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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
  • Splicing Factor HCC1 3 4
  • CAPER Alpha 3 4
  • RNPC2 3 4
  • HCC1 3 4
  • RNA-Binding Region-Containing Protein 2 4
  • RNA-Binding Motif Protein 39 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. Among its related pathways are 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 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

Additional gene information for RBM39 Gene

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

Genomics for RBM39 Gene

GeneHancer (GH) Regulatory Elements for RBM39 Gene

Promoters and enhancers for RBM39 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J035738 Promoter/Enhancer 3.3 UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 664.3 +0.6 613 7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 RBM39 CPNE1 RBM12 ERGIC3 AAR2 TRPC4AP RPL36P4 EDEM2 PHF20 EIF6
GH20J035764 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 90.4 -27.2 -27209 9.2 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF416 ZNF548 SP3 PHF20 ENSG00000283527 CPNE1 RBM12 RBM39 NCOA6 ERGIC3 TRPC4AP AAR2 DLGAP4-AS1
GH20J035410 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 51.6 +330.6 330551 2.1 HDGF PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 UQCC1 TRPC4AP RBM12 RBM39 CPNE1 ERGIC3 AAR2 RPL36P4 PROCR EIF6
GH20J035951 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 50.4 -211.5 -211524 3.8 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 CNBD2 SCAND1 CPNE1 RBM39 RBM12 TRPC4AP RPL36P4 SOGA1 ERGIC3 DSN1
GH20J035283 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 45.1 +457.2 457156 3.9 MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D EIF6 FAM83C-AS1 RBM12 RBM39 ERGIC3 NCOA6 CPNE1 TRPC4AP AAR2 RPL36P4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBM39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RBM39 gene promoter:
  • Pax-6
  • AP-1
  • FOXF2
  • NF-AT2
  • Hlf
  • NF-AT
  • NF-AT1
  • NF-AT3
  • NF-AT4

Genomic Locations for RBM39 Gene

Genomic Locations for RBM39 Gene
40,990 bases
Minus strand
38,728 bases
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:
    Recommended name:
    RNA-binding protein 39
    Protein Accession:
    Secondary Accessions:
    • A2RRD3
    • A5D8W2
    • B0BLV3
    • E1P5S0
    • E1P5S1
    • Q14499

    Protein attributes for RBM39 Gene

    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.
    • 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


neXtProt entry for RBM39 Gene

Post-translational modifications for RBM39 Gene

  • Ubiquitination at Lys244, posLast=232232, and posLast=178178
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RBM39 Gene

Domains & Families for RBM39 Gene

Gene Families for RBM39 Gene

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

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the splicing factor SR 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.

Phenotypes From GWAS Catalog for RBM39 Gene

Gene Ontology (GO) - Molecular Function for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,HDA 22658674
GO:0005515 protein binding IPI 15798186
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

Clone 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

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 RBM39 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
  • Nucleoplasm (2)
  • Microtubule organizing center (1)
  • Microtubules (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005815 microtubule organizing center IDA --
GO:0015630 microtubule cytoskeleton IDA --
GO:0016607 nuclear speck IMP,IDA 28437394
genes like me logo Genes that share ontologies with RBM39: view

Pathways & Interactions for RBM39 Gene

SuperPathways for RBM39 Gene

SuperPathway 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:

Clone 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: -
SP5: -
SP7: - - - - - -
SP8: - - - - -
SP9: - - - - - - -
SP10: - - -
SP11: - -
SP12: - -

ExUns: 17a · 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22
SP3: -
SP4: -
SP6: - - - -

Relevant External Links for RBM39 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RBM39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, 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:


SOURCE GeneReport for Unigene cluster for RBM39 Gene:


mRNA Expression by UniProt/SwissProt for RBM39 Gene:

Tissue specificity: Widely expressed. Highly expressed in pancreas, skeletal muscle, lung and brain. Expressed at intermediate level in kidney, liver and heart.

Evidence on tissue expression from TISSUES for RBM39 Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Lung(2.9)
  • Intestine(2.7)
  • Muscle(2.6)
  • Bone marrow(2.5)
  • Spleen(2.5)
  • Kidney(2.3)
  • Heart(2.2)
  • Lymph node(2.2)
  • Eye(2.1)
  • Thyroid gland(2.1)
  • Adrenal gland(2)
  • Gall bladder(2)
  • Skin(2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with RBM39: 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 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
(Pan troglodytes)
Mammalia RBM39 33
  • 99.81 (n)
(Monodelphis domestica)
Mammalia RBM39 34
  • 97 (a)
(Canis familiaris)
Mammalia RBM39 34 33
  • 95.66 (n)
(Bos Taurus)
Mammalia RBM39 34 33
  • 95.48 (n)
(Rattus norvegicus)
Mammalia LOC100910882 33
  • 93.33 (n)
(Mus musculus)
Mammalia Rbm39 16 34 33
  • 93.08 (n)
(Ornithorhynchus anatinus)
Mammalia RBM39 34
  • 68 (a)
(Gallus gallus)
Aves -- 34
  • 98 (a)
-- 34
  • 98 (a)
(Anolis carolinensis)
Reptilia RBM39 34
  • 97 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2265 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.4395 33
(Danio rerio)
Actinopterygii rbm39a 34
  • 82 (a)
rbm39b 34
  • 76 (a)
Dr.1040 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1045 33
fruit fly
(Drosophila melanogaster)
Insecta CG11266 34
  • 48 (a)
(Caenorhabditis elegans)
Secernentea Y55F3AM.3 34
  • 41 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP13 34
  • 19 (a)
RNA15 34
  • 18 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G16940 33
  • 54.17 (n)
(Oryza sativa)
Liliopsida Os.24932 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
Cin.4013 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4013 33
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

Gene Tree for RBM39 (if available)
Gene Tree for RBM39 (if available)
Evolutionary constrained regions (ECRs) for RBM39: view image

Paralogs for RBM39 Gene

Paralogs for RBM39 Gene

(11) SIMAP similar genes for RBM39 Gene using alignment to 14 proteins:

  • E1P5S2_HUMAN
  • F2Z2Z5_HUMAN
  • F2Z3E6_HUMAN
  • F8WF24_HUMAN
  • F8WF73_HUMAN
  • H0Y4X3_HUMAN
  • H0Y6I9_HUMAN
  • Q5QP21_HUMAN
  • Q5QP22_HUMAN
  • Q5QP23_HUMAN 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 Variation AA Info Type
rs1000068547 -- 35,726,630(-) C/A genic_downstream_transcript_variant, intron_variant
rs1000084264 -- 35,741,778(-) T/C intron_variant
rs1000104482 -- 35,727,317(-) T/TT genic_downstream_transcript_variant, intron_variant
rs1000137611 -- 35,713,680(-) A/C genic_downstream_transcript_variant, intron_variant
rs1000144872 -- 35,707,981(-) T/C genic_downstream_transcript_variant, intron_variant

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)

Additional Variant Information for RBM39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for RBM39 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
colorectal adenoma
  • adenoma of large intestine
- elite association - COSMIC cancer census association via MalaCards
Search RBM39 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 EM (The Journal of clinical investigation 1993) 2 3 4 58
  2. Cancer-relevant splicing factor CAPERα engages the essential splicing factor SF3b155 in a specific ternary complex. (PMID: 24795046) Loerch S … Kielkopf CL (The Journal of biological chemistry 2014) 3 4 58
  3. The origins, evolution, and functional potential of alternative splicing in vertebrates. (PMID: 21551269) Mudge JM … Harrow J (Molecular biology and evolution 2011) 2 3 58
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  5. Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta. (PMID: 15694343) Dowhan DH … O'Malley BW (Molecular cell 2005) 2 3 58

Products for RBM39 Gene

Sources for RBM39 Gene