Ddx42 DEAD box helicase 42 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddx42provided by MGI
Official Full Name: DEAD box helicase 42provided by MGI
Primary source: MGI:MGI:1919297
See related: Ensembl:ENSMUSG00000020705 AllianceGenome:MGI:1919297
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: RHELP; RNAHP; SF3b125; 1810047H21Rik; B430002H05Rik
Summary: Predicted to enable RNA binding activity and RNA helicase activity. Predicted to be involved in U2-type prespliceosome assembly; protein localization; and regulation of apoptotic process. Predicted to be located in cytosol and nuclear speck. Predicted to be part of U2-type prespliceosome. Predicted to be active in nucleus. Orthologous to human DDX42 (DEAD-box helicase 42). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 21.4), CNS E14 (RPKM 14.0) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 E1; 11 68.89 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (106107715..106139966)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (106216887..106249140)

Chromosome 11 - NC_000077.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Gene trapped (1)
Targeted (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_15367-15368:1017691706:1 (e-PCR)
- UniSTS:267828

RH124310 (e-PCR)
- UniSTS:161132

AW319508 (e-PCR)
- UniSTS:180352

RH127156 (e-PCR)
- UniSTS:167052

AU045295 (e-PCR)
- UniSTS:160177

NoName (e-PCR)
- UniSTS:236759

UniSTS:238045 (e-PCR)
- UniSTS:238045

Gene Ontology Provided by MGI

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 binding	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	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

Process	Evidence Code	Pubs
involved_in U2-type prespliceosome assembly	ISO Inferred from Sequence Orthology more info
involved_in U2-type prespliceosome assembly	ISS Inferred from Sequence or Structural Similarity 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 protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of U2-type prespliceosome	ISO Inferred from Sequence Orthology more info
part_of U2-type prespliceosome	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ATP-dependent RNA helicase DDX42

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 42; DEAD box protein 42; RNA helicase-related protein

NP_001348569.1

EC 3.6.4.13

NP_001348571.1

EC 3.6.4.13

NP_001348572.1

EC 3.6.4.13

NP_001348573.1

EC 3.6.4.13

NP_082350.3

EC 3.6.4.13

XP_030102205.1

EC 3.6.4.13

XP_036012900.1

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_001361640.1 → NP_001348569.1 ATP-dependent RNA helicase DDX42 isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

AL604045

Conserved Domains (2) summary

PTZ00110
Location:30 → 489

PTZ00110; helicase; Provisional

cl11081
Location:481 → 726

dermokine
NM_001361642.1 → NP_001348571.1 ATP-dependent RNA helicase DDX42 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.

Source sequence(s)

AL604045

Conserved Domains (1) summary

COG0513
Location:76 → 343

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
NM_001361643.1 → NP_001348572.1 ATP-dependent RNA helicase DDX42 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).

Source sequence(s)

AK134182, AL596331, AL604045

Conserved Domains (2) summary

PRK10590
Location:9 → 414

PRK10590; ATP-dependent RNA helicase RhlE; Provisional

cd17952
Location:1 → 196

DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42
NM_001361644.1 → NP_001348573.1 ATP-dependent RNA helicase DDX42 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).

Source sequence(s)

AL604045

Conserved Domains (2) summary

PRK10590
Location:9 → 414

PRK10590; ATP-dependent RNA helicase RhlE; Provisional

cd17952
Location:1 → 196

DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42
NM_028074.4 → NP_082350.3 ATP-dependent RNA helicase DDX42 isoform a

See identical proteins and their annotated locations for NP_082350.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AI836088, AK007805, AK049311

Consensus CDS

CCDS48956.1

UniProtKB/Swiss-Prot

Q3TAN3, Q3TE60, Q810A7, Q8BWZ7, Q9D8Q2

Related

ENSMUSP00000021046.6, ENSMUST00000021046.6

Conserved Domains (3) summary

PRK10590
Location:254 → 678

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 ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

106107715..106139966

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157007.1 → XP_036012900.1 ATP-dependent RNA helicase DDX42 isoform X1

Conserved Domains (2) summary

PTZ00110
Location:30 → 489

PTZ00110; helicase; Provisional

cl11081
Location:481 → 726

dermokine
XM_030246345.2 → XP_030102205.1 ATP-dependent RNA helicase DDX42 isoform X2

Conserved Domains (2) summary

PRK10590
Location:9 → 414

PRK10590; ATP-dependent RNA helicase RhlE; Provisional

cd17952
Location:1 → 196

DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42