Ddx39b DEAD box helicase 39b [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddx39bprovided by MGI
Official Full Name: DEAD box helicase 39bprovided by MGI
Primary source: MGI:MGI:99240
See related: Ensembl:ENSMUSG00000019432 AllianceGenome:MGI:99240
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: Bat1; Bat-1; Bat1a; D6S81Eh; D17H6S81E; D17H6S81E-1; 0610030D10Rik
Summary: Predicted to enable several functions, including ATP-dependent protein binding activity; RNA helicase activity; and snRNA binding activity. Predicted to be involved in several processes, including RNA metabolic process; positive regulation of cell growth involved in cardiac muscle cell development; and positive regulation of macromolecule biosynthetic process. Predicted to act upstream of or within mRNA processing and mRNA transport. Located in nuclear speck. Is expressed in embryo. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human DDX39B (DExD-box helicase 39B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 289.9), limb E14.5 (RPKM 249.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 B1; 17 18.6 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (35460722..35472683)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (35241746..35253707)

Chromosome 17 - NC_000083.7 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?

DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-kappaB and sensitize to alkylating chemotherapy.
Title: DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy.
Ectopic UAP56 upregulated HSF4-controlled HSP25 and alpha B-crystallin proteins expression, while knocking down UAP56 by shRNA reversed it.
Title: Heat shock factor 4 regulates the expression of HSP25 and alpha B-crystallin by associating with DEXD/H-box RNA helicase UAP56.
These results imply that murine leukemia virus requires UAP56, THOC5 and THOC7, in addition to NXF1, for nuclear export of viral transcripts.
Title: Murine leukemia virus uses TREX components for efficient nuclear export of unspliced viral transcripts.
Mx proteins exert their antiviral activity against IAV by interfering with the function of the RNA helicases UAP56 and URH49
Title: Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49.

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Variation

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Alleles

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

Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Bat1_microsatellite (e-PCR)
- UniSTS:240926

D17H6S81E-1 (e-PCR), detects polymorphism
- UniSTS:142121

RH126881 (e-PCR)
- UniSTS:209757

RH144334 (e-PCR)
- UniSTS:233579

Gene Ontology Provided by MGI

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 activity, acting on RNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables U4 snRNA binding	ISO Inferred from Sequence Orthology more info
enables U6 snRNA binding	ISO Inferred from Sequence Orthology 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	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
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in RNA secondary structure unwinding	ISO Inferred from Sequence Orthology more info
involved_in RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth involved in cardiac muscle cell development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular associated smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in spliceosomal complex assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of U4 snRNP	ISO Inferred from Sequence Orthology more info
part_of U6 snRNP	ISO Inferred from Sequence Orthology more info
colocalizes_with cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of spliceosomal complex	ISO Inferred from Sequence Orthology more info
part_of transcription export complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: spliceosome RNA helicase Ddx39b

Names: 56 kDa U2AF65-associated protein; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B; DEAD box protein UAP56; HLA-B-associated transcript 1A; nuclear RNA helicase Bat1; spliceosome RNA helicase Bat1

NP_001239386.1

EC 3.6.4.13

NP_062667.1

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_001252457.1 → NP_001239386.1 spliceosome RNA helicase Ddx39b

See identical proteins and their annotated locations for NP_001239386.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

CR974444

Consensus CDS

CCDS28695.1

UniProtKB/Swiss-Prot

Q8HW97, Q9Z1N5

UniProtKB/TrEMBL

Q3T9L0, Q3TIE4, Q3TPL7, Q3U837, Q3UVN0

Related

ENSMUSP00000134178.2, ENSMUST00000172549.2

Conserved Domains (2) summary

cd18787
Location:262 → 391

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

cd17950
Location:44 → 251

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39
NM_019693.3 → NP_062667.1 spliceosome RNA helicase Ddx39b

See identical proteins and their annotated locations for NP_062667.1

Status: VALIDATED

Description

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

Source sequence(s)

AA231260, AK051034, CN716634, CR974444

Consensus CDS

CCDS28695.1

UniProtKB/Swiss-Prot

Q8HW97, Q9Z1N5

UniProtKB/TrEMBL

Q3T9L0, Q3TIE4, Q3TPL7, Q3U837, Q3UVN0

Related

ENSMUSP00000070682.6, ENSMUST00000068056.12

Conserved Domains (2) summary

cd18787
Location:262 → 391

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

cd17950
Location:44 → 251

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