Ddx4 DEAD-box helicase 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ddx4provided by RGD
Official Full Name: DEAD-box helicase 4provided by RGD
Primary source: RGD:1308793
See related: EnsemblRapid:ENSRNOG00000026686 AllianceGenome:RGD:1308793
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RVLG
Summary: Predicted to enable several functions, including ATP hydrolysis activity; RNA helicase activity; and molecular condensate scaffold activity. Involved in response to benzoic acid; response to retinoic acid; and spermatogenesis. Located in chromatoid body and perinuclear region of cytoplasm. Orthologous to human DDX4 (DEAD-box helicase 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Restricted expression toward (RPKM 372.3) See more
Orthologs: human mouse all
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Genomic context

Location:: 2q14

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (45961174..46016097, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (44227946..44282867, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (44447610..44504263, complement)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The protective effect of platelet-rich plasma administrated on ovarian function in female rats with Cy-induced ovarian damage.
Title: The protective effect of platelet-rich plasma administrated on ovarian function in female rats with Cy-induced ovarian damage.

Submit: New GeneRIF Correction

General gene information

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Markers

AV206478 (e-PCR)
- UniSTS:165893

G65195 (e-PCR)
- UniSTS:225859

PMC208779P1 (e-PCR)
- UniSTS:271981

Ddx4 (e-PCR), detects polymorphism
- UniSTS:142841

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity 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 helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation 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
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables molecular condensate scaffold activity	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
involved_in flagellated sperm motility	ISO Inferred from Sequence Orthology more info
involved_in gamete generation	IBA Inferred from Biological aspect of Ancestor more info
involved_in germ cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within male meiosis I	ISO Inferred from Sequence Orthology more info
involved_in male meiosis I	ISO Inferred from Sequence Orthology more info
involved_in male meiosis I	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in male meiotic nuclear division	ISS Inferred from Sequence or Structural Similarity more info
involved_in piRNA processing	ISO Inferred from Sequence Orthology more info
involved_in piRNA processing	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in response to benzoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to retinoic acid	HEP more info	PubMed
involved_in response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in secondary piRNA processing	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in transposable element silencing by piRNA-mediated DNA methylation	ISO Inferred from Sequence Orthology more info
involved_in transposable element silencing by piRNA-mediated DNA methylation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_positive_effect transposable element silencing by piRNA-mediated heterochromatin formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_positive_effect transposable element silencing by piRNA-mediated heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in P granule	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatoid body	IDA Inferred from Direct Assay more info	PubMed
located_in chromatoid body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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 perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in pi-body	ISO Inferred from Sequence Orthology more info
located_in pi-body	ISS Inferred from Sequence or Structural Similarity more info
located_in piP-body	ISO Inferred from Sequence Orthology more info
located_in piP-body	ISS Inferred from Sequence or Structural Similarity more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: probable ATP-dependent RNA helicase DDX4

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 4; DEAD box protein 4; putative ATP-dependent RNA helicase DDX4; vasa homolog; vasa-like gene protein

NP_001071115.2

EC 3.6.4.13

XP_038958110.1

EC 3.6.4.13

XP_038958111.1

EC 3.6.4.13

XP_038958112.1

EC 3.6.4.13

XP_038958113.1

EC 3.6.4.13

XP_038958115.1

EC 3.6.4.13

XP_038958116.1

EC 3.6.4.13

XP_063137794.1

EC 3.6.4.13

XP_063137795.1

EC 3.6.4.13

XP_063137797.1

EC 3.6.4.13

XP_063137798.1

EC 3.6.4.13

XP_063137799.1

EC 3.6.4.13

XP_063137800.1

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_001077647.2 → NP_001071115.2 probable ATP-dependent RNA helicase DDX4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q64060

UniProtKB/TrEMBL

A0A8I5ZVB9

Related

ENSRNOP00000083389.1, ENSRNOT00000117202.2

Conserved Domains (2) summary

PTZ00110
Location:121 → 668

PTZ00110; helicase; Provisional

cd18052
Location:242 → 494

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

45961174..46016097 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039102188.2 → XP_038958116.1 probable ATP-dependent RNA helicase DDX4 isoform X11

UniProtKB/Swiss-Prot

Q64060

Conserved Domains (2) summary

PTZ00110
Location:121 → 654

PTZ00110; helicase; Provisional

cd18052
Location:228 → 480

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4
XM_039102185.2 → XP_038958113.1 probable ATP-dependent RNA helicase DDX4 isoform X8

UniProtKB/Swiss-Prot

Q64060

Conserved Domains (2) summary

PTZ00110
Location:121 → 673

PTZ00110; helicase; Provisional

cd18052
Location:247 → 499

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4
XM_039102182.2 → XP_038958110.1 probable ATP-dependent RNA helicase DDX4 isoform X3

UniProtKB/TrEMBL

C7E3F3

Conserved Domains (2) summary

cd18787
Location:520 → 649

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd18052
Location:262 → 514

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4
XM_039102187.2 → XP_038958115.1 probable ATP-dependent RNA helicase DDX4 isoform X9

UniProtKB/Swiss-Prot

Q64060

UniProtKB/TrEMBL

A0A8I5ZVB9

Conserved Domains (2) summary

PTZ00110
Location:121 → 668

PTZ00110; helicase; Provisional

cd18052
Location:242 → 494

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4
XM_039102184.2 → XP_038958112.1 probable ATP-dependent RNA helicase DDX4 isoform X4

UniProtKB/TrEMBL

C7E3F3, H9BFH0

Related

ENSRNOP00000013035.7, ENSRNOT00000013035.8

Conserved Domains (2) summary

cd18787
Location:515 → 644

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd18052
Location:257 → 509

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4
XM_063281730.1 → XP_063137800.1 probable ATP-dependent RNA helicase DDX4 isoform X10
XM_063281729.1 → XP_063137799.1 probable ATP-dependent RNA helicase DDX4 isoform X7
XM_063281727.1 → XP_063137797.1 probable ATP-dependent RNA helicase DDX4 isoform X5
XM_063281728.1 → XP_063137798.1 probable ATP-dependent RNA helicase DDX4 isoform X6
XM_063281725.1 → XP_063137795.1 probable ATP-dependent RNA helicase DDX4 isoform X2
XM_063281724.1 → XP_063137794.1 probable ATP-dependent RNA helicase DDX4 isoform X1
XM_039102183.1 → XP_038958111.1 probable ATP-dependent RNA helicase DDX4 isoform X3

UniProtKB/TrEMBL

C7E3F3

Conserved Domains (2) summary

cd18787
Location:520 → 649

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd18052
Location:262 → 514

DEADc_DDX4; DEAD-box helicase domain of DEAD box protein 4