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

Gene ID: 53817, updated on 14-Nov-2024

Summary

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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 hydrolysis activity; ATP-dependent protein binding activity; and RNA 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. 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, Nov 2024]
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

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See Ddx39b in Genome Data Viewer
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_000083.7Genomic Context describing neighboring genes Neighboring gene microRNA 6974 Neighboring gene STARR-positive B cell enhancer ABC_E11642 Neighboring gene lymphotoxin A Neighboring gene nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1 Neighboring gene STARR-positive B cell enhancer ABC_E5601 Neighboring gene STARR-positive B cell enhancer ABC_E7528 Neighboring gene STARR-positive B cell enhancer ABC_E1942 Neighboring gene ATPase, H+ transporting, lysosomal V1 subunit G2 Neighboring gene STARR-positive B cell enhancer ABC_E10948 Neighboring gene predicted gene, 22589 Neighboring gene microRNA 6975 Neighboring gene predicted gene, 25128 Neighboring gene microRNA 8094 Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:35395114-35395315 Neighboring gene STARR-positive B cell enhancer ABC_E2487 Neighboring gene STARR-positive B cell enhancer ABC_E5603 Neighboring gene histocompatibility 2, D region locus 1 Neighboring gene vacuolar protein sorting 52 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy. Szymura SJ, et al. BMC Biol, 2020 Mar 24. PMID 32209106, Free PMC Article
  2. Plk1-mediated phosphorylation of UAP56 regulates the stability of UAP56. Xiong F, et al. Mol Biol Rep, 2012 Feb. PMID 21637952
  3. Fine mapping of the crossover-sites in the C4-H-2D region of H-2 recombinant mouse strains. Snoek M, et al. Immunogenetics, 1991. PMID 1684177
  4. Murine leukemia virus uses TREX components for efficient nuclear export of unspliced viral transcripts. Sakuma T, et al. Viruses, 2014 Mar 10. PMID 24618812, Free PMC Article
  5. Heat shock factor 4 regulates the expression of HSP25 and alpha B-crystallin by associating with DEXD/H-box RNA helicase UAP56. Cui X, et al. Cell Stress Chaperones, 2018 Jul. PMID 29164525, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC19235, MGC38799

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 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 ATP-dependent activity, acting on RNA ISO
Inferred from Sequence Orthology
more info
  
enables ATP-dependent protein binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent protein binding ISO
Inferred from Sequence Orthology
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 RNA helicase activity ISO
Inferred from Sequence Orthology
more info
  
enables U4 snRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables U4 snRNA binding ISO
Inferred from Sequence Orthology
more info
  
enables U6 snRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables U6 snRNA binding 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
  
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 protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in RNA secondary structure unwinding IEA
Inferred from Electronic Annotation
more info
  
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 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 ISO
Inferred from Sequence Orthology
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in spliceosomal complex assembly ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of U4 snRNP IEA
Inferred from Electronic Annotation
more info
  
part_of U4 snRNP ISO
Inferred from Sequence Orthology
more info
  
part_of U6 snRNP IEA
Inferred from Electronic Annotation
more info
  
part_of U6 snRNP ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex ISO
Inferred from Sequence Orthology
more info
  
part_of transcription export complex IEA
Inferred from Electronic Annotation
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
NP_062667.1

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)

  1. 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

  2. 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

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

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    35460722..35472683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Z1N5.1 GenPept UniProtKB/Swiss-Prot:Q9Z1N5

Gene LinkOut

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