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Aliases for DDX39B Gene

Aliases for DDX39B Gene

  • DExD-Box Helicase 39B 2 3 5
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39B 2 3
  • HLA-B-Associated Transcript 1 Protein 3 4
  • 56 KDa U2AF65-Associated Protein 3 4
  • ATP-Dependent RNA Helicase P47 3 4
  • DEAD-Box Helicase 39B 2 3
  • UAP56 3 4
  • BAT1 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
  • D6S81E 3

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 (DExD-Box Helicase 39B) is a Protein Coding gene. Diseases associated with DDX39B include Plasmodium Vivax Malaria. Among its related pathways are RNA Polymerase II Transcription Termination and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and hydrolase activity. 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

Additional gene information for DDX39B Gene

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

Genomics for DDX39B Gene

GeneHancer (GH) Regulatory Elements for DDX39B Gene

Promoters and enhancers for DDX39B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I031538 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 685.9 +1.3 1336 4.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 DDX39B DDX39B-AS1 GC06M031543 GC06M031550 GC06M031555 GC06M031573 GC06M031962 GC06M031965 GC06M031970 PIR32498
GH06I031813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 111.4 -283.4 -283401 25.6 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 C6orf48 HSPA1B HSPA1A HSPA1L GC06P032039 ATF6B DDX39B LY6G5B LSM2 BAG6
GH06I031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 106.6 -195.0 -194980 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 DDX39B LY6G5B ATF6B LSM2 CSNK2B SKIV2L GPANK1 BAG6
GH06I030715 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 107.6 +822.9 822949 7.7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 MDC1 TUBB DDX39B TRIM39 DHX16 LY6G5B PPP1R10 ZNRD1 PAIP1P1 NRM
GH06I031725 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 100.3 -186.1 -186106 5.6 HDGF HNRNPUL1 PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 DDAH2 DDX39B LY6G5B ATF6B LSM2 SKIV2L PBX2 NFKBIL1 CSNK2B MSH5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX39B on UCSC Golden Path with GeneCards custom track

Genomic Locations for DDX39B Gene

Genomic Locations for DDX39B Gene
chr6:31,530,219-31,542,475
(GRCh38/hg38)
Size:
12,257 bases
Orientation:
Minus strand
chr6:31,497,996-31,510,252
(GRCh37/hg19)

Genomic View for DDX39B Gene

Genes around DDX39B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX39B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX39B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

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. Interacts with LUZP4.
    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

Post-translational modifications for DDX39B Gene

  • Ubiquitination at Lys33 and Lys241

No data available for DME Specific Peptides for DDX39B Gene

Domains & Families for DDX39B Gene

Gene Families for DDX39B Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transporters

Graphical View of Domain Structure for InterPro Entry

Q13838

UniProtKB/Swiss-Prot:

DX39B_HUMAN :
  • The helicase C-terminal domain mediates interaction with ALYREF/THOC4.
  • Belongs to the DEAD box helicase family. DECD subfamily.
Domain:
  • The helicase C-terminal domain mediates interaction with ALYREF/THOC4.
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

Phenotypes From GWAS Catalog for DDX39B Gene

Gene Ontology (GO) - Molecular Function for DDX39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IEA 22658674
GO:0004004 ATP-dependent RNA helicase activity TAS,IDA 17562711
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 11979277
genes like me logo Genes that share ontologies with DDX39B: view
genes like me logo Genes that share phenotypes with DDX39B: view

miRNA for DDX39B Gene

miRTarBase miRNAs that target DDX39B

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX39B gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

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 TAS,IDA 21859714
GO:0005654 nucleoplasm TAS --
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

Pathways & Interactions for DDX39B Gene

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

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:0001889 liver development IEA --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with DDX39B: view

No data available for SIGNOR curated interactions for DDX39B Gene

Drugs & Compounds for DDX39B Gene

(4) Drugs for DDX39B Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Isopropyl alcohol Approved, Investigational Pharma Target 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for DDX39B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX39B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DDX39B Gene



Protein tissue co-expression partners for DDX39B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX39B Gene:

DDX39B

SOURCE GeneReport for Unigene cluster for DDX39B Gene:

Hs.254042

Evidence on tissue expression from TISSUES for DDX39B Gene

  • Nervous system(4.7)
  • Kidney(4.5)
  • Liver(4.5)
  • Muscle(4.4)
  • Lung(4.1)
  • Intestine(3.5)
  • Pancreas(3.3)
  • Eye(3.2)
  • Skin(2.9)
genes like me logo Genes that share expression patterns with DDX39B: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia DDX39B 33 34
  • 99.84 (n)
cow
(Bos Taurus)
Mammalia DDX39B 33 34
  • 95.79 (n)
dog
(Canis familiaris)
Mammalia DDX39B 33 34
  • 94.86 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DDX39B 34
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx39b 33 16 34
  • 92.13 (n)
rat
(Rattus norvegicus)
Mammalia Ddx39b 33
  • 91.9 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX39B 34
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX39B 34
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx39b 33
  • 80.53 (n)
MGC75726 33
zebrafish
(Danio rerio)
Actinopterygii ddx39b 34
  • 92 (a)
OneToOne
bat1 33
  • 79.67 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta Hel25E 33 34
  • 75.85 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009075 33
  • 73.04 (n)
worm
(Caenorhabditis elegans)
Secernentea hel-1 34
  • 76 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR260C 33
  • 62.92 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E21935g 33
  • 61.92 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SUB2 33 34 36
  • 61.32 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G11170 33
  • 67.47 (n)
soybean
(Glycine max)
eudicotyledons Gma.2711 33
rice
(Oryza sativa)
Liliopsida Os01g0550000 33
  • 66.9 (n)
Os.14280 33
wheat
(Triticum aestivum)
Liliopsida Ta.2127 33
corn
(Zea mays)
Liliopsida Zm.3715 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10395 34
  • 82 (a)
OneToMany
bread mold
(Neurospora crassa)