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    Ddx23 DEAD-box helicase 23 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300208, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Ddx23provided by RGD
    Official Full Name
    DEAD-box helicase 23provided by RGD
    Primary source
    RGD:1308685
    See related
    EnsemblRapid:ENSRNOG00000060154 AllianceGenome:RGD:1308685
    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
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in R-loop processing and mRNA splicing, via spliceosome. Predicted to be located in chromatin; nucleolus; and nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex; U5 snRNP; and catalytic step 2 spliceosome. Orthologous to human DDX23 (DEAD-box helicase 23). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Muscle (RPKM 283.0), Thymus (RPKM 238.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ddx23 in Genome Data Viewer
    Location:
    7q36
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (131676636..131693917, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (129797620..129814909, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (140325453..140342730, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene cystatin C, pseudogene 1 Neighboring gene adenylate cyclase 6 Neighboring gene tubulin, alpha 1C Neighboring gene calcium voltage-gated channel auxiliary subunit beta 3 Neighboring gene uncharacterized LOC103692978 Neighboring gene Rho family GTPase 1 Neighboring gene coiled-coil domain containing 65

    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 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. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. Teigelkamp S, et al. RNA, 1997 Nov. PMID 9409622, Free PMC Article
    2. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Laggerbauer B, et al. Proc Natl Acad Sci U S A, 1998 Apr 14. PMID 9539711, Free PMC Article
    3. Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. Sridhara SC, et al. Cell Rep, 2017 Jan 10. PMID 28076779
    4. Functions of the DExD/H-box proteins in nuclear pre-mRNA splicing. Chang TH, et al. Biochim Biophys Acta, 2013 Aug. PMID 23454554
    5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT enables helicase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in R-loop processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of U4/U6 x U5 tri-snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U5 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX23
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 23
    NP_001100263.2
    XP_006257405.1

    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_001106793.2 → NP_001100263.2  probable ATP-dependent RNA helicase DDX23

      See identical proteins and their annotated locations for NP_001100263.2

      Status: VALIDATED

      Source sequence(s)
      BC169082, CB612721, CO570626
      UniProtKB/TrEMBL
      A6KC96, G3V9M1
      Related
      ENSRNOP00000072026.3, ENSRNOT00000089612.3
      Conserved Domains (3) summary
      TIGR01622
      Location:79 → 207
      SF-CC1; splicing factor, CC1-like family
      cd18787
      Location:638 → 767
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17945
      Location:401 → 627
      DEADc_DDX23; DEAD-box helicase domain of DEAD box protein 23

    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_086025.1 Reference GRCr8

      Range
      131676636..131693917 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006257343.5 → XP_006257405.1  probable ATP-dependent RNA helicase DDX23 isoform X1

      See identical proteins and their annotated locations for XP_006257405.1

      UniProtKB/TrEMBL
      A6KC96, G3V9M1
      Conserved Domains (3) summary
      TIGR01622
      Location:79 → 207
      SF-CC1; splicing factor, CC1-like family
      cd18787
      Location:638 → 767
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17945
      Location:401 → 627
      DEADc_DDX23; DEAD-box helicase domain of DEAD box protein 23
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
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