Spliceosome RNA helicase DDX39B (DDX39B)
The protein contains 428 amino acids for an estimated molecular weight of 48991 Da.
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. 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 acti (updated: April 7, 2021)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
(right-click above to access to more options from the contextual menu)
Biological Process
Liver development
MRNA 3'-end processing
MRNA export from nucleus
MRNA splicing, via spliceosome
Negative regulation of DNA damage checkpoint
Positive regulation of cell growth involved in cardiac muscle cell development
Positive regulation of DNA biosynthetic process
Positive regulation of DNA-templated transcription, elongation
Positive regulation of translation
Positive regulation of vascular associated smooth muscle cell proliferation
RNA export from nucleus
RNA secondary structure unwinding
RNA splicing
Spliceosomal complex assembly
Viral mRNA export from host cell nucleus
The reference OMIM entry for this protein is 142560
Dead box polypeptide 39b; ddx39b
Hla-b-associated transcript 1; bat1
U2af65-associated protein, 56-kd; uap56
D6s81e
DESCRIPTION
UAP56 (BAT1) is an essential splicing factor that is recruited to the pre-mRNA dependent on U2AF65 (191318) and is required for the U2 snRNP-branchpoint interaction. UAP56 is a member of the DEAD box family of RNA-dependent ATPases, which mediate ATP hydrolysis during several steps of pre-mRNA splicing (Fleckner et al., 1997).CLONING
By chromosome walking with overlapping cosmids, Spies et al. (1989) isolated a 435-kb DNA segment that was centromeric to HLA-B (142830) in the human major histocompatibility complex. The presence of additional genes was suggested by a large cluster of CpG islands. With cosmid probes, 5 distinct transcripts were detected in RNA samples from a variety of cell lines, and the corresponding cDNA clones were isolated and designated 'HLA-B-associated transcripts' (BAT1 through BAT5, 142620). Peelman et al. (1995) sequenced both human and pig BAT1 and showed that the genes are members of the DEAD-box family of ATP-dependent RNA helicases, which are involved in a number of cellular functions including initiation of translation, RNA splicing, and ribosome assembly. Proteins of this family have 9 conserved amino acid motifs but differ at their amino and carboxyl ends. From studies of other family members, the first block is involved in ATP binding, the fifth block may be an ATPase, the sixth block is needed for RNA helicase activity, and the ninth block is involved with ATP hydrolysis-independent RNA interactions during unwinding. The gene contains 10 exons spanning about 10 kb of genomic DNA and encodes a 428-amino acid protein. Peelman et al. (1995) detected 3 different length mRNAs (4.1, 17, and 0.9 kb) in all tissues analyzed, although at different relative levels. The protein is highly conserved, with 98% identity to the p47 rat liver nuclear protein and 99% identity to the pig BAT1 homolog. Peelman et al. (1995) showed that a recombinant epitope-tagged BAT1 construct was expressed in COS cells and showed localization of the protein to the nucleus. Fleckner et al. (1997) cloned a human 56-kD U2AF65-associated protein that they termed UAP56. Using a yeast 2-hybrid assay, Fleckner et al. (1997) identified UAP56 as the splicing factor that interacts with U2AF65 amino acids 138 to 183. UAP56 encodes a protein of 428 amino acids containing the 7 consensus motifs characteristic of DEAD box RNA helicases.GENE FUNCTION
Spies et al. (1989) raised the question of whether variation at one of the BAT genes, rather than at HLA-B itself, determines susceptibility to ankylosing spondylitis (106300). Allcock et al. (2001) used antisense DNA corresponding to exons 2 through 5 of the BAT1 gene and showed that after antigenic stimulation, monocytic and T-cell lines produced higher levels of the acute phase cytokines TNF, interleukin-1 (IL1; see 147760), and IL6 (147620) than cells containing the transfecting vector alone. These results suggested that BAT1 is a negative regulator of inflammation. Fleckner et al. (1997) demonstrated that UAP56 is an essential splicing factor that is required for U2 snRNP-branchpoint interaction. It is a component of the spliceosome. Luo et al. (2001) demonstrated that UAP56 interacts directly and highly specifically with ALY (THOC4; 604171). Moreover, UAP56 is present together with ALY in a spliced mRNA-protein complex (mRNP). Excess UAP56 is a potent dominant-negative inhibitor of mRNA export. Excess UAP56 also inhibits the recruitment of ALY to the sp ... More on the omim web site
April 10, 2021: Protein entry updated
Automatic update: Entry updated from uniprot information.
May 12, 2019: Protein entry updated
Automatic update: OMIM entry 142560 was added.
Feb. 23, 2019: Protein entry updated
Automatic update: comparative model was added.
Feb. 23, 2019: Protein entry updated
Automatic update: model status changed
Oct. 19, 2018: Additional information
Initial protein addition to the database. This entry was referenced in Bryk and co-workers. (2017).