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RBM39 RNA binding motif protein 39 [ Homo sapiens (human) ]

Gene ID: 9584, updated on 7-Apr-2024

Summary

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Official Symbol
RBM39provided by HGNC
Official Full Name
RNA binding motif protein 39provided by HGNC
Primary source
HGNC:HGNC:15923
See related
Ensembl:ENSG00000131051 MIM:604739; AllianceGenome:HGNC:15923
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HCC1; CAPER; RNPC2; FSAP59; CAPERalpha
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 103.4), lymph node (RPKM 47.1) and 25 other tissues See more
Orthologs
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Genomic context

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See RBM39 in Genome Data Viewer
Location:
20q11.22
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35701347..35742260, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37422322..37463242, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34289269..34330182, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NFS1 cysteine desulfurase Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34286841-34287500 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34287501-34288160 Neighboring gene reactive oxygen species modulator 1 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17795 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:34330085-34330770 Neighboring gene ribosome production factor 2 homolog pseudogene 1 Neighboring gene MPRA-validated peak4202 silencer Neighboring gene uncharacterized LOC124904972

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases. Eléouët M, et al. Biochim Biophys Acta Gene Regul Mech, 2023 Mar. PMID 36535628
  2. Tumor-associated antigen CAPERα and microvessel density in hepatocellular carcinoma. Dai L, et al. Oncotarget, 2016 Mar 29. PMID 26934653, Free PMC Article
  3. Overexpression of HCC1/CAPERα may play a role in lung cancer carcinogenesis. Chai Y, et al. Tumour Biol, 2014 Jul. PMID 24643682, Free PMC Article
  4. CAPER, a novel regulator of human breast cancer progression. Mercier I, et al. Cell Cycle, 2014. PMID 24621503, Free PMC Article
  5. CAPER-α alternative splicing regulates the expression of vascular endothelial growth factor₁₆₅ in Ewing sarcoma cells. Huang G, et al. Cancer, 2012 Apr 15. PMID 22009261, Free PMC Article

See all (234) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RBM39: A druggable metabolic sensor linking RNA splicing, transcriptional regulation, and metabolic reprogramming in cancer.
    Title: RBM39: A druggable metabolic sensor linking RNA splicing, transcriptional regulation, and metabolic reprogramming in cancer.
  2. Regulatory role of RBM39 in acute myeloid leukemia: Mediation through the PI3K/AKT pathway.
    Title: Regulatory role of RBM39 in acute myeloid leukemia: Mediation through the PI3K/AKT pathway.
  3. Arginine reprograms metabolism in liver cancer via RBM39.
    Title: Arginine reprograms metabolism in liver cancer via RBM39.
  4. Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.
    Title: Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39.
  5. Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases.
    Title: Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases.
  6. The transcription factor c-Jun inhibits RBM39 to reprogram pre-mRNA splicing during genotoxic stress.
    Title: The transcription factor c-Jun inhibits RBM39 to reprogram pre-mRNA splicing during genotoxic stress.
  7. Identification of a small molecule splicing inhibitor targeting UHM domains.
    Title: Identification of a small molecule splicing inhibitor targeting UHM domains.
  8. Inhibiting an RBM39/MLL1 epigenomic regulatory complex with dominant-negative peptides disrupts cancer cell transcription and proliferation.
    Title: Inhibiting an RBM39/MLL1 epigenomic regulatory complex with dominant-negative peptides disrupts cancer cell transcription and proliferation.
  9. The splicing factors U2AF65 and CAPERalpha engage multivalent interactions through their low complexity RS domains. The resulting assemblies can bridge the U2snRNP component SF3b155 with repeated polypyrimidine tracts in introns, to promote alternative splicing.
    Title: U2AF(65) assemblies drive sequence-specific splice site recognition.
  10. aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high-affinity ligand
    Title: Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, RNA binding motif protein 39 (RBM39), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with RBM39 is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ44170, DKFZp781C0423

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RS domain binding IEA
Inferred from Electronic Annotation
more info
  
enables U1 snRNP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
  
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of protein-containing complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding protein 39
Names
CAPER alpha
RNA-binding region (RNP1, RRM) containing 2
coactivator of activating protein-1 and estrogen receptors
epididymis secretory sperm binding protein
functional spliceosome-associated protein 59
hepatocellular carcinoma protein 1
splicing factor HCC1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029955.2 RefSeqGene

    Range
    5000..45913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242599.2 → NP_001229528.1  RNA-binding protein 39 isoform c

    See identical proteins and their annotated locations for NP_001229528.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (c) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AK299678, AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS56186.1
    UniProtKB/TrEMBL
    B4DRA0
    Related
    ENSP00000436747.2, ENST00000528062.7
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 496
    SF-CC1; splicing factor, CC1-like family

  2. NM_001242600.2 → NP_001229529.1  RNA-binding protein 39 isoform d

    See identical proteins and their annotated locations for NP_001229529.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (d) lacks two internal segments, compared to isoform a.
    Source sequence(s)
    AK299165, AL357374, BC131543, BC141835, C75555, DC346351
    UniProtKB/TrEMBL
    B4DRA0
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 490
    SF-CC1; splicing factor, CC1-like family

  3. NM_001323422.2 → NP_001310351.1  RNA-binding protein 39 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555
    UniProtKB/TrEMBL
    B4E1M7
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 486
    SF-CC1; splicing factor, CC1-like family

  4. NM_001323423.2 → NP_001310352.1  RNA-binding protein 39 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    UniProtKB/TrEMBL
    Q6MZY7, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1 → 361
    SF-CC1; splicing factor, CC1-like family

  5. NM_001323424.2 → NP_001310353.1  RNA-binding protein 39 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL357374, C75555, DA189970
    UniProtKB/TrEMBL
    B4E1M7
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 517
    SF-CC1; splicing factor, CC1-like family

  6. NM_004902.4 → NP_004893.1  RNA-binding protein 39 isoform b

    See identical proteins and their annotated locations for NP_004893.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (b, also called CC1.3) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS13265.1
    UniProtKB/TrEMBL
    B4E1M7
    Related
    ENSP00000354437.6, ENST00000361162.10
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 512
    SF-CC1; splicing factor, CC1-like family

  7. NM_184234.3 → NP_909122.1  RNA-binding protein 39 isoform a

    See identical proteins and their annotated locations for NP_909122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a, also called CC1.4).
    Source sequence(s)
    AL357374, BC141835, C75555, DC346351
    Consensus CDS
    CCDS13266.1
    UniProtKB/Swiss-Prot
    A2RRD3, A5D8W2, B0BLV3, E1P5S0, E1P5S1, Q14498, Q14499
    UniProtKB/TrEMBL
    A0A384NQ03, B4E1M7
    Related
    ENSP00000253363.6, ENST00000253363.11
    Conserved Domains (1) summary
    TIGR01622
    Location:46 → 518
    SF-CC1; splicing factor, CC1-like family

RNA

  1. NR_040722.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL357374, BC141835, BX640812, C75555, DC346351

  2. NR_040723.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) includes an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL357374, BC141835, BX537770, C75555, DC346351
    Related
    ENST00000639702.1

  3. NR_040724.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) includes an additional exon in the 5' region, and uses an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL357374, BC141835, BX640714, C75555, DC346351

  4. NR_136587.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL357374, DA189970

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    35701347..35742260 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028138.3 → XP_016883627.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    B4DRA0

  2. XM_047440604.1 → XP_047296560.1  RNA-binding protein 39 isoform X4

  3. XM_006723891.5 → XP_006723954.1  RNA-binding protein 39 isoform X4

    See identical proteins and their annotated locations for XP_006723954.1

    UniProtKB/TrEMBL
    Q6MZY7, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1 → 361
    SF-CC1; splicing factor, CC1-like family

  4. XM_047440605.1 → XP_047296561.1  RNA-binding protein 39 isoform X4

  5. XM_024452023.2 → XP_024307791.1  RNA-binding protein 39 isoform X5

    UniProtKB/TrEMBL
    Q6MZY7, Q6N037, Q7Z3L0
    Conserved Domains (1) summary
    TIGR01622
    Location:1 → 355
    SF-CC1; splicing factor, CC1-like family

  6. XM_047440602.1 → XP_047296558.1  RNA-binding protein 39 isoform X2

    Related
    ENSP00000344581.6, ENST00000338163.10

  7. XM_047440603.1 → XP_047296559.1  RNA-binding protein 39 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    37422322..37463242 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324247.1 → XP_054180222.1  RNA-binding protein 39 isoform X1

  2. XM_054324250.1 → XP_054180225.1  RNA-binding protein 39 isoform X4

  3. XM_054324252.1 → XP_054180227.1  RNA-binding protein 39 isoform X4

  4. XM_054324251.1 → XP_054180226.1  RNA-binding protein 39 isoform X4

  5. XM_054324253.1 → XP_054180228.1  RNA-binding protein 39 isoform X5

    UniProtKB/TrEMBL
    Q6N037

  6. XM_054324248.1 → XP_054180223.1  RNA-binding protein 39 isoform X2

  7. XM_054324249.1 → XP_054180224.1  RNA-binding protein 39 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_184237.1: Suppressed sequence

    Description
    NM_184237.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_184241.1: Suppressed sequence

    Description
    NM_184241.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  3. NM_184244.1: Suppressed sequence

    Description
    NM_184244.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14498.2 GenPept UniProtKB/Swiss-Prot:Q14498

Gene LinkOut

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