U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 360815, updated on 14-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Ddx54provided by RGD
    Official Full Name
    DEAD-box helicase 54provided by RGD
    Primary source
    RGD:1562539
    See related
    EnsemblRapid: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; nuclear 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, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 116.4), Adrenal (RPKM 104.3) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Ddx54 in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. DEAD-box helicase 54 regulates microglial inflammatory response in rats with chronic constriction injuries through NF-κB/NLRP3 signaling axis. Liu P, et al. J Neurophysiol, 2023 Aug 1. PMID 37377223
    2. 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
    3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    4. Defining the membrane proteome of NK cells. Ghosh D, et al. J Mass Spectrom, 2010 Jan. PMID 19946888
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (6) citations in PubMed

    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

    Go to the top of the page Help

    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 ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader 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 chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    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 chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in motile cilium 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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    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.

    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
      ENSRNOP00000080555.2, ENSRNOT00000111779.2

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

      UniProtKB/TrEMBL
      D3ZHY6
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools