DDX42 DEAD-box helicase 42 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX42provided by HGNC
Official Full Name: DEAD-box helicase 42provided by HGNC
Primary source: HGNC:HGNC:18676
See related: Ensembl:ENSG00000198231 MIM:613369; AllianceGenome:HGNC:18676
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: RHELP; RNAHP; SF3B8; DDX42P; SF3b125
Summary: This gene encodes a member of the Asp-Glu-Ala-Asp (DEAD) box protein family. Members of this protein family are putative RNA helicases, and 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. Members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 27.4), ovary (RPKM 25.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q23.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (63773800..63819317)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (64644531..64690152)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (61851530..61896677)

Chromosome 17 - NC_000017.11 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 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?

[The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses].
Title: [The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses].
Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
Title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses.
Title: The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses.
Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42.
Title: Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42.
expression of N-terminal DDX42 is able to overcome Japanese encephalitis virus-induced antagonism of IFN responses and so may be important for Japanese encephalitis virus pathogenesis
Title: Interferon antagonist function of Japanese encephalitis virus NS4A and its interaction with DEAD-box RNA helicase DDX42.
characterization of protein associated with the human 17S U2 snRNP and one of its stable subunits, SF3b; may facilitate the assembly of the 17S U2 snRNP
Title: Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein.
Ddx42p represents the first example of a human DEAD box protein possessing RNA helicase, protein displacement and RNA annealing activities.
Title: Ddx42p--a human DEAD box protein with RNA chaperone activities.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH75315 (e-PCR)
- UniSTS:90112

A007J39 (e-PCR)
- UniSTS:55908

D17S1492E (e-PCR)
- UniSTS:151697

RH80617 (e-PCR)
- UniSTS:88526

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 binding	IDA Inferred from Direct Assay 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 protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in U2-type prespliceosome assembly	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 protein localization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Cajal body	IEA Inferred from Electronic Annotation more info
part_of U2-type prespliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor 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 DDX42

Names: DEAD (Asp-Glu-Ala-Asp) box helicase 42; DEAD (Asp-Glu-Ala-Asp) box polypeptide 42; SF3b DEAD box protein; splicing factor 3B-associated 125 kDa protein; splicing factor 3b, subunit 8

NP_031398.2

EC 3.6.4.13

NP_987095.1

EC 3.6.4.13

XP_047291237.1

EC 3.6.4.13

XP_047291238.1

EC 3.6.4.13

XP_047291239.1

EC 3.6.4.13

XP_054170905.1

EC 3.6.4.13

XP_054170906.1

EC 3.6.4.13

XP_054170907.1

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_007372.3 → NP_031398.2 ATP-dependent RNA helicase DDX42

See identical proteins and their annotated locations for NP_031398.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AC015651, BC015505, BC093081

Consensus CDS

CCDS32704.1

UniProtKB/Swiss-Prot

A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8

Related

ENSP00000464050.1, ENST00000578681.5

Conserved Domains (3) summary

PRK10590
Location:254 → 688

PRK10590; ATP-dependent RNA helicase RhlE; Provisional

cd00079
Location:470 → 601

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:255 → 459

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_203499.3 → NP_987095.1 ATP-dependent RNA helicase DDX42

See identical proteins and their annotated locations for NP_987095.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AB036090, AC015651, BC015505, DA440475

Consensus CDS

CCDS32704.1

UniProtKB/Swiss-Prot

A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8

Related

ENSP00000374574.2, ENST00000389924.7

Conserved Domains (3) summary

PRK10590
Location:254 → 688

PRK10590; ATP-dependent RNA helicase RhlE; Provisional

cd00079
Location:470 → 601

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:255 → 459

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 ...