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

    Gene ID: 9584, updated on 3-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35701347..35742260, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37422322..37463242, complement)
    RS_2024_09 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 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. Novel nuclear autoantigen with splicing factor motifs identified with antibody from hepatocellular carcinoma. Imai H, et al. J Clin Invest, 1993 Nov. PMID 8227358, Free PMC Article
    2. 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
    3. CAPER, a novel regulator of human breast cancer progression. Mercier I, et al. Cell Cycle, 2014. PMID 24621503, Free PMC Article
    4. 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
    5. Proteomic analysis of nuclei isolated from cancer cell lines treated with indenoisoquinoline NSC 724998, a novel topoisomerase I inhibitor. Han B, et al. J Proteome Res, 2010 Aug 6. PMID 20515076, Free PMC Article

    See all (265) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer.
      Title: MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer.
    2. 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.
    3. 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.
    4. Arginine reprograms metabolism in liver cancer via RBM39.
      Title: Arginine reprograms metabolism in liver cancer via RBM39.
    5. 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.
    6. 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.
    7. 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.
    8. Identification of a small molecule splicing inhibitor targeting UHM domains.
      Title: Identification of a small molecule splicing inhibitor targeting UHM domains.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    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_2024_08

    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

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