Ddx39a DExD-box helicase 39A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ddx39aprovided by RGD
Official Full Name: DExD-box helicase 39Aprovided by RGD
Primary source: RGD:619920
See related: EnsemblRapid:ENSRNOG00000004373 AllianceGenome:RGD:619920
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ddxl; Ddx39
Summary: Predicted to enable several functions, including ATP hydrolysis activity; RNA helicase activity; and identical protein binding activity. Predicted to be involved in gene expression; negative regulation of RNA export from nucleus; and negative regulation of innate immune response. Predicted to be located in cytoplasm and nuclear speck. Predicted to be active in nucleus. Orthologous to human DDX39A (DExD-box helicase 39A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 370.9), Spleen (RPKM 223.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (41323465..41331413, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (24418743..24427422, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (24846530..24854886)

Chromosome 19 - NC_086037.1 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?

Overexpression of SOCS3 was found to reduce the level of calcium ionophore-induced phosphorylation of ERK1/2 and c-Jun transcription factor
Title: SOCS3 suppresses the expression of IL-4 cytokine by inhibiting the phosphorylation of c-Jun through the ERK signaling pathway in rat mast cell line RBL-2H3.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Ddx39 (e-PCR), detects polymorphism
- UniSTS:479096

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-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	ISO Inferred from Sequence Orthology 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 helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of RNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of innate immune response	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	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	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: ATP-dependent RNA helicase DDX39A

Names: ATP-dependent RNA helicase DDX39; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A; DEAD box protein 39; DEAD-box helicase 39A; nuclear RNA helicase, DECD variant of DEAD box family

NP_446015.2

EC 3.6.4.13

XP_038953975.1

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_053563.2 → NP_446015.2 ATP-dependent RNA helicase DDX39A

See identical proteins and their annotated locations for NP_446015.2

Status: PROVISIONAL

Source sequence(s)

BC086328

UniProtKB/Swiss-Prot

O70498, Q5U216

UniProtKB/TrEMBL

A0A8I6A2E4, A6IYD0

Related

ENSRNOP00000068949.1, ENSRNOT00000090312.3

Conserved Domains (2) summary

cd18787
Location:261 → 390

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

cd17950
Location:43 → 250

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39

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_086037.1 Reference GRCr8

Range

41323465..41331413 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039098047.2 → XP_038953975.1 ATP-dependent RNA helicase DDX39A isoform X1

UniProtKB/TrEMBL

A0A8L2QK42

Related

ENSRNOP00000110804.1, ENSRNOT00000149968.1

Conserved Domains (1) summary

COG0513
Location:27 → 247

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]