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DDX54 DEAD-box helicase 54 [ Homo sapiens (human) ]

Gene ID: 79039, updated on 7-Apr-2024

Summary

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Official Symbol
DDX54provided by HGNC
Official Full Name
DEAD-box helicase 54provided by HGNC
Primary source
HGNC:HGNC:20084
See related
Ensembl:ENSG00000123064 MIM:611665; AllianceGenome:HGNC:20084
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DP97
Summary
This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The nucleolar protein encoded by this gene interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. Alternative splice variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 11.3), spleen (RPKM 9.8) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12q24.13
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (113157173..113185478, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (113133817..113162122, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (113594978..113623283, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113495773-113496561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113503073-113503631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113504873-113505373 Neighboring gene deltex E3 ubiquitin ligase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113535297-113535838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7061 Neighboring gene RAS protein activator like 1 Neighboring gene MPRA-validated peak1969 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113592609-113593108 Neighboring gene MPRA-validated peak1971 silencer Neighboring gene cilia and flagella associated protein 73 Neighboring gene microRNA 7106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7063 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:113623217-113623866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113623867-113624517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113624518-113625167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113629297-113629950 Neighboring gene Sharpr-MPRA regulatory region 6569 Neighboring gene RBPJ interacting and tubulin associated 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:113639865-113640756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7067 Neighboring gene IQ motif containing D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7068

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A DEAD-box RNA helicase Ddx54 protein in oligodendrocytes is indispensable for myelination in the central nervous system. Zhan R, et al. J Neurosci Res, 2013 Mar. PMID 23239230
  2. DP97, a DEAD box DNA/RNA helicase, is a target gene-selective co-regulator of the constitutive androstane receptor. Kanno Y, et al. Biochem Biophys Res Commun, 2012 Sep 14. PMID 22910411
  3. SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth. Zhang Y, et al. Dig Dis Sci, 2021 Jun. PMID 32712782
  4. Paralog Studies Augment Gene Discovery: DDX and DHX Genes. Paine I, et al. Am J Hum Genet, 2019 Aug 1. PMID 31256877, Free PMC Article
  5. 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

See all (120) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
    Title: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
  2. Missense mutation in DDX54 gene is associated with neurodevelopmental disorder.
    Title: Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
  3. Ddx54 plays an important role in central nervous system myelination, presumably in myelin sheath formation after the differentiation of oligodendrocytes.
    Title: A DEAD-box RNA helicase Ddx54 protein in oligodendrocytes is indispensable for myelination in the central nervous system.
  4. DP97 was found to be a gene (or promoter)-selective co-activator for hCAR
    Title: DP97, a DEAD box DNA/RNA helicase, is a target gene-selective co-regulator of the constitutive androstane receptor.
  5. Identifies dead box polypeptide 54 as a 14-3-3-binding protein.
    Title: Rapid identification of 14-3-3-binding proteins by protein microarray analysis.
  6. Identifies DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 (locus 79039) as a novel nucleolar protein in HeLa cells.
    Title: Directed proteomic analysis of the human nucleolus.
  7. Identifies DEAD box polypeptide 54 (similar to RIKEN cDNA 2410015A15 gene) as one of 213 different nucleolar proteins in HeLa cells.
    Title: Functional proteomic analysis of human nucleolus.
  8. Kinetic analysis of DEAD box helicases, including DEAD box polypeptide 54, in response to transcription inhibition.
    Title: Nucleolar proteome dynamics.
  9. Includes the identification of DEAD box polypeptide 54 phosphopeptides following the stimulation of HeLa cells with epidermal growth factor.
    Title: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC2835

Gene Ontology Provided by GOA

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 HDA PubMed 
enables RNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear estrogen receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables signaling receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in intracellular estrogen receptor signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
  
located_in membrane HDA PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ATP-dependent RNA helicase DDX54
Names
ATP-dependent RNA helicase DP97
DEAD (Asp-Glu-Ala-Asp) box polypeptide 54
DEAD box RNA helicase 97 kDa
DEAD box helicase 97 KDa
DEAD box polypeptide, 97kD
DEAD box protein 54
apoptosis related protein 5
NP_001104792.1
NP_076977.3

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_001111322.2 → NP_001104792.1  ATP-dependent RNA helicase DDX54 isoform 1

    See identical proteins and their annotated locations for NP_001104792.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF478457, BC005848
    Consensus CDS
    CCDS44984.1
    UniProtKB/Swiss-Prot
    Q8TDD1
    Related
    ENSP00000323858.7, ENST00000314045.11
    Conserved Domains (4) summary
    PRK01297
    Location:1 → 469
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cd00079
    Location:315 → 441
    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:98 → 300
    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:714 → 774
    DBP10CT; DBP10CT (NUC160) domain

  2. NM_024072.4 → NP_076977.3  ATP-dependent RNA helicase DDX54 isoform 2

    See identical proteins and their annotated locations for NP_076977.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AF478457, BC005848
    Consensus CDS
    CCDS31907.1
    UniProtKB/Swiss-Prot
    Q86YT8, Q8TDD1, Q9BRZ1
    Related
    ENSP00000304072.5, ENST00000306014.10
    Conserved Domains (4) summary
    PRK01297
    Location:1 → 469
    PRK01297; ATP-dependent RNA helicase RhlB; Provisional
    cd00079
    Location:315 → 441
    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:98 → 300
    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:714 → 774
    DBP10CT; DBP10CT (NUC160) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    113157173..113185478 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    113133817..113162122 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TDD1.2 GenPept UniProtKB/Swiss-Prot:Q8TDD1

Gene LinkOut

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

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