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DDX39B DExD-box helicase 39B [ Homo sapiens (human) ]

Gene ID: 7919, updated on 6-Jan-2019

Summary

Official Symbol
DDX39Bprovided by HGNC
Official Full Name
DExD-box helicase 39Bprovided by HGNC
Primary source
HGNC:HGNC:13917
See related
Ensembl:ENSG00000198563 MIM:142560
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BAT1; UAP56; D6S81E
Summary
This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in endometrium (RPKM 76.9), ovary (RPKM 76.7) and 25 other tissues See more
Orthologs

Genomic context

See DDX39B in Genome Data Viewer
Location:
6p21.33
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (31530219..31542475, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31497996..31510252, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase A pseudogene 9 Neighboring gene ATP6V1G2-DDX39B readthrough (NMD candidate) Neighboring gene ribosomal protein L15 pseudogene 4 Neighboring gene mitochondrial coiled-coil domain 1 Neighboring gene small nucleolar RNA, C/D box 117 Neighboring gene DDX39B antisense RNA 1 Neighboring gene small nucleolar RNA, C/D box 84 Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene NFKB inhibitor like 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Rev rev HIV-1 Rev specifically inhibits the association of ALY/REF and UAP56 with spliced RRE-containing RNA PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Exon junction complex (EJC), organism-specific biosystem (from KEGG)
    Exon junction complex (EJC), organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exon junction complex (EJC), conserved biosystem (from KEGG)
    Exon junction complex (EJC), conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • TREX complex, organism-specific biosystem (from KEGG)
    TREX complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • TREX complex, conserved biosystem (from KEGG)
    TREX complex, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
ATP-dependent protein binding IDA
Inferred from Direct Assay
more info
PubMed 
ATPase activity EXP
Inferred from Experiment
more info
PubMed 
RNA binding HDA PubMed 
RNA-dependent ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
U4 snRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
U6 snRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
RNA export from nucleus TAS
Traceable Author Statement
more info
 
RNA secondary structure unwinding IDA
Inferred from Direct Assay
more info
PubMed 
RNA splicing IDA
Inferred from Direct Assay
more info
PubMed 
liver development IEA
Inferred from Electronic Annotation
more info
 
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
mRNA export from nucleus IGI
Inferred from Genetic Interaction
more info
PubMed 
mRNA splicing, via spliceosome IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA-templated transcription, elongation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell growth involved in cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of translation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of vascular smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
spliceosomal complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
viral mRNA export from host cell nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with U4 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with U6 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription export complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
spliceosome RNA helicase DDX39B
Names
56 kDa U2AF65-associated protein
ATP-dependent RNA helicase p47
DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
DEAD-box helicase 39B
HLA-B-associated transcript 1 protein
nuclear RNA helicase (DEAD family)
spliceosome RNA helicase BAT1
NP_004631.1
NP_542165.1

NCBI Reference Sequences (RefSeq)

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_004640.7NP_004631.1  spliceosome RNA helicase DDX39B

    See identical proteins and their annotated locations for NP_004631.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    BM993499, DA272922, Z37166
    Consensus CDS
    CCDS4697.1
    UniProtKB/Swiss-Prot
    Q13838
    UniProtKB/TrEMBL
    A0A024RCM3
    Related
    ENSP00000379475.1, ENST00000396172.5
    Conserved Domains (1) summary
    COG0513
    Location:31413
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
  2. NM_080598.5NP_542165.1  spliceosome RNA helicase DDX39B

    See identical proteins and their annotated locations for NP_542165.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternative splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL662801, BC000361, BM993499, DA048099, DA272922
    Consensus CDS
    CCDS4697.1
    UniProtKB/Swiss-Prot
    Q13838
    UniProtKB/TrEMBL
    A0A024RCM3
    Related
    ENSP00000416269.1, ENST00000458640.5
    Conserved Domains (1) summary
    COG0513
    Location:31413
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

RNA

  1. NR_037852.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK298194, BM993499, DA048099, DA272922

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    31530219..31542475 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    2862768..2871733 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    3007552..3019805 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

    Range
    2777992..2790245 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p12 ALT_REF_LOCI_4

    Range
    2835292..2847528 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

    Range
    2872162..2884414 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    2786081..2798331 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    2829503..2841759 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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