DDX47 DEAD-box helicase 47 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX47provided by HGNC
Official Full Name: DEAD-box helicase 47provided by HGNC
Primary source: HGNC:HGNC:18682
See related: Ensembl:ENSG00000213782 MIM:615428; AllianceGenome:HGNC:18682
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: RRP3; E4-DBP; HQ0256; MSTP162
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 protein encoded by this gene can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 25.1), lymph node (RPKM 21.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (12813346..12829981)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (12686924..12703560)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (12966280..12982915)

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?

BIOINFORMATICS APPLICATIONS UNDER CONDITION CONTROL: HIGH DIAGNOSTIC VALUE OF DDX47 IN REAL MEDICAL SETTINGS.
Title: BIOINFORMATICS APPLICATIONS UNDER CONDITION CONTROL: HIGH DIAGNOSTIC VALUE OF DDX47 IN REAL MEDICAL SETTINGS.
DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.
Title: DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.
GABARAP and DDX 47 are involved in the apoptotic process
Title: GABAA receptor-associated protein (GABARAP) induces apoptosis by interacting with DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 47 (DDX 47).

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 (DDX47), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with DDX47 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A002Q26 (e-PCR)
- UniSTS:40280

SHGC-80741 (e-PCR)
- UniSTS:102274

D12S929 (e-PCR)
- UniSTS:149930

D12S1235E (e-PCR)
- UniSTS:151482

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 more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in extrinsic apoptotic signaling pathway via death domain receptors	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	HDA more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: probable ATP-dependent RNA helicase DDX47

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 47; DEAD box polypeptide 47; DEAD box protein 47; E4-DEAD box protein

NP_057439.2

EC 3.6.4.13

NP_957518.1

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_016355.4 → NP_057439.2 probable ATP-dependent RNA helicase DDX47 isoform 1

See identical proteins and their annotated locations for NP_057439.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AL136666, BC009379

Consensus CDS

CCDS8655.1

UniProtKB/Swiss-Prot

B3KXP4, G5E955, Q96GM0, Q96NV8, Q9H0S4, Q9UI98

UniProtKB/TrEMBL

Q9H4E3

Related

ENSP00000350698.3, ENST00000358007.7

Conserved Domains (3) summary

PRK11192
Location:24 → 446

PRK11192; ATP-dependent RNA helicase SrmB; Provisional

cd00079
Location:237 → 366

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:26 → 227

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 ...
NM_201224.2 → NP_957518.1 probable ATP-dependent RNA helicase DDX47 isoform 2

See identical proteins and their annotated locations for NP_957518.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, as compared to variant 1. The encoded isoform (2) is thus missing an internal segment, as compared to isoform 1.

Source sequence(s)

AF078843, AL136666, BC009379

Consensus CDS

CCDS8656.1

UniProtKB/TrEMBL

Q9H4E3

Related

ENSP00000319578.6, ENST00000352940.8

Conserved Domains (3) summary

PRK11192
Location:24 → 397

PRK11192; ATP-dependent RNA helicase SrmB; Provisional

cd00079
Location:184 → 317

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:26 → 227

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 ...