Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), transcript variant 2, mRNA. RefSeq Summary (NM_080598): 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]. Transcript (Including UTRs) Position: hg19 chr6:31,497,996-31,510,252 Size: 12,257 Total Exon Count: 11 Strand: - Coding Region Position: hg19 chr6:31,498,211-31,508,309 Size: 10,099 Coding Exon Count: 10
ID:DX39B_HUMAN DESCRIPTION: RecName: Full=Spliceosome RNA helicase DDX39B; EC=3.6.4.13; AltName: Full=56 kDa U2AF65-associated protein; AltName: Full=ATP-dependent RNA helicase p47; AltName: Full=DEAD box protein UAP56; AltName: Full=HLA-B-associated transcript 1 protein; FUNCTION: Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It 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. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4. 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 and ALYREF/THOC4. 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; SUBUNIT: Homodimer, and heterodimer with DDX39A. Component of the THO complex, which is composed of THOC1, THOC2, THOC5, THOC6 and THOC7. Together with THOC3, ALYREF/THOC4 and DDX39B, THO forms the transcription/export (TREX) complex. Component of the spliceosome. Interacts directly with U2AF2. Interacts directly with ALYREF/THOC4 and is necessARy for ALYREF/THOC4 recruitment to spliced mRNA. Interacts with RBM8A, RNPS1 and SRRM1. Interacts with FYTTD1/UIF and THOC1. Interacts with human cytomegalovirus/HHV-5 protein UL69. SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. 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. SEQUENCE CAUTION: Sequence=CAI17665.2; Type=Erroneous gene model prediction;
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q13838
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
BC004350 - Homo sapiens cDNA clone IMAGE:3536103. AK222912 - Homo sapiens mRNA for HLA-B associated transcript 1 variant, clone: HRC02604. BC013006 - Homo sapiens HLA-B associated transcript 1, mRNA (cDNA clone MGC:3991 IMAGE:3010263), complete cds. Z37166 - H.sapiens BAT1 mRNA for nuclear RNA helicase (DEAD family). BC000361 - Homo sapiens HLA-B associated transcript 1, mRNA (cDNA clone MGC:8674 IMAGE:2964517), complete cds. AK298194 - Homo sapiens cDNA FLJ53073 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-). AB209217 - Homo sapiens mRNA for HLA-B associated transcript 1 variant protein. JD381427 - Sequence 362451 from Patent EP1572962. JD454504 - Sequence 435528 from Patent EP1572962. JD276483 - Sequence 257507 from Patent EP1572962. JD124427 - Sequence 105451 from Patent EP1572962. JD339533 - Sequence 320557 from Patent EP1572962. JD469887 - Sequence 450911 from Patent EP1572962. JD495458 - Sequence 476482 from Patent EP1572962. JD043342 - Sequence 24366 from Patent EP1572962. BT009909 - Homo sapiens HLA-B associated transcript 1 mRNA, complete cds. DQ891881 - Synthetic construct clone IMAGE:100004511; FLH180891.01X; RZPDo839H02134D HLA-B associated transcript 1 (BAT1) gene, encodes complete protein. KJ897793 - Synthetic construct Homo sapiens clone ccsbBroadEn_07187 hypothetical protein, encodes complete protein. DQ895067 - Synthetic construct Homo sapiens clone IMAGE:100009527; FLH180887.01L; RZPDo839H02133D HLA-B associated transcript 1 (BAT1) gene, encodes complete protein. AB528305 - Synthetic construct DNA, clone: pF1KE1035, Homo sapiens BAT1 gene for HLA-B associated transcript 1, without stop codon, in Flexi system. AK127767 - Homo sapiens cDNA FLJ45868 fis, clone OCBBF3004487, highly similar to Probable ATP-dependent RNA helicase p47. DQ581701 - Homo sapiens piRNA piR-49813, complete sequence. AK295854 - Homo sapiens cDNA FLJ54084 complete cds, moderately similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-). AK316469 - Homo sapiens cDNA, FLJ79368 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-). AK295634 - Homo sapiens cDNA FLJ54033 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-). AK294939 - Homo sapiens cDNA FLJ53763 complete cds, highly similar to Spliceosome RNA helicase BAT1 (EC 3.6.1.-). JD469310 - Sequence 450334 from Patent EP1572962. JD211352 - Sequence 192376 from Patent EP1572962. JD538060 - Sequence 519084 from Patent EP1572962. DQ598822 - Homo sapiens piRNA piR-36888, complete sequence.
Biochemical and Signaling Pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes hsa03040 - Spliceosome
Reactome (by CSHL, EBI, and GO)
Protein Q13838 (Reactome details) participates in the following event(s):
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B) R-HSA-72185 mRNA polyadenylation R-HSA-72180 Cleavage of mRNA at the 3'-end R-HSA-72187 mRNA 3'-end processing R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-72202 Transport of Mature Transcript to Cytoplasm R-HSA-8953854 Metabolism of RNA R-HSA-109688 Cleavage of Growing Transcript in the Termination Region R-HSA-73856 RNA Polymerase II Transcription Termination R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription)
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
