Q13838
PR
Gene name |
DDX39B |
Protein name |
Spliceosome RNA helicase DDX39B |
Names |
56 kDa U2AF65-associated protein, ATP-dependent RNA helicase p47, DEAD box protein UAP56, HLA-B-associated transcript 1 protein |
Species |
Homo sapiens (Human) |
KEGG Pathway |
hsa:7919 |
EC number |
3.6.4.13: Acting on ATP; involved in cellular and subcellular movement |
Protein Class |
|
Descriptions
The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.
Autoinhibitory domains (AIDs)
Target domain |
|
Relief mechanism |
|
Assay |
cis-regPred |
Accessory elements
No accessory elements
Autoinhibited structure
Activated structure
10 structures for Q13838
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 1T5I | X-ray | 190 A | A | 259-428 | PDB |
| 1T6N | X-ray | 194 A | A/B | 34-251 | PDB |
| 1XTI | X-ray | 195 A | A | 46-428 | PDB |
| 1XTJ | X-ray | 270 A | A | 44-423 | PDB |
| 1XTK | X-ray | 240 A | A | 45-428 | PDB |
| 7APK | EM | 330 A | H/P/h/p | 1-428 | PDB |
| 7ZNK | EM | 390 A | H/P/h/p | 1-428 | PDB |
| 7ZNL | EM | 345 A | H/P/h/p | 1-428 | PDB |
| 8ENK | X-ray | 250 A | A/B | 44-428 | PDB |
| AF-Q13838-F1 | Predicted | AlphaFoldDB |
109 variants for Q13838
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
|
CA363303968 rs1379005393 |
2 | A>T | No |
gnomAD ClinGen |
|
|
CA136875402 rs371622727 |
3 | E>D | No |
ESP TOPMed gnomAD ClinGen |
|
|
rs1390209603 CA363303916 |
8 | N>S | No |
gnomAD ClinGen |
|
| TCGA novel | 9 | E>D | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA136875398 rs12178599 |
13 | Y>N | No |
ClinGen Ensembl |
|
|
CA3713313 rs771879483 |
14 | E>D | No |
ExAC gnomAD ClinGen |
|
| TCGA novel | 16 | D>A | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs1463442829 CA363303845 |
16 | D>E | No |
gnomAD ClinGen |
|
|
rs747849603 CA3713312 |
18 | V>M | No |
ExAC ClinGen |
|
|
CA3713310 rs754842685 |
22 | A>G | No |
ExAC TOPMed gnomAD ClinGen |
|
|
CA3713311 rs778941682 |
22 | A>P | No |
ExAC gnomAD ClinGen |
|
|
rs989941493 CA136875385 |
24 | G>A | No |
TOPMed ClinGen |
|
|
rs989941493 CA363303779 |
24 | G>E | No |
TOPMed ClinGen |
|
| TCGA novel | 25 | D>H | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 26 | G>E | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA136875378 rs760564961 |
27 | A>S | No |
ClinGen Ensembl |
|
|
rs757540967 CA3713307 |
27 | A>V | No |
ClinGen ExAC gnomAD |
|
|
CA3713306 rs375215990 |
31 | A>G | No |
ESP ExAC TOPMed gnomAD ClinGen |
|
|
CA136875373 rs375215990 |
31 | A>V | No |
ClinGen ESP ExAC TOPMed gnomAD |
|
| TCGA novel | 32 | K>R | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA363303707 rs1461003672 |
33 | K>E | No |
gnomAD ClinGen |
|
|
CA363303699 rs1231892701 |
34 | D>H | No |
TOPMed ClinGen |
|
|
rs764412505 CA3713305 |
43 | H>Y | No |
ExAC gnomAD ClinGen |
|
|
CA363303606 rs1277612570 |
44 | S>T | No |
TOPMed ClinGen |
|
|
rs752959659 CA3713303 |
48 | R>C | No |
ExAC TOPMed gnomAD ClinGen |
|
|
rs1302662028 CA363303552 |
50 | F>L | No |
gnomAD ClinGen |
|
|
rs776349707 CA3713300 |
58 | R>W | No |
ExAC gnomAD ClinGen |
|
|
CA3713299 rs770536861 |
59 | A>G | No |
ExAC gnomAD ClinGen |
|
|
CA363303475 rs1188222078 |
60 | I>V | No |
gnomAD ClinGen |
|
| TCGA novel | 62 | D>Y | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 64 | G>V | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs1413964269 CA363303242 |
89 | A>T | No |
gnomAD ClinGen |
|
|
rs766929998 CA3713256 |
110 | V>L | No |
ExAC gnomAD ClinGen |
|
|
CA363303087 rs1449996789 |
112 | G>A | No |
TOPMed gnomAD ClinGen |
|
|
CA363303088 rs1449996789 |
112 | G>E | No |
TOPMed gnomAD ClinGen |
|
|
rs1297610972 CA363302843 |
119 | M>V | No |
gnomAD ClinGen |
|
|
CA3713194 rs756160298 |
122 | T>I | No |
ExAC gnomAD ClinGen |
|
|
rs763152729 CA3713191 |
135 | R>H | No |
ExAC ClinGen |
|
|
CA363302686 rs1433553103 |
140 | M>I | No |
TOPMed ClinGen |
|
|
CA136874645 rs933102807 |
140 | M>T | No |
TOPMed ClinGen |
|
|
CA3713190 rs775570418 |
140 | M>V | No |
ExAC gnomAD ClinGen |
|
|
CA363302673 rs1297460988 |
142 | N>S | No |
TOPMed ClinGen |
|
|
rs754655043 CA3713179 |
145 | V>G | No |
ExAC gnomAD ClinGen |
|
|
CA3713178 rs748938626 |
146 | A>G | No |
ExAC gnomAD ClinGen |
|
|
rs1428928229 CA363302628 |
147 | V>G | No |
TOPMed ClinGen |
|
|
CA3713177 rs75750725 |
150 | G>C | No |
ClinGen ExAC |
|
|
rs1157967310 CA363302607 |
150 | G>V | No |
gnomAD ClinGen |
|
| rs777891843 | 150 | G>W | Variant assessed as Somatic; 0.0001048 impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs1433238480 CA363302603 |
151 | G>V | No |
gnomAD ClinGen |
|
|
CA363302583 rs1191236674 |
154 | I>M | No |
gnomAD ClinGen |
|
|
rs755993810 CA3713175 |
159 | E>D | No |
ExAC gnomAD ClinGen |
|
|
rs1248579937 CA363302543 |
160 | V>M | No |
ClinGen gnomAD |
|
|
CA3713174 rs373225565 |
163 | K>N | No |
ESP ExAC gnomAD ClinGen |
|
| rs758489522 | 163 | K>missing | Variant assessed as Somatic; 0.0 impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA3713172 rs757158055 |
166 | P>L | Variant assessed as Somatic; 4.626e-05 impact. [NCI-TCGA] | No |
ExAC gnomAD ClinGen NCI-TCGA |
|
CA3713171 rs757158055 |
166 | P>R | No |
ExAC gnomAD ClinGen |
|
|
CA363302499 rs1260344667 |
166 | P>S | No |
gnomAD ClinGen |
|
|
CA363302434 rs759729035 |
176 | I>M | No |
ExAC TOPMed gnomAD ClinGen |
|
| TCGA novel | 178 | A>* | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 181 | R>* | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA363302397 rs1241135162 |
183 | K>E | No |
TOPMed ClinGen |
|
|
rs1303812682 CA363302371 |
186 | N>S | No |
gnomAD ClinGen |
|
|
CA136873509 rs1007941500 |
188 | K>I | No |
TOPMed ClinGen |
|
|
CA3713166 rs766550277 |
189 | H>L | No |
ExAC gnomAD ClinGen |
|
|
CA363302347 rs1376897344 |
190 | I>V | No |
gnomAD ClinGen |
|
|
rs1171131572 CA363302270 |
200 | K>E | No |
gnomAD ClinGen |
|
| TCGA novel | 200 | K>T | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 205 | L>= | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA3713128 rs746746089 |
207 | M>I | No |
ExAC gnomAD ClinGen |
|
| TCGA novel | 208 | R>C | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs267600954 CA136872889 |
216 | R>C | Variant assessed as Somatic; 0.0 impact. [NCI-TCGA] | No |
gnomAD ClinGen NCI-TCGA |
|
CA3713126 rs758214637 |
219 | P>L | No |
ExAC gnomAD ClinGen |
|
|
rs1157085249 CA363301969 |
240 | R>C | No |
gnomAD ClinGen |
|
|
rs768637863 CA3713058 |
252 | D>H | No |
ExAC TOPMed gnomAD ClinGen |
|
| TCGA novel | 266 | Y>C | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA363301761 rs1562406919 |
267 | V>M | No |
ClinGen Ensembl |
|
|
CA363301722 rs1165387206 |
272 | N>S | No |
TOPMed ClinGen |
|
|
CA3713053 rs777865377 |
273 | E>Q | No |
ExAC ClinGen |
|
|
CA363301610 rs745700709 COSM372287 |
288 | N>I | lung [Cosmic] | No |
ExAC TOPMed gnomAD ClinGen cosmic curated |
|
rs745700709 CA3713050 |
288 | N>S | Variant assessed as Somatic; 4.622e-05 impact. [NCI-TCGA] | No |
ExAC TOPMed gnomAD ClinGen NCI-TCGA |
|
rs745700709 CA3713051 |
288 | N>T | No |
ExAC TOPMed gnomAD ClinGen |
|
|
CA363301572 rs1439556909 |
292 | I>V | No |
gnomAD ClinGen |
|
|
CA363301510 rs1350950718 |
301 | I>V | No |
gnomAD ClinGen |
|
|
rs1261913596 CA363301479 |
305 | Q>H | No |
gnomAD ClinGen |
|
| TCGA novel | 319 | R>H | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 325 | E>D | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs777307555 CA3713004 |
329 | R>Q | No |
ExAC gnomAD ClinGen |
|
|
CA3713005 rs746480137 |
329 | R>W | No |
ClinGen ExAC gnomAD |
|
| TCGA novel | 342 | V>A | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs754920476 CA3713000 |
344 | T>N | No |
ExAC gnomAD ClinGen |
|
|
CA363301204 rs1316566294 |
344 | T>S | No |
gnomAD ClinGen |
|
|
CA363301188 rs1175604539 |
347 | F>L | No |
gnomAD ClinGen |
|
|
CA3712994 rs370219054 |
355 | R>Q | No |
ESP ExAC TOPMed gnomAD ClinGen |
|
| TCGA novel | 357 | N>D | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs770168629 CA3712991 |
370 | T>A | No |
ExAC gnomAD ClinGen |
|
| TCGA novel | 376 | A>S | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 376 | A>T | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
| TCGA novel | 380 | R>Q | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
CA363300890 rs938725414 |
380 | R>W | No |
TOPMed gnomAD ClinGen |
|
|
CA363300823 rs1421720981 |
388 | I>V | No |
ClinGen gnomAD |
|
|
TCGA novel rs11543322 CA136870126 |
391 | V>L | Variant assessed as Somatic; impact. [NCI-TCGA] | No |
ClinGen Ensembl NCI-TCGA |
|
rs1236357354 CA363300775 |
393 | D>E | No |
gnomAD ClinGen |
|
| TCGA novel | 398 | K>N | Variant assessed as Somatic; impact. [NCI-TCGA] | No | NCI-TCGA |
|
rs778633305 CA3712963 |
398 | K>R | No |
ClinGen ExAC TOPMed gnomAD |
|
|
rs778633305 CA363300731 |
398 | K>T | No |
ExAC TOPMed gnomAD ClinGen |
|
|
CA363300555 rs1450155021 |
418 | I>L | No |
TOPMed ClinGen |
|
|
CA363300539 rs1284972330 |
420 | I>V | No |
gnomAD ClinGen |
|
|
CA3712961 rs749151547 |
422 | S>F | No |
ClinGen ExAC |
|
|
CA3712936 rs757082591 |
428 | R>Q | No |
ExAC gnomAD ClinGen |
No associated diseases with Q13838
4 regional properties for Q13838
Functions
| Description | ||
|---|---|---|
| EC Number | 3.6.4.13 | Acting on ATP; involved in cellular and subcellular movement |
| Subcellular Localization |
|
|
| PANTHER Family | ||
| PANTHER Subfamily | ||
| PANTHER Protein Class | ||
| PANTHER Pathway Category | No pathway information available | |
8 GO annotations of cellular component
| Name | Definition |
|---|---|
| cytoplasm | The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. |
| nuclear speck | A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy. |
| nucleoplasm | That part of the nuclear content other than the chromosomes or the nucleolus. |
| nucleus | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
| spliceosomal complex | Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA. |
| transcription export complex | The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans. |
| U4 snRNP | A ribonucleoprotein complex that contains small nuclear RNA U4, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U4 snRNP, most of which remain associated with the U4 snRNA both while the U4 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes. |
| U6 snRNP | A ribonucleoprotein complex that contains small nuclear RNA U6, the Lsm2-8 heptameric ring complex, as well as several proteins that are unique to the U6 snRNP, most of which remain associated with the U6 snRNA both while the U6 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes. |
9 GO annotations of molecular function
| Name | Definition |
|---|---|
| ATP binding | Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. |
| ATP hydrolysis activity | Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. |
| ATP-dependent activity, acting on RNA | Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction. |
| ATP-dependent protein binding | Binding to a protein or protein complex using energy from ATP hydrolysis. |
| identical protein binding | Binding to an identical protein or proteins. |
| RNA binding | Binding to an RNA molecule or a portion thereof. |
| RNA helicase activity | Unwinding of an RNA helix, driven by ATP hydrolysis. |
| U4 snRNA binding | Binding to a U4 small nuclear RNA (U4 snRNA). |
| U6 snRNA binding | Binding to a U6 small nuclear RNA (U6 snRNA). |
9 GO annotations of biological process
| Name | Definition |
|---|---|
| mRNA export from nucleus | The directed movement of mRNA from the nucleus to the cytoplasm. |
| mRNA splicing, via spliceosome | The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced. |
| negative regulation of DNA damage checkpoint | Any process that stops, prevents, or reduces the frequency, rate or extent of a DNA damage checkpoint. |
| positive regulation of DNA-templated transcription, elongation | Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase. |
| RNA export from nucleus | The directed movement of RNA from the nucleus to the cytoplasm. |
| RNA secondary structure unwinding | The process in which a secondary structure of RNA are broken or 'melted'. |
| RNA splicing | The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. |
| spliceosomal complex assembly | The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions. |
| viral mRNA export from host cell nucleus | The directed movement of intronless viral mRNA from the host nucleus to the cytoplasm for translation. |
26 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| Q07478 | SUB2 | ATP-dependent RNA helicase SUB2 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PR |
| Q3T147 | DDX39B | Spliceosome RNA helicase DDX39B | Bos taurus (Bovine) | PR |
| Q5ZHZ0 | DDX39B | Spliceosome RNA helicase DDX39B | Gallus gallus (Chicken) | PR |
| P60024 | DDX39B | Spliceosome RNA helicase DDX39B | Pan troglodytes (Chimpanzee) | PR |
| Q5WR10 | DDX39B | Spliceosome RNA helicase DDX39B | Canis lupus familiaris (Dog) (Canis familiaris) | PR |
| P38919 | EIF4A3 | Eukaryotic initiation factor 4A-III | Homo sapiens (Human) | PR |
| Q9NQI0 | DDX4 | Probable ATP-dependent RNA helicase DDX4 | Homo sapiens (Human) | SS |
| O15523 | DDX3Y | ATP-dependent RNA helicase DDX3Y | Homo sapiens (Human) | SS |
| O00571 | DDX3X | ATP-dependent RNA helicase DDX3X | Homo sapiens (Human) | EV |
| Q9UHL0 | DDX25 | ATP-dependent RNA helicase DDX25 | Homo sapiens (Human) | PR |
| Q9UMR2 | DDX19B | ATP-dependent RNA helicase DDX19B | Homo sapiens (Human) | PR |
| Q9NUU7 | DDX19A | ATP-dependent RNA helicase DDX19A | Homo sapiens (Human) | PR |
| P17844 | DDX5 | Probable ATP-dependent RNA helicase DDX5 | Homo sapiens (Human) | PR |
| O00148 | DDX39A | ATP-dependent RNA helicase DDX39A | Homo sapiens (Human) | PR |
| Q9UJV9 | DDX41 | Probable ATP-dependent RNA helicase DDX41 | Homo sapiens (Human) | PR |
| Q8VDW0 | Ddx39a | ATP-dependent RNA helicase DDX39A | Mus musculus (Mouse) | PR |
| Q9Z1N5 | Ddx39b | Spliceosome RNA helicase Ddx39b | Mus musculus (Mouse) | PR |
| Q29024 | DDX39B | Spliceosome RNA helicase DDX39B | Sus scrofa (Pig) | PR |
| Q5U216 | Ddx39a | ATP-dependent RNA helicase DDX39A | Rattus norvegicus (Rat) | PR |
| Q63413 | Ddx39b | Spliceosome RNA helicase Ddx39b | Rattus norvegicus (Rat) | PR |
| Q5TM17 | DDX39B | Spliceosome RNA helicase DDX39B | Macaca mulatta (Rhesus macaque) | PR |
| Q5JK84 | AIP2 | DEAD-box ATP-dependent RNA helicase 15 | Oryza sativa subsp japonica (Rice) | PR |
| Q0JM17 | AIP1 | DEAD-box ATP-dependent RNA helicase 56 | Oryza sativa subsp japonica (Rice) | PR |
| Q18212 | hel-1 | Spliceosome RNA helicase DDX39B homolog | Caenorhabditis elegans | PR |
| Q56XG6 | RH15 | DEAD-box ATP-dependent RNA helicase 15 | Arabidopsis thaliana (Mouse-ear cress) | PR |
| Q9LFN6 | RH56 | DEAD-box ATP-dependent RNA helicase 56 | Arabidopsis thaliana (Mouse-ear cress) | PR |
| 10 | 20 | 30 | 40 | 50 | 60 |
| MAENDVDNEL | LDYEDDEVET | AAGGDGAEAP | AKKDVKGSYV | SIHSSGFRDF | LLKPELLRAI |
| 70 | 80 | 90 | 100 | 110 | 120 |
| VDCGFEHPSE | VQHECIPQAI | LGMDVLCQAK | SGMGKTAVFV | LATLQQLEPV | TGQVSVLVMC |
| 130 | 140 | 150 | 160 | 170 | 180 |
| HTRELAFQIS | KEYERFSKYM | PNVKVAVFFG | GLSIKKDEEV | LKKNCPHIVV | GTPGRILALA |
| 190 | 200 | 210 | 220 | 230 | 240 |
| RNKSLNLKHI | KHFILDECDK | MLEQLDMRRD | VQEIFRMTPH | EKQVMMFSAT | LSKEIRPVCR |
| 250 | 260 | 270 | 280 | 290 | 300 |
| KFMQDPMEIF | VDDETKLTLH | GLQQYYVKLK | DNEKNRKLFD | LLDVLEFNQV | VIFVKSVQRC |
| 310 | 320 | 330 | 340 | 350 | 360 |
| IALAQLLVEQ | NFPAIAIHRG | MPQEERLSRY | QQFKDFQRRI | LVATNLFGRG | MDIERVNIAF |
| 370 | 380 | 390 | 400 | 410 | 420 |
| NYDMPEDSDT | YLHRVARAGR | FGTKGLAITF | VSDENDAKIL | NDVQDRFEVN | ISELPDEIDI |
| SSYIEQTR |