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    Ddx54 DEAD-box helicase 54 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360815, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Ddx54provided by RGD
    Official Full Name
    DEAD-box helicase 54provided by RGD
    Primary source
    RGD:1562539
    See related
    Ensembl:ENSRNOG00000001377 AllianceGenome:RGD:1562539
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1562539
    Summary
    Predicted to enable several functions, including RNA helicase activity; estrogen receptor binding activity; and transcription corepressor activity. Predicted to be involved in rRNA processing. Predicted to be located in Golgi apparatus and nucleoplasm. Predicted to be active in nucleolus. Orthologous to human DDX54 (DEAD-box helicase 54). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 116.4), Adrenal (RPKM 104.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    12q16
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (41595298..41610560, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (35934713..35949956, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (41469642..41484887, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene RAS protein activator like 1 Neighboring gene NADH:ubiquinone oxidoreductase subunit A1, pseudogene 2 Neighboring gene cilia and flagella associated protein 73 Neighboring gene RBPJ interacting and tubulin associated 1 Neighboring gene IQ motif containing D

    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. Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). Rajendran RR, et al. J Biol Chem, 2003 Feb 14. PMID 12466272
    2. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    3. Defining the membrane proteome of NK cells. Ghosh D, et al. J Mass Spectrom, 2010 Jan. PMID 19946888
    4. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DEAD-box helicase 54 regulates microglial inflammatory response in rats with chronic constriction injuries through NF-kappaB/NLRP3 signaling axis.
      Title: DEAD-box helicase 54 regulates microglial inflammatory response in rats with chronic constriction injuries through NF-κB/NLRP3 signaling axis.
    Submit: New GeneRIF Correction

    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
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear estrogen receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables signaling receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in RNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    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
    ATP-dependent RNA helicase DDX54
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 54
    NP_001178477.1
    XP_006249459.2
    XP_006249460.2

    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_001191548.1 → NP_001178477.1  ATP-dependent RNA helicase DDX54

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/TrEMBL
      D3ZHY6
      Conserved Domains (4) summary
      COG0513
      Location:69 → 536
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd00079
      Location:314 → 440
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cd00268
      Location:97 → 299
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
      pfam08147
      Location:705 → 765
      DBP10CT; DBP10CT (NUC160) domain

    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_086030.1 Reference GRCr8

      Range
      41595298..41610560 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006249397.4 → XP_006249459.2  ATP-dependent RNA helicase DDX54 isoform X1

      UniProtKB/TrEMBL
      D3ZHY6
      Related
      ENSRNOP00000001859.8

    2. XM_006249398.4 → XP_006249460.2  ATP-dependent RNA helicase DDX54 isoform X2

      UniProtKB/TrEMBL
      D3ZHY6
    Nucleotide Protein Strain
    Heading Accession and Version

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