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DDX39B Gene

protein-coding   GIFtS: 57
GCID: GC06M031522

DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39B

(Previous name: HLA-B associated transcript 1)
(Previous symbol: BAT1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 39B1 2     HLA-B Associated Transcript 11
BAT11 2 3 5     U2AF65-Associated Protein 561
56 KDa U2AF65-Associated Protein2 3     Nuclear RNA Helicase (DEAD Family)2
UAP562 3     Spliceosome RNA Helicase BAT12
ATP-Dependent RNA Helicase P472 3     Spliceosome RNA Helicase DDX39B2
HLA-B-Associated Transcript 1 Protein2 3     EC 3.6.4.133
D6S81E2 5     DEAD Box Protein UAP563

External Ids:    HGNC: 139171   Entrez Gene: 79192   Ensembl: ENSG000001985637   OMIM: 1425605   UniProtKB: Q138383   

Export aliases for DDX39B gene to outside databases

Previous GC identifer: GC06M031500


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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, and chronic venous leg ulcers. GO annotations related to this gene include U6 snRNA binding and ATP-dependent RNA helicase activity. An important paralog of this gene is DDX20.

UniProtKB/Swiss-Prot: DX39B_HUMAN, Q13838
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 Kaposi's 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
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

Gene Wiki entry for DDX39B (BAT1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NC_018917.2  NT_007592.16  NT_113891.3  NT_167244.2  NT_167245.2  NT_167246.2  NT_167247.2  
NT_167248.2  NT_167249.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for DDX39B
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDDX39B promoter sequence
   Search Chromatin IP Primers for DDX39B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DDX39B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.33

DDX39B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX39B gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M031522:  view genomic region     (about GC identifiers)

Start:
31,497,996 bp from pter      End:
31,510,252 bp from pter
Size:
12,257 bases      Orientation:
minus strand

Selected alternative locations (see all 7):
Chr6-,NT_167247 2,877,747-2,889,999      Chr6-,NT_167244 2,812,684-2,821,649      Chr6-,NT_167248 2,791,677-2,803,927     
Chr6-,NT_113891.2 3,007,658-3,019,911      Chr6-,NT_167249 2,828,801-2,841,057      Chr6-,NT_167245 2,783,577-2,795,830     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for DDX39B

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DX39B_HUMAN, Q13838 (See protein sequence)
Recommended Name: Spliceosome RNA helicase DDX39B  
Size: 428 amino acids; 48991 Da
Subunit: 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
Sequence caution: Sequence=CAI17665.2; Type=Erroneous gene model prediction;
5 PDB 3D structures from and Proteopedia for DDX39B:
1T5I (3D)        1T6N (3D)        1XTI (3D)        1XTJ (3D)        1XTK (3D)    
Secondary accessions: B0S8C0 O43496 Q0EFA1 Q2L6F9 Q53GL9 Q5RJ64 Q5RJ66 Q5ST94 Q5STB4 Q5STB5
Q5STB7 Q5STB8 Q5STU4 Q5STU5 Q5STU6 Q5STU8 Q71V76
Alternative splicing: 2 isoforms:  Q13838-1   Q13838-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for DDX39B: NX_Q13838

Explore proteomics data for DDX39B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys33, Lys36, Lys53, Lys90, Lys131, Lys241, Lys268, Lys334, Lys384
  • Modification sites at PhosphoSitePlus

  • See DDX39B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_004631.1  NP_542165.1  

    ENSEMBL proteins: 
     ENSP00000436220   ENSP00000365347   ENSP00000416269   ENSP00000379475   ENSP00000406422  
     ENSP00000408000   ENSP00000399371   ENSP00000392672   ENSP00000410313   ENSP00000416350  
     ENSP00000405707   ENSP00000409426   ENSP00000393984   ENSP00000399841   ENSP00000405245  
     ENSP00000412582   ENSP00000392669   ENSP00000400328   ENSP00000391946  

    DDX39B Human Recombinant Protein Products:

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    Novus Biologicals DDX39B Proteins
    Novus Biologicals DDX39B Lysates
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    Browse Sino Biological Cell Lysates
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    Browse Proteins at Cloud-Clone Corp.

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    Browse ELISAs at Cloud-Clone Corp.
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    DDX: DEAD-boxes

    5 InterPro protein domains:
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR027417 P-loop_NTPase
     IPR014014 RNA_helicase_DEAD_Q_motif
     IPR014001 Helicase_ATP-bd
     IPR001650 Helicase_C

    Graphical View of Domain Structure for InterPro Entry Q13838

    ProtoNet protein and cluster: Q13838

    UniProtKB/Swiss-Prot: DX39B_HUMAN, Q13838
    Domain: The helicase C-terminal domain mediates interaction with ALYREF/THOC4
    Similarity: Belongs to the DEAD box helicase family. DECD subfamily
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    DDX39B for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DX39B_HUMAN, Q13838
    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 Kaposi's 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
    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
    Catalytic activity: ATP + H(2)O = ADP + phosphate
    Biophysicochemical properties: Kinetic parameters: KM=3.3 uM for ATP; Vmax=0.126 uM/min/mg enzyme with ATP as
    substrate;

         Enzyme Number (IUBMB): EC 3.6.4.131

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding ----
    GO:0004004ATP-dependent RNA helicase activity IDA17562711
    GO:0004386helicase activity ----
    GO:0005515protein binding IPI15047853
         
    DDX39B for ontologies           About GeneDecksing


    Phenotypes:
         4 GenomeRNAi human phenotypes for DDX39B:
     G0/1 arrest  Increased G1 DNA content  Synthetic lethal with Ras  Synthetic lethal with cisplati 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DDX39B
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for DDX39B

    miRNA
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    miRTarBase miRNAs that target DDX39B:
    hsa-mir-93-5p (MIRT028060)

    Block miRNA regulation of human, mouse, rat DDX39B using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate DDX39B:
    hsa-miR-142-3p hsa-miR-205 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-323-5p hsa-miR-3129-5p hsa-miR-876-3p hsa-miR-412
    SwitchGear 3'UTR luciferase reporter plasmidDDX39B 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat DDX39B

    Gene Editing
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    Sino Biological Human cDNA Clone for DDX39B
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX39B

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX39B


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DX39B_HUMAN, Q13838: 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): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000346transcription export complex IDA15833825
    GO:0005634nucleus IDA--
    GO:0005681spliceosomal complex IDA18593880
    GO:0005687colocalizes with U4 snRNP IDA18593880
    GO:0005688colocalizes with U6 snRNP IDA18593880

    DDX39B for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for DDX39B About    
    See pathways by source

    SuperPathContained pathways About
    1Influenza A
    Influenza A0.34
    2Spliceosome
    Spliceosome
    3RNA transport
    RNA transport
    4mRNA surveillance pathway
    mRNA surveillance pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    4 Kegg Pathways  (Kegg details for DDX39B):
        RNA transport
    mRNA surveillance pathway
    Spliceosome
    Influenza A


    DDX39B for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DDX39B
    Interactions:

        Search GeneGlobe Interaction Network for DDX39B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for DDX39B (Q138382, 3 ENSP000003794754) via UniProtKB, MINT, STRING, and/or I2D (see all 879)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDX39AO001482, 3, ENSP000002427764MINT-62737 MINT-7945693 MINT-62639 MINT-62813 MINT-7947479 I2D: score=4 STRING: ENSP00000242776
    HNRNPLLQ8WVV92, 3, ENSP000003870884MINT-62644 MINT-62818 MINT-62742 I2D: score=4 STRING: ENSP00000387088
    RPS15AP622442, 3, ENSP000003186464MINT-62817 MINT-62741 MINT-62643 I2D: score=4 STRING: ENSP00000318646
    DNAJC14Q6Y2X32, 3MINT-62641 MINT-62739 MINT-62815 I2D: score=2 
    DDX19AQ9NUU72, 3, ENSP000003061174MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000306117
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly IDA18593880
    GO:0000398mRNA splicing, via spliceosome IGI15047853
    GO:0006200ATP catabolic process TAS7601445
    GO:0006406mRNA export from nucleus IGI15047853
    GO:0008380RNA splicing IDA18593880

    DDX39B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
    About This Section

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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for DDX39B (DX39B)

    1 DrugBank Compound for DDX39B    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Adenosine-5'-Diphosphate-- 20398-34-9target--17139284 17016423 10592235

    1 Novoseek inferred chemical compound relationship for DDX39B gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    atp 24 15 18411249 (4), 17984224 (3), 17562711 (3), 20116367 (1) (see all 5)



    DDX39B for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for DDX39B gene (2 alternative transcripts): 
    NM_004640.6  NM_080598.5  

    Unigene Cluster for DDX39B:

    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
    Hs.254042  [show with all ESTs]
    Unigene Representative Sequence: NR_037853
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 25):
    ENST00000474961 ENST00000484566 ENST00000376177 ENST00000462256(uc003ntr.3 uc003ntx.2 uc011dnp.1)
    ENST00000458640(uc003ntu.3) ENST00000396172(uc003ntt.3 uc011dnn.2)
    ENST00000462421 ENST00000417023 ENST00000478365 ENST00000482195 ENST00000431908
    ENST00000481456(uc003ntw.2 uc011dno.1) ENST00000427214 ENST00000428098
    ENST00000419338 ENST00000456662 ENST00000428450 ENST00000449757
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    Primer
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    Additional mRNA sequence: 

    AK222912.1 AK295634.1 AK295854.1 AK298194.1 AK316469.1 BC000361.2 BC013006.2 BT009909.1 
    NR_037852.1 NR_037853.1 Z37166.1 

    Selected DOTS entries (see all 72):

    DT.97777677  DT.100878283  DT.100878272  DT.100878254  DT.102841810  DT.452348  DT.91965128  DT.100878266 
    DT.95274923  DT.100728870  DT.121310725  DT.312157  DT.121310196  DT.95274904  DT.121310204  DT.100878269 
    DT.100878279  DT.100878253  DT.85104878  DT.100878262  DT.100878268  DT.100878271  DT.121310070  DT.121310049 

    Selected AceView cDNA sequences (see all 157):

    CR590279 BC000361 CR614717 CR606599 NM_138282 BC004350 F15253 BX445405 
    CR620111 BT009909 CR612427 CR612476 NM_004640 CR618145 BC013006 NM_080598 
    C20601 CR596330 CR600093 AA230211 BC047791 AJ243199 CR601722 NM_130463 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DDX39B (see all 26)    About this scheme

    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:                                                                                                                    -     -     -     -     -     -     -   

    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:                                                  -                                                                                             


    ECgene alternative splicing isoforms for DDX39B

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    DDX39B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    DDX39B Expression
    About this image


    DDX39B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Ovary (Reproductive System)
             Primary Oocyte Primary Follicle
     
     Bone (Muscoskeletal System)
             Mandibular Condyle
     
     Gonad
             Primary Oocyte Primary Follicle
    DDX39B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DDX39B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.254042
        Custom PCR Arrays for DDX39B
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    OriGene qPCR primer pairs and template standards for DDX39B
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX39B

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for DDX39B gene from Selected species (see all 26)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ddx39b1 , 5 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B1, 5 92.13(n)1
    99.53(a)1
      17 (18.60 cM)5
    538171  NM_001252457.11  NP_001239386.11 
     352417465 
    lizard
    (Anolis carolinensis)
    Reptilia DDX39B6
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B
    97(a)
    1 ↔ 1
    2(194066457-194077229)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia MGC757262 hypothetical protein MGC75726 80.36(n)    BC061280.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC055240.12   -- 79.35(n)   393917  BC055240.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Hel25E1 Helicase at 25E 75.85(n)
    85.51(a)
      33781  NM_164646.3  NP_723089.1 
    worm
    (Caenorhabditis elegans)
    Secernentea hel-16
    Protein HEL-1, isoform a (hel-1) mRNA, complete cd...
    76(a)
    1 → many
    II(8326849-8328870) WBGene00001840
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SUB2(YDL084W)4
    SUB21
    Component of the TREX complex required for nuclear more4
    SUB21
    61.32(n)1
    66.03(a)1
      4(305237-306577)4
    8514751, 4  NP_010199.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G111701 AT5G11170 67.47(n)
    72.77(a)
      830986  NM_121155.3  NP_568244.2 
    rice
    (Oryza sativa)
    Liliopsida Os.142802 Oryza sativa (japonica cultivar-group) cDNA clone0 more 72.66(n)    AK122050.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DDX39B gene
    DDX202  DDX39A2  
    Selected SIMAP similar genes for DDX39B using alignment to 19 protein entries:     DX39B_HUMAN (see all proteins) (see all similar genes):
    DKFZp547B159    BAT1    DDX39    DDX39A    EIF4A2    DDX56
    DDX47    DDX54    EIF4A3    DDX27    E4-DBP    DDX19B
    EIF4A1    DDX23    DDX20    DDX46    DDX5    DDX19A

    DDX39B for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for DDX39B
    PGOHUM00000242507


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    1 SNPs for DDX39B    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1400325091,2
    C--31298997(+) ATAATC/TATTTT 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for DDX39B (31497996 - 31510252 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for DDX39B:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1042e201CNV Deletion23290073
    nsv830627CNV Loss17160897
    nsv470809CNV Loss18288195
    dgv6580n71CNV Gain21882294
    dgv213e55CNV Gain17911159
    esv690CNV CNV17122850
    essv13266CNV CNV17122850

    Human Gene Mutation Database (HGMD): DDX39B
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DDX39B
    DNA2.0 Custom Variant and Variant Library Synthesis for DDX39B

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 142560    OMIM disorders: --

    Selected diseases for DDX39B (see all 30):    
    About MalaCards
    rheumatoid arthritis    chronic venous leg ulcers    toxic epidermal necrolysis    stevens-johnson syndrome
    arthritis    autoimmune hepatitis    leprosy    lupus erythematosus
    fanconi's anemia    dilated cardiomyopathy    atopic dermatitis    kaposi's sarcoma
    dermatitis    influenza    neuropathy    type 1 diabetes
    myocardial infarction    hepatitis    hepatitis c virus    systemic lupus erythematosus


    DDX39B for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for DDX39B gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    autoimmune diseases 30.5 1 1352699 (1)
    rheumatoid arthritis 18.3 3 18381799 (2), 1672123 (1)
    necrosis 17.6 5 8081366 (1), 18381799 (1), 7601445 (1)
    lupus erythematosus systemic 7.01 2 1672123 (1), 16971954 (1)
    tumors 0 4 18381799 (1), 7601445 (1)


    Export disorders for DDX39B gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

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    PubMed articles for DDX39B gene, integrated from 10 sources (see all 141):
    (articles sorted by number of sources associating them with DDX39B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family. (PubMed id 7601445)1, 2, 3, 9 Peelman L.... Spies T. (Genomics 1995)
    2. Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. (PubMed id 15296731)1, 2, 9 Zhao R.... Blumenthal T. (Structure 2004)
    3. Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor. (PubMed id 17562711)1, 2, 9 Shen J.... Zhao R. (J. Biol. Chem. 2007)
    4. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. (PubMed id 11675789)1, 2, 9 Luo M.-J.... Reed R. (Nature 2001)
    5. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. (PubMed id 9242493)1, 2, 9 Fleckner J.... Green M.R. (Genes Dev. 1997)
    6. UIF, a new mRNA export adaptor that works together with REF/ALY, requires FACT for recruitment to mRNA. (PubMed id 19836239)1, 2, 9 Hautbergue G.M.... Wilson S.A. (Curr. Biol. 2009)
    7. Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication. (PubMed id 18974867)1, 2, 9 Boyne J.R.... Whitehouse A. (PLoS Pathog. 2008)
    8. The UL69 transactivator protein of human cytomegalovirus interacts with DEXD/H-Box RNA helicase UAP56 to promote cytoplasmic accumulation of unspliced RNA. (PubMed id 16478985)1, 2, 9 Lischka P.... Stamminger T. (Mol. Cell. Biol. 2006)
    9. Crystal structure of the human ATP-dependent splicing and export factor UAP56. (PubMed id 15585580)1, 2, 9 Shi H.... Xu R.-M. (Proc. Natl. Acad. Sci. U.S.A. 2004)
    10. Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49. (PubMed id 21859714)1, 2 Wisskirchen C....Pavlovic J. (J. Biol. Chem. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7919 HGNC: 13917 AceView: BAT1andATP6V1G2 Ensembl:ENSG00000198563 euGenes: HUgn7919
    ECgene: DDX39B Kegg: 7919 H-InvDB: DDX39B

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for DDX39B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for DDX39B gene:
    Search GeneIP for patents involving DDX39B

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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