER 3

External Ids for RBM39 Gene

Previous HGNC Symbols for RBM39 Gene

  • RNPC2

Previous GeneCards Identifiers for RBM39 Gene

  • GC20M033755
  • GC20M034291
  • GC20M031068

Summaries for RBM39 Gene

Entrez Gene Summary for RBM39 Gene

  • This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and alternative splicing, and it is also a transcriptional coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011]

GeneCards Summary for RBM39 Gene

RBM39 (RNA Binding Motif Protein 39) is a Protein Coding gene. Diseases associated with RBM39 include Colorectal Adenoma and Hepatocellular Carcinoma. Among its related pathways are mRNA Splicing - Major Pathway. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is RBM23.

UniProtKB/Swiss-Prot for RBM39 Gene

  • Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Gene Wiki entry for RBM39 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RBM39 Gene

Genomics for RBM39 Gene

Regulatory Elements for RBM39 Gene

Enhancers for RBM39 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
- Elite enhancer/Elite enhancer-gene association

Enhancers around RBM39 on UCSC Golden Path with GeneCards custom track

Promoters for RBM39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RBM39 on UCSC Golden Path with GeneCards custom track

Genomic Location for RBM39 Gene

Chromosome:
20
Start:
35,703,609 bp from pter
End:
35,742,336 bp from pter
Size:
38,728 bases
Orientation:
Minus strand

Genomic View for RBM39 Gene

Genes around RBM39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBM39 Gene

Proteins for RBM39 Gene

  • Protein details for RBM39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14498-RBM39_HUMAN
    Recommended name:
    RNA-binding protein 39
    Protein Accession:
    Q14498
    Secondary Accessions:
    • A2RRD3
    • A5D8W2
    • B0BLV3
    • E1P5S0
    • E1P5S1
    • Q14499

    Protein attributes for RBM39 Gene

    Size:
    530 amino acids
    Molecular mass:
    59380 Da
    Quaternary structure:
    • Interacts with NCOA6 (By similarity). Interacts with RSRC1 (via Arg/Ser-rich domain). Interacts with SF3B1.
    Miscellaneous:
    • Antibodies against RNPC2 are present in sera from a patient with hepatocellular carcinoma who developed several autoantibodies.

    Three dimensional structures from OCA and Proteopedia for RBM39 Gene

    Alternative splice isoforms for RBM39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBM39 Gene

Post-translational modifications for RBM39 Gene

  • Ubiquitination at Lys 178, Lys 232, and Lys 244
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RBM39 Gene

Domains & Families for RBM39 Gene

Gene Families for RBM39 Gene

Graphical View of Domain Structure for InterPro Entry

Q14498

UniProtKB/Swiss-Prot:

RBM39_HUMAN :
  • Contains 3 RRM (RNA recognition motif) domains.
  • Belongs to the splicing factor SR family.
Domain:
  • Contains 3 RRM (RNA recognition motif) domains.
Family:
  • Belongs to the splicing factor SR family.
genes like me logo Genes that share domains with RBM39: view

Function for RBM39 Gene

Molecular function for RBM39 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.

Gene Ontology (GO) - Molecular Function for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005515 protein binding IPI 15798186
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with RBM39: view
genes like me logo Genes that share phenotypes with RBM39: view

Animal Model Products

CRISPR Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBM39 Gene

Localization for RBM39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM39 Gene

Nucleus speckle. Note=Concentrated in nuclear speckles. Colocalizes with the core spliceosomal snRNP proteins.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RBM39 Gene COMPARTMENTS Subcellular localization image for RBM39 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005815 microtubule organizing center IDA --
GO:0015630 microtubule cytoskeleton IDA --
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with RBM39: view

Pathways & Interactions for RBM39 Gene

SuperPathways for RBM39 Gene

Superpath Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with RBM39: view

Pathways by source for RBM39 Gene

1 BioSystems pathway for RBM39 Gene

Gene Ontology (GO) - Biological Process for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006396 RNA processing TAS 8227358
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with RBM39: view

No data available for SIGNOR curated interactions for RBM39 Gene

Drugs & Compounds for RBM39 Gene

No Compound Related Data Available

Transcripts for RBM39 Gene

Unigene Clusters for RBM39 Gene

RNA binding motif protein 39:
Representative Sequences:

CRISPR Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RBM39 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^
SP1: - - - - - - - - -
SP2: -
SP3:
SP4:
SP5: -
SP6:
SP7: - - - - - -
SP8: - - - - -
SP9: - - - - - - -
SP10: - - -
SP11: - -
SP12: - -
SP13:

ExUns: 17a · 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22
SP1:
SP2:
SP3: -
SP4: -
SP5:
SP6: - - - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for RBM39 Gene

GeneLoc Exon Structure for
RBM39
ECgene alternative splicing isoforms for
RBM39

Expression for RBM39 Gene

mRNA expression in normal human tissues for RBM39 Gene

Protein differential expression in normal tissues from HIPED for RBM39 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RBM39 Gene



Protein tissue co-expression partners for RBM39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RBM39 Gene:

RBM39

SOURCE GeneReport for Unigene cluster for RBM39 Gene:

Hs.282901

mRNA Expression by UniProt/SwissProt for RBM39 Gene:

Q14498-RBM39_HUMAN
Tissue specificity: Widely expressed. Highly expressed in pancreas, skeletal muscle, lung and brain. Expressed at intermediate level in kidney, liver and heart.
genes like me logo Genes that share expression patterns with RBM39: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for RBM39 Gene

Orthologs for RBM39 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RBM39 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia RBM39 34
  • 95.48 (n)
  • 100 (a)
RBM39 35
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RBM39 34
  • 95.66 (n)
  • 100 (a)
RBM39 35
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rbm39 34
  • 93.08 (n)
  • 99.81 (a)
Rbm39 16
Rbm39 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RBM39 34
  • 99.81 (n)
  • 100 (a)
rat
(Rattus norvegicus)
Mammalia LOC100910882 34
  • 93.33 (n)
  • 99.81 (a)
oppossum
(Monodelphis domestica)
Mammalia RBM39 35
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RBM39 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 35
  • 98 (a)
OneToMany
-- 35
  • 98 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia RBM39 35
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2265 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.4395 34
zebrafish
(Danio rerio)
Actinopterygii Dr.1040 34
rbm39a 35
  • 82 (a)
OneToMany
rbm39b 35
  • 76 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1045 34
fruit fly
(Drosophila melanogaster)
Insecta CG11266 35
  • 48 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y55F3AM.3 35
  • 41 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP13 35
  • 19 (a)
ManyToMany
RNA15 35
  • 18 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G16940 34
  • 54.17 (n)
  • 48.91 (a)
rice
(Oryza sativa)
Liliopsida Os.24932 34
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4013 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 59 (a)
OneToMany
Species where no ortholog for RBM39 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)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RBM39 Gene

ENSEMBL:
Gene Tree for RBM39 (if available)
TreeFam:
Gene Tree for RBM39 (if available)

Paralogs for RBM39 Gene

Paralogs for RBM39 Gene

Pseudogenes.org Pseudogenes for RBM39 Gene

genes like me logo Genes that share paralogs with RBM39: view

Variants for RBM39 Gene

Sequence variations from dbSNP and Humsavar for RBM39 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1803701 - 35,705,259(-) AGGAG(C/T)TATTC nc-transcript-variant, reference, missense
rs15039 -- 35,704,444(-) TTTTT(C/T)TTTCT nc-transcript-variant, utr-variant-3-prime
rs1538426 -- 35,740,352(+) AGACT(A/G)TTAGA intron-variant, utr-variant-5-prime
rs1052506 -- 35,731,492(-) TTGTC(A/C)CCGTG intron-variant
rs1056196 -- 35,739,237(-) ATGGA(A/T)AATTT intron-variant, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for RBM39 Gene

Variant ID Type Subtype PubMed ID
dgv4303n100 CNV gain 25217958
esv3645720 CNV gain 21293372
nsv526188 CNV gain 19592680

Variation tolerance for RBM39 Gene

Residual Variation Intolerance Score: 19.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.27% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RBM39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM39 Gene

Disorders for RBM39 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RBM39 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
colorectal adenoma
  • adenoma of large intestine
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
intestinal benign neoplasm
  • intestinal tumors
- elite association - COSMIC cancer census association via MalaCards
Search RBM39 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RBM39

Human Genome Epidemiology (HuGE) Navigator
RBM39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RBM39
genes like me logo Genes that share disorders with RBM39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBM39 Gene

Publications for RBM39 Gene

  1. Novel nuclear autoantigen with splicing factor motifs identified with antibody from hepatocellular carcinoma. (PMID: 8227358) Imai H. … Tan E.M. (J. Clin. Invest. 1993) 2 3 4 65
  2. Cancer-relevant splicing factor CAPERalpha engages the essential splicing factor SF3b155 in a specific ternary complex. (PMID: 24795046) Loerch S. … Kielkopf C.L. (J. Biol. Chem. 2014) 3 4 65
  3. The origins, evolution, and functional potential of alternative splicing in vertebrates. (PMID: 21551269) Mudge J.M. … Harrow J. (Mol. Biol. Evol. 2011) 2 3 65
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 65
  5. Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta. (PMID: 15694343) Dowhan D.H. … O'Malley B.W. (Mol. Cell 2005) 2 3 65

Products for RBM39 Gene

Sources for RBM39 Gene

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