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

Gene ID: 362251, updated on 10-Jul-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
EnsemblRapid: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
    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
    A0A8J8XIU1, 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, A0A8J8XIU1
    Related
    ENSRNOP00000026964.7, ENSRNOT00000026964.9

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

Nucleotide Protein Strain
Heading Accession and Version

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