RBM39: RNA Binding Motif Protein 39
A splicing factor with roles in cancer and transcriptional regulation
Gene Information Card
| Symbol | RBM39 |
|---|---|
| Full Name | RNA Binding Motif Protein 39 |
| Gene Type | Protein coding |
| Chromosomal Location | 20q11.22 |
| NCBI Gene ID | 9584 ncbi.nlm.nih.gov/gene/9584 |
| Ensembl ID | ENSG00000131051 |
| UniProt ID | Q14498 |
| OMIM ID | 604739 |
| HGNC ID | 9900 |
| Aliases | CAPER, CAPERalpha, FSAP59, HCC1, RNPC2 |
Description
RBM39 (RNA Binding Motif Protein 39) encodes a member of the U2AF-like family of splicing factors. The protein contains an RNA recognition motif (RRM) and a serine/arginine-rich (SR) domain, and is involved in pre-mRNA splicing, transcriptional coactivation, and regulation of alternative splicing. It interacts with nuclear receptors and other transcription factors, and has been implicated in cancer progression and viral replication.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (various types) | RBM39 overexpression or mutation alters splicing of oncogenes and tumor suppressors | PMID: 30700909 |
| Acute myeloid leukemia | RBM39 fusions (e.g., RBM39-MKL1) drive leukemogenesis | PMID: 17554309 |
| Viral infection | RBM39 interacts with viral proteins to modulate host splicing | PMID: 25464849 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 15.2 | High |
| Lymph node | 12.8 | High |
| Bone marrow | 11.5 | High |
| Brain | 6.3 | Medium |
| Liver | 4.1 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 14.5 | Cervical cancer cell line |
| K562 | 13.2 | Leukemia cell line |
| HEK293 | 10.8 | Embryonic kidney cell line |
| MCF7 | 9.4 | Breast cancer cell line |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1015C>T (p.Arg339Trp) | Missense | <0.1% | Altered RNA binding affinity |
| c.1246G>A (p.Gly416Arg) | Missense | <0.1% | Unknown functional effect |
| RBM39-MKL1 fusion | Gene fusion | Rare | Oncogenic in acute megakaryoblastic leukemia |
Mutation functional classification
Loss of Function (LOF)
Not well characterized; some missense mutations may reduce splicing activity.
Gain of Function (GOF)
Overexpression in cancers suggests potential oncogenic gain-of-function.
Dominant Negative (DN)
Fusion proteins like RBM39-MKL1 may act as dominant-negative splicing regulators.
View complete mutation data：
Gene Ontology (GO)
| • RNA binding | • mRNA splicing |
| • via spliceosome | • nucleus |
| • protein binding | • alternative mRNA splicing |
| • transcription coactivator activity |
Pathways
• mRNA Splicing - Major Pathway
• Processing of Capped Intron-Containing Pre-mRNA
• Gene Expression
Protein Summary
RBM39 is a 530-amino acid nuclear protein with an N-terminal RNA recognition motif (RRM) and a C-terminal SR-rich domain. It functions as a splicing factor and transcriptional coactivator, shuttling between nuclear speckles and the nucleoplasm. The protein interacts with U2AF65 and other spliceosomal components, and its activity is regulated by phosphorylation. RBM39 is overexpressed in multiple cancers and is a target for anti-cancer therapies using sulfonamide compounds that promote its degradation.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| RBM39 Knockout HEK293 Cell Line | EDJ-KQ50884 | Human | 9584 | Details Get a Quote |
| RBM39 Knockout HeLa Cell Line | EDJ-KQ55201 | Human | 9584 | Details Get a Quote |
| RBM39 Knockout A-549 Cell Line | EDJ-KQ63683 | Human | 9584 | Details Get a Quote |
| RBM39 Knockout HCT 116 Cell Line | EDJ-KQ72145 | Human | 9584 | Details Get a Quote |
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