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

Summary

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

Location:: 12q24.13

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (113157173..113185478, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (113133817..113162122, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (113594978..113623283, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
Title: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
Missense mutation in DDX54 gene is associated with neurodevelopmental disorder.
Title: Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
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.
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.
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.
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.
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.
Kinetic analysis of DEAD box helicases, including DEAD box polypeptide 54, in response to transcription inhibition.
Title: Nucleolar proteome dynamics.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 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	HDA more info	PubMed
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
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 chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in 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 more info	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

EC 3.6.4.13

NP_076977.3

EC 3.6.4.13

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)

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
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