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Aliases for DDX39B Gene

Aliases for DDX39B Gene

  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39B 2 3
  • BAT1 3 4 6
  • HLA-B-Associated Transcript 1 Protein 3 4
  • 56 KDa U2AF65-Associated Protein 3 4
  • ATP-Dependent RNA Helicase P47 3 4
  • D6S81E 3 6
  • UAP56 3 4
  • Nuclear RNA Helicase (DEAD Family) 3
  • Spliceosome RNA Helicase DDX39B 3
  • HLA-B Associated Transcript 1 2
  • Spliceosome RNA Helicase BAT1 3
  • U2AF65-Associated Protein 56 2
  • DEAD Box Protein UAP56 4
  • EC 3.6.4.13 4

External Ids for DDX39B Gene

Previous HGNC Symbols for DDX39B Gene

  • BAT1

Previous GeneCards Identifiers for DDX39B Gene

  • GC06M031500
  • GC06M031522

Summaries for DDX39B Gene

Entrez Gene Summary for DDX39B Gene

  • 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]

GeneCards Summary for DDX39B Gene

DDX39B (DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39B) is a Protein Coding gene. Diseases associated with DDX39B include rheumatoid arthritis. Among its related pathways are RNA transport and Spliceosome. GO annotations related to this gene include ATP-dependent RNA helicase activity and U6 snRNA binding. An important paralog of this gene is DDX39A.

UniProtKB/Swiss-Prot for DDX39B Gene

  • Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5 end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. The TREX complex is essential for the export of Kaposis sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability

  • Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5 or 3 overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly with [PubMed:23299939] reporting a stimulatory effect

Gene Wiki entry for DDX39B Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX39B Gene

Genomics for DDX39B Gene

Genomic Location for DDX39B Gene

Start:
31,530,219 bp from pter
End:
31,542,475 bp from pter
Size:
12,257 bases
Orientation:
Minus strand

Genomic View for DDX39B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDX39B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

No data available for Regulatory Elements for DDX39B Gene

Proteins for DDX39B Gene

  • Protein details for DDX39B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13838-DX39B_HUMAN
    Recommended name:
    Spliceosome RNA helicase DDX39B
    Protein Accession:
    Q13838
    Secondary Accessions:
    • B0S8C0
    • O43496
    • Q0EFA1
    • Q2L6F9
    • Q53GL9
    • Q5RJ64
    • Q5RJ66
    • Q5ST94
    • Q5STB4
    • Q5STB5
    • Q5STB7
    • Q5STB8
    • Q5STU4
    • Q5STU5
    • Q5STU6
    • Q5STU8
    • Q71V76

    Protein attributes for DDX39B Gene

    Size:
    428 amino acids
    Molecular mass:
    48991 Da
    Quaternary structure:
    • Homodimer, and heterodimer with DDX39A. Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have dynamic structure involving ATP-dependent remodeling; in the complex bridges ALYREF/THOC4 and the THO complex, and, in a ATP-dependent manner, ALYREF/THOC4 and SARNP/CIP29. Component of the spliceosome. Interacts directly with U2AF2. Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1, MX1 and POLDIP3. Interacts with human cytomegalovirus/HHV-5 protein UL69.
    SequenceCaution:
    • Sequence=CAI17665.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for DDX39B Gene

    Alternative splice isoforms for DDX39B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX39B Gene

Proteomics data for DDX39B Gene at MOPED

Post-translational modifications for DDX39B Gene

  • Ubiquitination at Lys33, Lys36, Lys53, Lys90, Lys131, Lys241, Lys268, Lys334, and Lys384
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for DDX39B Gene

Domains for DDX39B Gene

Gene Families for DDX39B Gene

HGNC:
  • DDX :DEAD-boxes

Graphical View of Domain Structure for InterPro Entry

Q13838

UniProtKB/Swiss-Prot:

DX39B_HUMAN :
  • Q13838
Domain:
  • The helicase C-terminal domain mediates interaction with ALYREF/THOC4.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the DEAD box helicase family. DECD subfamily.
genes like me logo Genes that share domains with DDX39B: view

Function for DDX39B Gene

Molecular function for DDX39B Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.3 uM for ATP {ECO:0000269 PubMed:17562711}; Vmax=0.126 uM/min/mg enzyme with ATP as substrate {ECO:0000269 PubMed:17562711};
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5 end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. The TREX complex is essential for the export of Kaposis sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability
UniProtKB/Swiss-Prot Function:
Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5 or 3 overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly with [PubMed:23299939] reporting a stimulatory effect

Enzyme Numbers (IUBMB) for DDX39B Gene

Gene Ontology (GO) - Molecular Function for DDX39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding --
GO:0004004 ATP-dependent RNA helicase activity IDA 17562711
GO:0004386 helicase activity --
GO:0005515 protein binding IPI 11979277
genes like me logo Genes that share ontologies with DDX39B: view

Phenotypes for DDX39B Gene

genes like me logo Genes that share phenotypes with DDX39B: view

Animal Model Products

CRISPR Products

miRNA for DDX39B Gene

miRTarBase miRNAs that target DDX39B

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX39B

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for DDX39B Gene

Localization for DDX39B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX39B Gene

Nucleus. Nucleus speckle. Cytoplasm. Note=Can translocate to the cytoplasm in the presence of MX1. TREX complex assembly seems to occur in regions surrounding nuclear speckles known as perispeckles.

Gene Ontology (GO) - Cellular Components for DDX39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000346 transcription export complex IDA 15833825
GO:0005634 nucleus IDA 21859714
GO:0005654 nucleoplasm IDA --
GO:0005681 spliceosomal complex IDA 18593880
GO:0005687 colocalizes_with U4 snRNP IDA 18593880
genes like me logo Genes that share ontologies with DDX39B: view

No data available for Subcellular locations from COMPARTMENTS for DDX39B Gene

Pathways for DDX39B Gene

genes like me logo Genes that share pathways with DDX39B: view

Pathways by source for DDX39B Gene

Gene Ontology (GO) - Biological Process for DDX39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IDA 18593880
GO:0000398 mRNA splicing, via spliceosome IGI 15047853
GO:0006200 obsolete ATP catabolic process --
GO:0006406 mRNA export from nucleus IGI 15047853
GO:0008152 metabolic process --
genes like me logo Genes that share ontologies with DDX39B: view

Compounds for DDX39B Gene

(1) Drugbank Compounds for DDX39B Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Adenosine-5'-Diphosphate
20398-34-9 target

(1) Novoseek inferred chemical compound relationships for DDX39B Gene

Compound -log(P) Hits PubMed IDs
atp 24 12
genes like me logo Genes that share compounds with DDX39B: view

Transcripts for DDX39B Gene

Unigene Clusters for DDX39B Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX39B

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX39B Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^
SP1: - - - - -
SP2: - - - - - - -
SP3:
SP4:
SP5: - - - - - - -
SP6: - - - - - - -
SP7: - - - - - - -
SP8: - - - - -
SP9:
SP10: - - - - -
SP11: - - - - - - - - - - - - -
SP12: - - - - -
SP13: - - - - - -
SP14: - - - - - -
SP15: - - - -
SP16: - - -
SP17: -
SP18: - - - -
SP19: - - -
SP20: - -
SP21:
SP22: - -
SP23:
SP24:
SP25:
SP26: - - - - - - -

ExUns: 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c · 16d ^ 17a · 17b · 17c · 17d ^ 18a · 18b ^ 19a · 19b ^ 20 ^ 21a · 21b · 21c · 21d ^ 22 ^ 23
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5: -
SP6: - -
SP7: -
SP8: - -
SP9:
SP10:
SP11:
SP12:
SP13: -
SP14: -
SP15: -
SP16: -
SP17: -
SP18:
SP19:
SP20:
SP21:
SP22:
SP23: -
SP24: -
SP25:
SP26: -

Relevant External Links for DDX39B Gene

GeneLoc Exon Structure for
DDX39B
ECgene alternative splicing isoforms for
DDX39B

Expression for DDX39B Gene

mRNA expression in normal human tissues for DDX39B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX39B Gene

SOURCE GeneReport for Unigene cluster for DDX39B Gene Hs.254042

genes like me logo Genes that share expressions with DDX39B: view

Expression partners for DDX39B Gene

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for DDX39B Gene

Orthologs for DDX39B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX39B Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia DDX39B 35
  • 95.79 (n)
  • 99.77 (a)
DDX39B 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX39B 35
  • 94.86 (n)
  • 99.53 (a)
DDX39B 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx39b 35
  • 92.13 (n)
  • 99.53 (a)
Ddx39b 16
Ddx39b 36
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia DDX39B 35
  • 99.84 (n)
  • 100 (a)
DDX39B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddx39b 35
  • 91.9 (n)
  • 99.53 (a)
oppossum
(Monodelphis domestica)
Mammalia DDX39B 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX39B 36
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX39B 36
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx39b 35
  • 80.53 (n)
  • 94.63 (a)
MGC75726 35
zebrafish
(Danio rerio)
Actinopterygii -- 35
bat1 35
  • 79.67 (n)
  • 93.93 (a)
ddx39b 36
  • 92 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009075 35
  • 73.04 (n)
  • 84.95 (a)
fruit fly
(Drosophila melanogaster)
Insecta Hel25E 35
  • 75.85 (n)
  • 85.51 (a)
Hel25E 36
  • 84 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hel-1 36
  • 76 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR260C 35
  • 62.92 (n)
  • 65.55 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E21935g 35
  • 61.92 (n)
  • 64.37 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SUB2 35
  • 61.32 (n)
  • 66.03 (a)
SUB2 36
  • 61 (a)
OneToMany
SUB2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G11170 35
  • 67.47 (n)
  • 72.77 (a)
soybean
(Glycine max)
eudicotyledons Gma.2711 35
rice
(Oryza sativa)
Liliopsida Os.14280 35
Os01g0550000 35
  • 66.9 (n)
  • 74.7 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.2127 35
corn
(Zea mays)
Liliopsida Zm.3715 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3968 35
bread mold
(Neurospora crassa)
Ascomycetes NCU09076 35
  • 66.19 (n)
  • 67.06 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes uap56 35
  • 64.42 (n)
  • 70.67 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10395 36
  • 82 (a)
OneToMany
Species with no ortholog for DDX39B:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for DDX39B Gene

ENSEMBL:
Gene Tree for DDX39B (if available)
TreeFam:
Gene Tree for DDX39B (if available)

Paralogs for DDX39B Gene

Paralogs for DDX39B Gene

Pseudogenes.org Pseudogenes for DDX39B Gene

genes like me logo Genes that share paralogs with DDX39B: view

Variants for DDX39B Gene

Structural Variations from Database of Genomic Variants (DGV) for DDX39B Gene

Variant ID Type Subtype PubMed ID
esv690 CNV CNV 17122850
dgv1042e201 CNV Deletion 23290073
dgv213e55 CNV Gain 17911159
essv13266 CNV CNV 17122850
dgv6580n71 CNV Gain 21882294
nsv830627 CNV Loss 17160897
nsv470809 CNV Loss 18288195

Relevant External Links for DDX39B Gene

HapMap Linkage Disequilibrium report
DDX39B
Human Gene Mutation Database (HGMD)
DDX39B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations from dbSNP and Humsavar for DDX39B Gene

Disorders for DDX39B Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for DDX39B Gene in MalaCards »

(1) Diseases for DDX39B Gene including...

(5) Novoseek inferred disease relationships for DDX39B Gene

Disease -log(P) Hits PubMed IDs
autoimmune diseases 30.5 1
rheumatoid arthritis 18.3 3
necrosis 17.6 3
lupus erythematosus systemic 7.01 2
tumors 0 2
genes like me logo Genes that share disorders with DDX39B: view

No data available for OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Genatlas and External Links for DDX39B Gene

Publications for DDX39B Gene

  1. The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family. (PMID: 7601445) Peelman L. … Spies T. (Genomics 1995) 2 3 4 23
  2. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. (PMID: 11675789) Luo M.-J. … Reed R. (Nature 2001) 3 4 23
  3. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. (PMID: 9242493) Fleckner J. … Green M.R. (Genes Dev. 1997) 3 4 23
  4. Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. (PMID: 15296731) Zhao R. … Blumenthal T. (Structure 2004) 3 4 23
  5. Crystal structure of the human ATP-dependent splicing and export factor UAP56. (PMID: 15585580) Shi H. … Xu R.-M. (Proc. Natl. Acad. Sci. U.S.A. 2004) 3 4 23

Products for DDX39B Gene

Sources for DDX39B Gene

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