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

    Gene ID: 9584, updated on 10-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001242599.2NP_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:46496
      SF-CC1; splicing factor, CC1-like family
    2. NM_001242600.2NP_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:46490
      SF-CC1; splicing factor, CC1-like family
    3. NM_001323422.2NP_001310351.1  RNA-binding protein 39 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL357374, C75555
      UniProtKB/TrEMBL
      B4E1M7
      Conserved Domains (1) summary
      TIGR01622
      Location:46486
      SF-CC1; splicing factor, CC1-like family
    4. NM_001323423.2NP_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:1361
      SF-CC1; splicing factor, CC1-like family
    5. NM_001323424.2NP_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:46517
      SF-CC1; splicing factor, CC1-like family
    6. NM_004902.4NP_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:46512
      SF-CC1; splicing factor, CC1-like family
    7. NM_184234.3NP_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:46518
      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_017028138.3XP_016883627.1  RNA-binding protein 39 isoform X1

      UniProtKB/TrEMBL
      B4DRA0
    2. XM_047440604.1XP_047296560.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      Q6MZY7, Q7Z3L0
    3. XM_006723891.5XP_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:1361
      SF-CC1; splicing factor, CC1-like family
    4. XM_047440605.1XP_047296561.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      Q6MZY7, Q7Z3L0
    5. XM_024452023.2XP_024307791.1  RNA-binding protein 39 isoform X5

      UniProtKB/TrEMBL
      Q6MZY7, Q6N037, Q7Z3L0
      Conserved Domains (1) summary
      TIGR01622
      Location:1355
      SF-CC1; splicing factor, CC1-like family
    6. XM_047440602.1XP_047296558.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      G3XAC6
      Related
      ENSP00000344581.6, ENST00000338163.10
    7. XM_047440603.1XP_047296559.1  RNA-binding protein 39 isoform X3

      UniProtKB/TrEMBL
      G3XAC6

    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_054324247.1XP_054180222.1  RNA-binding protein 39 isoform X1

      UniProtKB/TrEMBL
      B4DRA0
    2. XM_054324250.1XP_054180225.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      Q6MZY7, Q7Z3L0
    3. XM_054324252.1XP_054180227.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      Q6MZY7, Q7Z3L0
    4. XM_054324251.1XP_054180226.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      Q6MZY7, Q7Z3L0
    5. XM_054324253.1XP_054180228.1  RNA-binding protein 39 isoform X5

      UniProtKB/TrEMBL
      Q6MZY7, Q6N037, Q7Z3L0
    6. XM_054324248.1XP_054180223.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      G3XAC6
    7. XM_054324249.1XP_054180224.1  RNA-binding protein 39 isoform X3

      UniProtKB/TrEMBL
      G3XAC6

    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.