ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for DDX3X

Gene summary

Gene information	Gene symbol	DDX3X
	Gene ID	1654
	Gene name	DEAD-box helicase 3 X-linked
	Synonyms	CAP-Rf\|DBX\|DDX14\|DDX3\|HLP2\|MRX102
	Cytomap	Xp11.4
	Type of gene	protein-coding
	Description	ATP-dependent RNA helicase DDX3XDEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linkedDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linkedDEAD box protein 3, X-chromosomalDEAD box, X isoformDEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3DEAD/H box-3helicase-
	Modification date	20200329
	UniProtAcc	A0A087WVZ1, A0A087WX09, A0A0D9SF53, A0A0D9SFB3, A0A0D9SG12, A0A0J9YVQ7, A0A2R8Y4A4, A0A2R8Y4D2, A0A2R8Y5G6, A0A2R8Y645, A0A2R8Y650, A0A2R8Y770, A0A2R8Y7T2, A0A2R8YCU0, A0A2R8YCW1, A0A2R8YDH3, A0A2R8YDT5, A0A2R8YF31, A0A2R8YF78, A0A2R8YF89, A0A2R8YFR4, A0A2R8YFS5, A0A2R8YGJ1, A0A2U3TZJ9, B5BTY4, F6S8Q4, O00571,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
DDX3X	GO:0009615	response to virus	18636090
DDX3X	GO:0010501	RNA secondary structure unwinding	22872150
DDX3X	GO:0010628	positive regulation of gene expression	10074132
DDX3X	GO:0030308	negative regulation of cell growth	16818630
DDX3X	GO:0031333	negative regulation of protein complex assembly	17667941
DDX3X	GO:0031954	positive regulation of protein autophosphorylation	30341167
DDX3X	GO:0032727	positive regulation of interferon-alpha production	30341167
DDX3X	GO:0032728	positive regulation of interferon-beta production	27980081
DDX3X	GO:0034063	stress granule assembly	21883093
DDX3X	GO:0034157	positive regulation of toll-like receptor 7 signaling pathway	30341167
DDX3X	GO:0034161	positive regulation of toll-like receptor 8 signaling pathway	30341167
DDX3X	GO:0035556	intracellular signal transduction	18636090
DDX3X	GO:0045727	positive regulation of translation	18596238\|22872150
DDX3X	GO:0045944	positive regulation of transcription by RNA polymerase II	16818630\|18636090\|28128295
DDX3X	GO:0071243	cellular response to arsenic-containing substance	21883093
DDX3X	GO:0071470	cellular response to osmotic stress	21883093
DDX3X	GO:0071902	positive regulation of protein serine/threonine kinase activity	23413191
DDX3X	GO:1902523	positive regulation of protein K63-linked ubiquitination	27980081

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Gene structures and expression levels for DDX3X

Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

ENSG00000215301

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
PCC	UP	ENST00000642801.1	DDX3X-233:retained_intron:DDX3X	2.357341e+01	3.083544e+00	6.542238e-06	9.474486e-04
STG	UP	ENST00000646627.1	DDX3X-262:protein_coding:DDX3X	1.853293e+01	2.352021e+01	1.375981e-19	2.350204e-16
CB	UP	ENST00000480592.6	DDX3X-205:retained_intron:DDX3X	1.879528e+02	8.936878e-01	7.836123e-11	5.160737e-09
CB	UP	ENST00000645338.1	DDX3X-249:retained_intron:DDX3X	5.416243e+02	9.869362e-01	4.600487e-08	1.098790e-06
CB	UP	ENST00000622198.5	DDX3X-213:lncRNA:DDX3X	2.452195e+00	1.783351e+00	5.694438e-07	9.288182e-06
CB	UP	ENST00000643820.1	DDX3X-234:retained_intron:DDX3X	8.432026e+00	9.863346e-01	2.268416e-06	3.007571e-05
CB	UP	ENST00000645080.1	DDX3X-246:nonsense_mediated_decay:DDX3X	3.850908e+01	2.252548e+00	4.093216e-06	4.946166e-05
CB	UP	ENST00000645253.1	DDX3X-248:retained_intron:DDX3X	2.933472e+01	1.066015e+00	1.015194e-05	1.067713e-04
CB	UP	ENST00000642687.1	DDX3X-229:retained_intron:DDX3X	1.299754e+02	9.522198e-01	1.128581e-05	1.167157e-04
CB	UP	ENST00000542215.5	DDX3X-206:nonsense_mediated_decay:DDX3X	3.885571e+00	1.687346e+00	3.892078e-05	3.326579e-04
CB	UP	ENST00000642589.1	DDX3X-226:retained_intron:DDX3X	1.351113e+02	9.728451e-01	4.492224e-05	3.755385e-04
CB	UP	ENST00000646822.1	DDX3X-264:retained_intron:DDX3X	1.012883e+02	1.569687e+00	1.054666e-04	7.746945e-04
CB	UP	ENST00000647219.1	DDX3X-266:retained_intron:DDX3X	1.568186e+00	2.192477e+00	2.530891e-04	1.624975e-03
CB	UP	ENST00000457138.7	DDX3X-203:protein_coding:DDX3X	1.308781e+02	1.218162e+00	6.724490e-04	3.701458e-03
CB	UP	ENST00000646093.1	DDX3X-255:retained_intron:DDX3X	2.506486e+00	1.098199e+00	8.035391e-04	4.297872e-03
CB	UP	ENST00000646940.1	DDX3X-265:retained_intron:DDX3X	2.500145e+02	9.133884e-01	8.985740e-04	4.718726e-03
CB	UP	ENST00000642424.1	DDX3X-225:protein_coding:DDX3X	2.643265e+02	1.128019e+00	1.208152e-03	6.057586e-03
CB	UP	ENST00000642624.1	DDX3X-228:retained_intron:DDX3X	1.308067e+00	2.005670e+00	1.248598e-03	6.224300e-03
CB	UP	ENST00000478993.5	DDX3X-204:nonsense_mediated_decay:DDX3X	5.360831e+00	1.379147e+00	3.624928e-03	1.507793e-02
CB	UP	ENST00000645574.1	DDX3X-252:retained_intron:DDX3X	3.313097e+01	1.064573e+00	6.364381e-03	2.399370e-02
CB	UP	ENST00000644109.1	DDX3X-239:protein_coding:DDX3X	2.624352e+01	8.243873e-01	8.756936e-03	3.117388e-02
CB	UP	ENST00000631641.2	DDX3X-222:retained_intron:DDX3X	1.869101e+00	1.486714e+00	1.401817e-02	4.566203e-02
TC	UP	ENST00000645338.1	DDX3X-249:retained_intron:DDX3X	3.562766e+02	8.222832e-01	1.057334e-04	1.686292e-03
TC	UP	ENST00000643821.1	DDX3X-235:protein_coding:DDX3X	1.814973e+01	8.066407e-01	2.925246e-04	3.768004e-03
TC	UP	ENST00000644073.1	DDX3X-237:protein_coding:DDX3X	6.006478e+00	2.701810e+00	2.337571e-03	1.888675e-02
TC	DOWN	ENST00000642801.1	DDX3X-233:retained_intron:DDX3X	4.011099e+02	-1.242681e+00	5.712602e-03	3.700507e-02
TC	UP	ENST00000441189.4	DDX3X-202:protein_coding:DDX3X	3.283683e+00	4.065838e+00	5.811968e-03	3.749864e-02
TC	UP	ENST00000457138.7	DDX3X-203:protein_coding:DDX3X	8.591563e+01	8.514484e-01	8.007296e-03	4.756452e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for DDX3X

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_105432	chrX	41337408:41337465:41337691:41339083:41341484:41341494	41337691:41339083
exon_skip_111054	chrX	41342808:41342836:41343289:41343351:41343737:41343822	41343289:41343351
exon_skip_119391	chrX	41342737:41342836:41343737:41343822:41344030:41344109	41343737:41343822
exon_skip_124119	chrX	41343737:41343822:41344030:41344128:41344239:41344399	41344030:41344128
exon_skip_138537	chrX	41343216:41343351:41343737:41343822:41344030:41344128	41343737:41343822
exon_skip_152377	chrX	41337408:41337465:41337691:41339083:41341484:41341616	41337691:41339083
exon_skip_178911	chrX	41342737:41342836:41343289:41343351:41343737:41343822	41343289:41343351
exon_skip_181206	chrX	41337408:41337465:41339039:41339083:41341484:41341616	41339039:41339083
exon_skip_190025	chrX	41341484:41341616:41341949:41342046:41342495:41342506	41341949:41342046
exon_skip_192038	chrX	41342737:41342836:41343221:41343351:41343737:41343822	41343221:41343351
exon_skip_196418	chrX	41337408:41337465:41339036:41339083:41341484:41341494	41339036:41339083
exon_skip_227909	chrX	41339039:41339083:41340636:41340814:41341484:41341494	41340636:41340814
exon_skip_23645	chrX	41334621:41334815:41336083:41336159:41337408:41337465	41336083:41336159
exon_skip_240622	chrX	41334610:41334815:41336083:41336159:41337408:41337465	41336083:41336159
exon_skip_242774	chrX	41334257:41334297:41337408:41337465:41341484:41341494	41337408:41337465
exon_skip_244954	chrX	41342737:41342836:41343216:41343351:41343737:41343822	41343216:41343351
exon_skip_245937	chrX	41342737:41342836:41343216:41343351:41344030:41344109	41343216:41343351
exon_skip_258231	chrX	41343289:41343351:41343737:41343822:41344030:41344109	41343737:41343822
exon_skip_259635	chrX	41342495:41342653:41342737:41342836:41343216:41343351	41342737:41342836
exon_skip_271423	chrX	41342808:41342836:41343216:41343351:41343737:41343822	41343216:41343351
exon_skip_27743	chrX	41343737:41343822:41344030:41344128:41344239:41344310	41344030:41344128
exon_skip_281288	chrX	41334257:41334297:41337408:41339083:41341484:41341494	41337408:41339083
exon_skip_286823	chrX	41337408:41337465:41339039:41339083:41341484:41341494	41339039:41339083
exon_skip_30096	chrX	41337408:41337465:41339036:41339083:41341484:41341616	41339036:41339083
exon_skip_31651	chrX	41342808:41342836:41343221:41343351:41343737:41343822	41343221:41343351
exon_skip_34011	chrX	41342550:41342653:41342737:41342836:41343737:41343822	41342737:41342836
exon_skip_35269	chrX	41343737:41343822:41344030:41344128:41344239:41344317	41344030:41344128
exon_skip_45170	chrX	41334257:41334297:41337408:41337465:41341484:41341616	41337408:41337465
exon_skip_65266	chrX	41341505:41341616:41341949:41342046:41342495:41342506	41341949:41342046
exon_skip_73708	chrX	41342495:41342653:41342737:41344128:41344239:41344399	41342737:41344128
exon_skip_77302	chrX	41334634:41334769:41336083:41336159:41337408:41337464	41336083:41336159
exon_skip_77907	chrX	41334257:41334297:41337408:41339083:41341484:41341616	41337408:41339083
exon_skip_81264	chrX	41337408:41337465:41337691:41338912:41339036:41339083	41337691:41338912

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for DDX3X

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000629496	41342737	41342836	Frame-shift
ENST00000644876	41342737	41342836	Frame-shift
ENST00000629496	41343216	41343351	Frame-shift
ENST00000644876	41343216	41343351	Frame-shift
ENST00000629496	41343737	41343822	Frame-shift
ENST00000644876	41343737	41343822	Frame-shift
ENST00000629496	41339036	41339083	In-frame
ENST00000644876	41339036	41339083	In-frame
ENST00000629496	41344030	41344128	In-frame
ENST00000644876	41344030	41344128	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000629496	41343737	41343822	Frame-shift
ENST00000644876	41343737	41343822	Frame-shift
ENST00000629496	41339036	41339083	In-frame
ENST00000644876	41339036	41339083	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000629496	41343216	41343351	Frame-shift
ENST00000644876	41343216	41343351	Frame-shift
ENST00000629496	41343737	41343822	Frame-shift
ENST00000644876	41343737	41343822	Frame-shift
ENST00000629496	41339036	41339083	In-frame
ENST00000644876	41339036	41339083	In-frame
ENST00000629496	41344030	41344128	In-frame
ENST00000644876	41344030	41344128	In-frame

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Infer the effects of exon skipping event on protein functional features for DDX3X

p-ENSG00000215301_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000629496	5053	662	41339036	41339083	584	630	35	50
ENST00000644876	6924	662	41339036	41339083	1074	1120	35	50
ENST00000629496	5053	662	41344030	41344128	1246	1343	255	288
ENST00000644876	6924	662	41344030	41344128	1736	1833	255	288

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000629496	5053	662	41339036	41339083	584	630	35	50
ENST00000644876	6924	662	41339036	41339083	1074	1120	35	50

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000629496	5053	662	41339036	41339083	584	630	35	50
ENST00000644876	6924	662	41339036	41339083	1074	1120	35	50
ENST00000629496	5053	662	41344030	41344128	1246	1343	255	288
ENST00000644876	6924	662	41344030	41344128	1736	1833	255	288

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	255	288	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4PXA
O00571	255	288	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4PXA
O00571	255	288	268	272	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	268	272	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	255	288	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	255	288	211	403	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
O00571	255	288	211	403	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
O00571	255	288	249	256	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	249	256	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	276	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	276	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	269	269	Mutagenesis	Note=Greatly impairs phosphorylation by TBK1 and fails to synergize with TBK1 in IFN-beta induction%3B when associated with A-181%3B A-183 and A-240. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18583960;Dbxref=PMID:18583960
O00571	255	288	269	269	Mutagenesis	Note=Greatly impairs phosphorylation by TBK1 and fails to synergize with TBK1 in IFN-beta induction%3B when associated with A-181%3B A-183 and A-240. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18583960;Dbxref=PMID:18583960
O00571	255	288	100	662	Region	Note=Interaction with GSK3B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18846110;Dbxref=PMID:18846110
O00571	255	288	100	662	Region	Note=Interaction with GSK3B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18846110;Dbxref=PMID:18846110
O00571	255	288	250	259	Region	Note=Involved in stimulation of ATPase activity by DNA and RNA%2C nucleic acid binding and unwinding and HIV-1 replication
O00571	255	288	250	259	Region	Note=Involved in stimulation of ATPase activity by DNA and RNA%2C nucleic acid binding and unwinding and HIV-1 replication
O00571	255	288	260	517	Region	Note=Necessary for interaction with XPO1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15507209;Dbxref=PMID:15507209
O00571	255	288	260	517	Region	Note=Necessary for interaction with XPO1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15507209;Dbxref=PMID:15507209

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	35	51	Alternative sequence	ID=VSP_042830;Note=In isoform 2. KGRYIPPHLRNREATKG->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	38	38	Mutagenesis	Note=Impairs interaction with EIF4E. No effect on translation of HIV-1 RNA%3B when associated with A-43. Y->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17667941,ECO:0000269\|PubMed:22872150;Dbxref=PMID:17667941,PMID:22872150
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	43	43	Mutagenesis	Note=Impairs interaction with EIF4E. Fails to induce stress granule assembly and to rescue cell viability after stress. No effect on translation of HIV-1 RNA%3B when associated with A-38. L->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|Pub
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	139	Region	Note=Required for TBK1 and IKBKE-dependent IFN-beta activation
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	2	100	Region	Note=Interaction with EIF4E
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	35	50	50	50	Sequence conflict	Note=K->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00571	255	288	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4PXA
O00571	255	288	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4PXA
O00571	255	288	268	272	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	268	272	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	255	288	2	662	Chain	ID=PRO_0000055009;Note=ATP-dependent RNA helicase DDX3X
O00571	255	288	211	403	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
O00571	255	288	211	403	Domain	Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00541
O00571	255	288	249	256	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	249	256	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	276	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	276	290	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2I4I
O00571	255	288	269	269	Mutagenesis	Note=Greatly impairs phosphorylation by TBK1 and fails to synergize with TBK1 in IFN-beta induction%3B when associated with A-181%3B A-183 and A-240. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18583960;Dbxref=PMID:18583960
O00571	255	288	269	269	Mutagenesis	Note=Greatly impairs phosphorylation by TBK1 and fails to synergize with TBK1 in IFN-beta induction%3B when associated with A-181%3B A-183 and A-240. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18583960;Dbxref=PMID:18583960
O00571	255	288	100	662	Region	Note=Interaction with GSK3B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18846110;Dbxref=PMID:18846110
O00571	255	288	100	662	Region	Note=Interaction with GSK3B;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18846110;Dbxref=PMID:18846110
O00571	255	288	250	259	Region	Note=Involved in stimulation of ATPase activity by DNA and RNA%2C nucleic acid binding and unwinding and HIV-1 replication
O00571	255	288	250	259	Region	Note=Involved in stimulation of ATPase activity by DNA and RNA%2C nucleic acid binding and unwinding and HIV-1 replication
O00571	255	288	260	517	Region	Note=Necessary for interaction with XPO1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15507209;Dbxref=PMID:15507209
O00571	255	288	260	517	Region	Note=Necessary for interaction with XPO1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15507209;Dbxref=PMID:15507209

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3'-UTR located exon skipping events that lost miRNA binding sites in DDX3X

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for DDX3X

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for DDX3X

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DDX3X

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for DDX3X

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for DDX3X

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for DDX3X

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for DDX3X

Gene structures and expression levels for DDX3X

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for DDX3X

Open reading frame (ORF) annotation in the exon skipping event for DDX3X

Infer the effects of exon skipping event on protein functional features for DDX3X

3'-UTR located exon skipping events that lost miRNA binding sites in DDX3X

SNVs in the skipped exons for DDX3X

AD stage-associated exon skippint events for DDX3X

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DDX3X

Correlation with RNA binding proteins (RBPs) for DDX3X

RelatedDrugs for DDX3X

RelatedDiseases for DDX3X