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    Rbm39 RNA binding motif protein 39 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362251, updated on 25-Apr-2024

    Summary

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    Symbol
    Rbm39provided by RGD
    Full Name
    RNA binding motif protein 39provided by RGD
    Primary source
    RGD:1310071
    See related
    Ensembl:ENSRNOG00000019848 AllianceGenome:RGD:1310071
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Rrm; Rnp1; Rnpc2
    Summary
    Predicted to enable RS domain binding activity and transcription coactivator activity. Predicted to be involved in regulation of mRNA splicing, via spliceosome. Predicted to act upstream of or within regulation of transcription by RNA polymerase II. Predicted to be located in centriolar satellite and nuclear speck. Predicted to be part of protein-containing complex. Orthologous to human RBM39 (RNA binding motif protein 39). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 828.0), Spleen (RPKM 712.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rbm39 in Genome Data Viewer
    Location:
    3q42
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (165123087..165156453, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (144662998..144696222, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (151691498..151724723, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene NFS1 cysteine desulfurase Neighboring gene reactive oxygen species modulator 1 Neighboring gene PHD finger protein 20 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene SCAN domain-containing 1 Neighboring gene cyclic nucleotide binding domain containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Isolation of suppressor genes that restore retrovirus susceptibility to a virus-resistant cell line. Gao G, et al. Retrovirology, 2004 Sep 28. PMID 15453907, Free PMC Article
    2. Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta. Dowhan DH, et al. Mol Cell, 2005 Feb 4. PMID 15694343
    3. Selective degradation of splicing factor CAPERα by anticancer sulfonamides. Uehara T, et al. Nat Chem Biol, 2017 Jun. PMID 28437394
    4. Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Han T, et al. Science, 2017 Apr 28. PMID 28302793
    5. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109490

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RS domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables U1 snRNP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding protein 39
    Names
    RNA-binding protein 39-like
    RNA-binding region (RNP1, RRM) containing 2
    RNA-binding region-containing 2

    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.

    mRNA and Protein(s)

    1. NM_001013207.2 → NP_001013225.1  RNA-binding protein 39

      See identical proteins and their annotated locations for NP_001013225.1

      Status: VALIDATED

      Source sequence(s)
      BC078917, BC091394
      UniProtKB/TrEMBL
      A0A8J8XIU1, D3ZR20, F1MA64, Q5BJP4
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 512
      SF-CC1; splicing factor, CC1-like family

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      165123087..165156453 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008762356.4 → XP_008760578.1  RNA-binding protein 39 isoform X5

      See identical proteins and their annotated locations for XP_008760578.1

      Conserved Domains (5) summary
      cd12284
      Location:230 → 302
      RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
      cd12285
      Location:395 → 479
      RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
      cd12537
      Location:130 → 214
      RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)
      TIGR01622
      Location:46 → 490
      SF-CC1; splicing factor, CC1-like family
      pfam15519
      Location:319 → 411
      RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

    2. XM_008762349.4 → XP_008760571.1  RNA-binding protein 39 isoform X3

      See identical proteins and their annotated locations for XP_008760571.1

      Conserved Domains (5) summary
      cd12284
      Location:230 → 302
      RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
      cd12285
      Location:401 → 485
      RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
      cd12537
      Location:130 → 214
      RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)
      TIGR01622
      Location:46 → 496
      SF-CC1; splicing factor, CC1-like family
      pfam15519
      Location:319 → 417
      RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

    3. XM_006235331.5 → XP_006235393.1  RNA-binding protein 39 isoform X1

      See identical proteins and their annotated locations for XP_006235393.1

      UniProtKB/TrEMBL
      A0A8J8XIU1, A0A8J8XIU8
      Related
      ENSRNOP00000026964.6
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 518
      SF-CC1; splicing factor, CC1-like family

    4. XM_063284182.1 → XP_063140252.1  RNA-binding protein 39 isoform X6

    5. XM_039105498.2 → XP_038961426.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      A0A8I6A8P3, A0A8J8XIU1
      Conserved Domains (1) summary
      TIGR01622
      Location:20 → 492
      SF-CC1; splicing factor, CC1-like family

    6. XM_008762350.4 → XP_008760572.1  RNA-binding protein 39 isoform X3

      See identical proteins and their annotated locations for XP_008760572.1

      Conserved Domains (5) summary
      cd12284
      Location:230 → 302
      RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
      cd12285
      Location:401 → 485
      RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
      cd12537
      Location:130 → 214
      RRM1_RBM23; RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)
      TIGR01622
      Location:46 → 496
      SF-CC1; splicing factor, CC1-like family
      pfam15519
      Location:319 → 417
      RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

    7. XM_063284180.1 → XP_063140250.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      D3ZR20, F1MA64, Q5BJP4

    8. XM_006235332.5 → XP_006235394.1  RNA-binding protein 39 isoform X1

      See identical proteins and their annotated locations for XP_006235394.1

      UniProtKB/TrEMBL
      A0A8J8XIU1, A0A8J8XIU8
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 518
      SF-CC1; splicing factor, CC1-like family

    9. XM_063284184.1 → XP_063140254.1  RNA-binding protein 39 isoform X6

    10. XM_063284181.1 → XP_063140251.1  RNA-binding protein 39 isoform X4

      UniProtKB/TrEMBL
      A0A8I6A8P3

    11. XM_063284183.1 → XP_063140253.1  RNA-binding protein 39 isoform X6

    Nucleotide Protein Strain
    Heading Accession and Version

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