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Aliases for RBM39 Gene

Aliases for RBM39 Gene

  • RNA Binding Motif Protein 39 2 3
  • RNPC2 3 4 6
  • 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
  • CAPER 3 6
  • 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

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 hepatocellular carcinoma. Among its related pathways are mRNA Splicing - Major Pathway. GO annotations related to this gene include RNA binding and nucleotide 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for RBM39 Gene

35,703,609 bp from pter
35,742,336 bp from pter
38,728 bases
Minus strand

Genomic View for RBM39 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for RBM39 Gene at MOPED

Post-translational modifications for RBM39 Gene

  • Ubiquitination at Lys178, Lys232, and Lys244
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RBM39 Gene

Domains for RBM39 Gene

Gene Families for RBM39 Gene

  • RBM :RNA binding motif (RRM) containing

Graphical View of Domain Structure for InterPro Entry



  • Q14498
  • Contains 3 RRM (RNA recognition motif) domains.
  • 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:0003676 nucleic acid binding --
GO:0003723 RNA binding --
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

Phenotypes for RBM39 Gene

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

Animal Model Products

CRISPR Products

miRNA for RBM39 Gene

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RBM39

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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

Jensen Localization Image for RBM39 Gene COMPARTMENTS Subcellular localization image for RBM39 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 1

Gene Ontology (GO) - Cellular Components for RBM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
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 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

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

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

Transcripts for RBM39 Gene

Unigene Clusters for RBM39 Gene

RNA binding motif protein 39:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for RBM39

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for RBM39

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: -
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 for RBM39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for RBM39 Gene

SOURCE GeneReport for Unigene cluster for RBM39 Gene Hs.282901

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

In Situ Assay Products

No data available for 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
(Pan troglodytes)
Mammalia RBM39 35
  • 99.81 (n)
  • 100 (a)
(Bos Taurus)
Mammalia RBM39 35
  • 95.48 (n)
  • 100 (a)
RBM39 36
  • 100 (a)
(Canis familiaris)
Mammalia RBM39 35
  • 95.66 (n)
  • 100 (a)
RBM39 36
  • 100 (a)
(Mus musculus)
Mammalia Rbm39 35
  • 93.08 (n)
  • 99.81 (a)
Rbm39 16
Rbm39 36
  • 100 (a)
(Monodelphis domestica)
Mammalia RBM39 36
  • 97 (a)
(Ornithorhynchus anatinus)
Mammalia RBM39 36
  • 68 (a)
(Rattus norvegicus)
Mammalia LOC100910882 35
  • 93.33 (n)
  • 99.81 (a)
(Gallus gallus)
Aves -- 36
  • 98 (a)
-- 36
  • 98 (a)
(Anolis carolinensis)
Reptilia RBM39 36
  • 97 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4395 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2265 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1045 35
(Danio rerio)
Actinopterygii Dr.1040 35
rbm39a 36
  • 82 (a)
rbm39b 36
  • 76 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG11266 36
  • 48 (a)
(Caenorhabditis elegans)
Secernentea Y55F3AM.3 36
  • 41 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP13 36
  • 19 (a)
RNA15 36
  • 18 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G16940 35
  • 54.17 (n)
  • 48.91 (a)
(Oryza sativa)
Liliopsida Os.24932 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4013 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 59 (a)
Species with no ortholog for RBM39:
  • 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)

Paralogs for RBM39 Gene

Paralogs for RBM39 Gene 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 MAF
rs15039 -- 35,704,444(-) TTTTT(C/T)TTTCT utr-variant-3-prime, nc-transcript-variant
rs1052506 -- 35,731,492(-) TTGTC(A/C)CCGTG intron-variant
rs1056196 -- 35,739,237(-) ATGGA(A/T)AATTT intron-variant, utr-variant-5-prime
rs1538426 -- 35,740,352(+) AGACT(A/G)TTAGA intron-variant, utr-variant-5-prime
rs1803701 - 35,705,259(-) AGGAG(C/T)TATTC missense, reference, nc-transcript-variant

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

Variant ID Type Subtype PubMed ID
nsv526188 CNV Gain 19592680

Relevant External Links for RBM39 Gene

HapMap Linkage Disequilibrium report

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

Disorders for RBM39 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for RBM39 Gene including...

Search for RBM39 Gene in MalaCards »

Relevant External Links for RBM39

Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with RBM39: view

No data available for UniProtKB/Swiss-Prot 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
  2. 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
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4
  4. A novel SR-related protein is required for the second step of pre- mRNA splicing. (PMID: 15798186) Cazalla D. … Caceres J.F. (Mol. Cell. Biol. 2005) 3 4
  5. 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

Products for RBM39 Gene

Sources for RBM39 Gene

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