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ENSG00000225073 Gene

protein-coding   GIFtS: 16
GCID: GC06Mj31485          (predicted)

ENSG00000225073


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(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
56 KDa U2AF65-Associated Protein3     ATP-Dependent RNA Helicase P473
BAT13     DEAD Box Protein UAP563
EC 3.6.4.133     HLA-B-Associated Transcript 1 Protein3
UAP563     

External Ids:    Ensembl: ENSG000002250737   UniProtKB: Q138383   

Export aliases for ENSG00000225073 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ENSG00000225073 Gene:
ENSG00000225073 is a protein-coding gene.

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




(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for ENSG00000225073
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidENSG00000225073 promoter sequence
   Search Chromatin IP Primers for ENSG00000225073

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ENSG00000225073


Genomic Location:
Chromosome:6   

Ensembl cytogenetic band:  HSCHR6_MHC_COXp21.33   

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06Mj31485:       (about GC identifiers)

Start:
31,485,454 bp from start of contig ALT_REF_LOCI_2      End:
31,501,810 bp from start of contig ALT_REF_LOCI_2
Size:
16,357 bases      Orientation:
minus strand

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, 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 ENSG00000225073:
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 ENSG00000225073: NX_Q13838

Explore proteomics data for ENSG00000225073 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ENSG00000225073 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


    ENSEMBL proteins: 
     ENSP00000431969   ENSP00000404228   ENSP00000400326   ENSP00000390999   ENSP00000393712  
     ENSP00000392644   ENSP00000437017   ENSP00000412286   ENSP00000413832   ENSP00000405489  
     ENSP00000392819   ENSP00000392922   ENSP00000409162   ENSP00000408908   ENSP00000409929  
     ENSP00000391580   ENSP00000402876   ENSP00000403593   ENSP00000450155   ENSP00000449425  

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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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    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


    Find genes that share domains with ENSG00000225073           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding ----
    GO:0004004ATP-dependent RNA helicase activity ----
    GO:0004386helicase activity ----
    GO:0005515protein binding ----
         
    Find genes that share ontologies with ENSG00000225073           About GenesLikeMe


    Animal Models:
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    (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 ----
    GO:0005634nucleus ----
    GO:0005681spliceosomal complex ----
    GO:0005687U4 snRNP ----
    GO:0005688U6 snRNP ----

    Find genes that share ontologies with ENSG00000225073           About GenesLikeMe


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ENSG00000225073
    Interactions:

        Search GeneGlobe Interaction Network for ENSG00000225073

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

    Selected Interacting proteins for ENSG00000225073 (Q138382, 3 ENSP000004003264) via UniProtKB, MINT, STRING, and/or I2D (see all 918)
    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 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly ----
    GO:0000398mRNA splicing, via spliceosome ----
    GO:0006406mRNA export from nucleus ----
    GO:0008380RNA splicing ----
    GO:0010501RNA secondary structure unwinding ----

    Find genes that share ontologies with ENSG00000225073           About GenesLikeMe



    (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)
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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 ENSG00000225073 (DX39B)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 24):
    ENST00000472840 ENST00000464411 ENST00000438578 ENST00000485571(uc011fde.2 uc011fdl.1 uc011fdm.1 uc011fdn.1)
    ENST00000456476(uc011fdi.2) ENST00000415689(uc011fdh.2 uc011fdg.2)
    ENST00000412106(uc011fdj.2 uc011fdp.1) ENST00000422243 ENST00000494127
    ENST00000467694 ENST00000427425 ENST00000482077(uc011fdk.1) ENST00000438449
    ENST00000455645 ENST00000420958 ENST00000451051 ENST00000442717 ENST00000439691

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    GeneLoc Exon Structure


    (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)
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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    ENSG00000225073 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ENSG00000225073 Protein Expression
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    (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)
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      --

    ENSEMBL Gene Tree for ENSG00000225073 (if available)
    TreeFam Gene Tree for ENSG00000225073 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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)
    About This Section

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    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing ENSG00000225073
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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)
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    PubMed articles for ENSG00000225073 gene, integrated from 10 sources (see all 31):
    (articles sorted by number of sources associating them with ENSG00000225073)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Aly and THO are required for assembly of the human TREX complex and association of TREX components with the spliced mRNA. (PubMed id 23222130)2 Chi B....Cheng H. (Nucleic Acids Res. 2013)
    2. Chtop is a component of the dynamic TREX mRNA export complex. (PubMed id 23299939)2 Chang C.T....Wilson S.A. (EMBO J. 2013)
    3. The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export. (PubMed id 22928037)2 Folco E.G.... Reed R. (PLoS ONE 2012)
    4. Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-I+-acetylation features. (PubMed id 22223895)2 Bienvenut W.V....Giglione C. (amp 2012)
    5. Genome instability and transcription elongation impairment in human cells depleted of THO/TREX. (PubMed id 22144908)2 DomA-nguez-SA!nchez M.S....Aguilera A. (PLoS Genet. 2011)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    7. Interferon-induced antiviral protein MxA interacts with the cellular RNA helicases UAP56 and URH49. (PubMed id 21859714)2 Wisskirchen C....Pavlovic J. (J. Biol. Chem. 2011)
    8. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. (PubMed id 20844015)2 Dufu K....Reed R. (amp 2010)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    10. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (Anal. Chem. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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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    Ensembl:ENSG00000225073

    (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)
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    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ENSG00000225073 gene:
    Search GeneIP for patents involving ENSG00000225073

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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