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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 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

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

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
GH20H035739 3.1 FANTOM5 Ensembl ENCODE dbSUPER 59.5 +0.6 613 7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D CPNE1 RBM12 RBM39 ERGIC3 AAR2 PHF20 EIF6 TRPC4AP RPL36P4 MYL9
GH20H035765 1.8 FANTOM5 ENCODE dbSUPER 75.5 -27.2 -27210 9 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF548 SP3 NFYC SSRP1 CPNE1 RBM12 RBM39 NCOA6 ERGIC3 PHF20 AAR2 DLGAP4-AS1 TRPC4AP PROCR
GH20H034954 1.4 ENCODE dbSUPER 43.6 +786.4 786392 2 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RBM12 RBM39 NCOA6 CPNE1 ERGIC3 ENSG00000272945 PROCR RPL36P4 MYH7B TRPC4AP
GH20H035874 1.9 FANTOM5 Ensembl ENCODE dbSUPER 27.6 -133.2 -133182 2 PKNOX1 ATF1 ARNT SIN3A FEZF1 BRCA1 ZNF2 GTF3C2 KLF7 ATF7 CPNE1 RBM39 RBM12 ERGIC3 RPL36P4 TRPC4AP NFS1 EIF6 DSN1 AAR2
GH20H035881 1.9 FANTOM5 Ensembl ENCODE dbSUPER 26.8 -141.5 -141450 4 HDGF PKNOX1 ARID4B SIN3A FEZF1 ZNF2 GTF3C2 ZNF121 ELK1 ZNF143 CPNE1 RBM39 RBM12 ERGIC3 RPL36P4 TRPC4AP EIF6 DSN1 AAR2 RNU6-937P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000136594 436 3001 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D

Genomic Location for RBM39 Gene

Chromosome:
20
Start:
35,701,347 bp from pter
End:
35,742,336 bp from pter
Size:
40,990 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 Lys178, Lys232, and isoforms=2, 3244
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RBM39 Gene

Domains & Families for RBM39 Gene

Gene Families for RBM39 Gene

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

Graphical View of Domain Structure for InterPro Entry

Q14498

UniProtKB/Swiss-Prot:

RBM39_HUMAN :
  • Belongs to the splicing factor SR family.
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,IDA 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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RBM39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
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 IDA,TAS --
GO:0005815 microtubule organizing center IDA --
GO:0015630 microtubule cytoskeleton IDA --
GO:0016607 nuclear speck IDA,IMP 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RBM39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 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, 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.

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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia RBM39 33
  • 99.81 (n)
oppossum
(Monodelphis domestica)
Mammalia RBM39 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RBM39 33 34
  • 95.66 (n)
cow
(Bos Taurus)
Mammalia RBM39 33 34
  • 95.48 (n)
rat
(Rattus norvegicus)
Mammalia LOC100910882 33
  • 93.33 (n)
mouse
(Mus musculus)
Mammalia Rbm39 33 16 34
  • 93.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RBM39 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 34
  • 98 (a)
OneToMany
-- 34
  • 98 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia RBM39 34
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2265 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.4395 33
zebrafish
(Danio rerio)
Actinopterygii rbm39a 34
  • 82 (a)
OneToMany
rbm39b 34
  • 76 (a)
OneToMany
Dr.1040 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1045 33
fruit fly
(Drosophila melanogaster)
Insecta CG11266 34
  • 48 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y55F3AM.3 34
  • 41 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP13 34
  • 19 (a)
ManyToMany
RNA15 34
  • 18 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G16940 33
  • 54.17 (n)
rice
(Oryza sativa)
Liliopsida Os.24932 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
OneToMany
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

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
rs1000068547 -- 35,726,630(+) TGAAA(A/C)CCCAA intron-variant
rs1000084264 -- 35,741,778(+) GACTA(C/T)ACCCG intron-variant
rs1000104482 -- 35,727,316(+) TGCAC(-/T)TATAG intron-variant
rs1000137611 -- 35,713,680(+) AAAAA(A/C)AAAAA intron-variant
rs1000144872 -- 35,707,981(+) CATAA(C/T)AACAA 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)

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

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

Disorder Aliases PubMed IDs
colorectal adenoma
  • adenoma of large intestine
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
- 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 EM (The Journal of clinical investigation 1993) 2 3 4 60
  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 60
  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 60
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60
  5. A novel SR-related protein is required for the second step of Pre-mRNA splicing. (PMID: 15798186) Cazalla D … Cáceres JF (Molecular and cellular biology 2005) 3 4 60

Products for RBM39 Gene

Sources for RBM39 Gene

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