U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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