ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TUBD1

Gene summary

Gene information	Gene symbol	TUBD1
	Gene ID	51174
	Gene name	tubulin delta 1
	Synonyms	TUBD
	Cytomap	17q23.1
	Type of gene	protein-coding
	Description	tubulin delta chaindelta-tubulin
	Modification date	20180523
	UniProtAcc	Q9UJT1
	Context	PubMed: TUBD1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene

GO ID

GO term

PubMed ID

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Exon skipping events across known transcript of Ensembl for TUBD1 from UCSC genome browser

Skipped exons in TCGA and GTEx 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.

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Gene isoform structures and expression levels for TUBD1

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for TUBD1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_292042	17	57937682:57937785:57941024:57941208:57943969:57944110	57941024:57941208	ENSG00000108423.10	ENST00000539018.1,ENST00000346141.6,ENST00000591548.1,ENST00000340993.6,ENST00000325752.3,ENST00000592426.1
exon_skip_292044	17	57937682:57937785:57941024:57941208:57955463:57955637	57941024:57941208	ENSG00000108423.10	ENST00000376094.4
exon_skip_292060	17	57941143:57941208:57943969:57944110:57951899:57952061	57943969:57944110	ENSG00000108423.10	ENST00000539018.1,ENST00000325752.3,ENST00000592426.1
exon_skip_292061	17	57941143:57941208:57943969:57944110:57955463:57955637	57943969:57944110	ENSG00000108423.10	ENST00000591548.1,ENST00000588009.1,ENST00000340993.6
exon_skip_292062	17	57941143:57941208:57943969:57944110:57963443:57963591	57943969:57944110	ENSG00000108423.10	ENST00000593110.1
exon_skip_292072	17	57943969:57944110:57951899:57952064:57955463:57955637	57951899:57952064	ENSG00000108423.10	ENST00000539018.1,ENST00000394239.3,ENST00000325752.3,ENST00000592426.1
exon_skip_292077	17	57943969:57944110:57955463:57955695:57958254:57958471	57955463:57955695	ENSG00000108423.10	ENST00000591548.1,ENST00000588009.1,ENST00000340993.6
exon_skip_292087	17	57943969:57944110:57963443:57963591:57970057:57970076	57963443:57963591	ENSG00000108423.10	ENST00000593110.1
exon_skip_292093	17	57955661:57955695:57958254:57958471:57962021:57962117	57958254:57958471	ENSG00000108423.10	ENST00000591548.1
exon_skip_292094	17	57955661:57955695:57958254:57958471:57963443:57963591	57958254:57958471	ENSG00000108423.10	ENST00000340993.6,ENST00000394239.3,ENST00000325752.3,ENST00000376094.4,ENST00000592426.1
exon_skip_292099	17	57958298:57958471:57962021:57962117:57963443:57963591	57962021:57962117	ENSG00000108423.10	ENST00000591548.1
exon_skip_292100	17	57958298:57958471:57963443:57963591:57968191:57968364	57963443:57963591	ENSG00000108423.10	ENST00000340993.6,ENST00000394239.3,ENST00000325752.3,ENST00000376094.4,ENST00000592426.1
exon_skip_292101	17	57958298:57958471:57963443:57963591:57970057:57970076	57963443:57963591	ENSG00000108423.10	ENST00000590498.1
exon_skip_292105	17	57963443:57963591:57968191:57968402:57970057:57970076	57968191:57968402	ENSG00000108423.10	ENST00000591611.1,ENST00000591548.1,ENST00000340993.6,ENST00000394239.3,ENST00000325752.3
exon_skip_292108	17	57968389:57968402:57969174:57969321:57970057:57970076	57969174:57969321	ENSG00000108423.10	ENST00000592145.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TUBD1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_292042	17	57937682:57937785:57941024:57941208:57943969:57944110	57941024:57941208	ENSG00000108423.10	ENST00000346141.6,ENST00000325752.3,ENST00000340993.6,ENST00000592426.1,ENST00000539018.1,ENST00000591548.1
exon_skip_292044	17	57937682:57937785:57941024:57941208:57955463:57955637	57941024:57941208	ENSG00000108423.10	ENST00000376094.4
exon_skip_292046	17	57937394:57937785:57943956:57944110:57951899:57952064	57943956:57944110	ENSG00000108423.10	ENST00000394239.3
exon_skip_292060	17	57941143:57941208:57943969:57944110:57951899:57952061	57943969:57944110	ENSG00000108423.10	ENST00000325752.3,ENST00000592426.1,ENST00000539018.1
exon_skip_292061	17	57941143:57941208:57943969:57944110:57955463:57955637	57943969:57944110	ENSG00000108423.10	ENST00000340993.6,ENST00000591548.1,ENST00000588009.1
exon_skip_292062	17	57941143:57941208:57943969:57944110:57963443:57963591	57943969:57944110	ENSG00000108423.10	ENST00000593110.1
exon_skip_292072	17	57943969:57944110:57951899:57952064:57955463:57955637	57951899:57952064	ENSG00000108423.10	ENST00000325752.3,ENST00000394239.3,ENST00000592426.1,ENST00000539018.1
exon_skip_292077	17	57943969:57944110:57955463:57955695:57958254:57958471	57955463:57955695	ENSG00000108423.10	ENST00000340993.6,ENST00000591548.1,ENST00000588009.1
exon_skip_292087	17	57943969:57944110:57963443:57963591:57970057:57970076	57963443:57963591	ENSG00000108423.10	ENST00000593110.1
exon_skip_292093	17	57955661:57955695:57958254:57958471:57962021:57962117	57958254:57958471	ENSG00000108423.10	ENST00000591548.1
exon_skip_292094	17	57955661:57955695:57958254:57958471:57963443:57963591	57958254:57958471	ENSG00000108423.10	ENST00000325752.3,ENST00000340993.6,ENST00000394239.3,ENST00000376094.4,ENST00000592426.1
exon_skip_292099	17	57958298:57958471:57962021:57962117:57963443:57963591	57962021:57962117	ENSG00000108423.10	ENST00000591548.1
exon_skip_292101	17	57958298:57958471:57963443:57963591:57970057:57970076	57963443:57963591	ENSG00000108423.10	ENST00000590498.1
exon_skip_292105	17	57963443:57963591:57968191:57968402:57970057:57970076	57968191:57968402	ENSG00000108423.10	ENST00000325752.3,ENST00000340993.6,ENST00000394239.3,ENST00000591548.1,ENST00000591611.1
exon_skip_292108	17	57968389:57968402:57969174:57969321:57970057:57970076	57969174:57969321	ENSG00000108423.10	ENST00000592145.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for TUBD1

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000325752	57968191	57968402	3UTR-3CDS
ENST00000325752	57941024	57941208	Frame-shift
ENST00000592426	57941024	57941208	Frame-shift
ENST00000325752	57958254	57958471	Frame-shift
ENST00000592426	57958254	57958471	Frame-shift
ENST00000325752	57963443	57963591	Frame-shift
ENST00000592426	57963443	57963591	Frame-shift
ENST00000325752	57943969	57944110	In-frame
ENST00000592426	57943969	57944110	In-frame
ENST00000325752	57951899	57952064	In-frame
ENST00000592426	57951899	57952064	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000325752	57968191	57968402	3UTR-3CDS
ENST00000325752	57941024	57941208	Frame-shift
ENST00000592426	57941024	57941208	Frame-shift
ENST00000325752	57958254	57958471	Frame-shift
ENST00000592426	57958254	57958471	Frame-shift
ENST00000325752	57943969	57944110	In-frame
ENST00000592426	57943969	57944110	In-frame
ENST00000325752	57951899	57952064	In-frame
ENST00000592426	57951899	57952064	In-frame

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Infer the effects of exon skipping event on protein functional features for TUBD1

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000325752	2489	453	57951899	57952064	1048	1212	256	311
ENST00000592426	1477	453	57951899	57952064	771	935	256	311
ENST00000325752	2489	453	57943969	57944110	1213	1353	311	358
ENST00000592426	1477	453	57943969	57944110	936	1076	311	358

Loci of skipped exons in GTEx 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
ENST00000325752	2489	453	57951899	57952064	1048	1212	256	311
ENST00000592426	1477	453	57951899	57952064	771	935	256	311
ENST00000325752	2489	453	57943969	57944110	1213	1353	311	358
ENST00000592426	1477	453	57943969	57944110	936	1076	311	358

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

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

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

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

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SNVs in the skipped exons for TUBD1

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

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

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-G3-A3CJ-01	exon_skip_292062 exon_skip_292060 exon_skip_292061	57943970	57944110	57944057	57944057	Frame_Shift_Del	T	-	p.M330fs
LIHC	TCGA-DD-A1EG-01		57951900	57952064	57951964	57951964	Frame_Shift_Del	A	-	p.F290fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958290	57958290	Frame_Shift_Del	T	-	p.M168fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958382	57958382	Frame_Shift_Del	A	-	p.F137fs
LIHC	TCGA-DD-A1EG-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958394	57958394	Frame_Shift_Del	A	-	p.F133fs
LIHC	TCGA-DD-A39Y-01	exon_skip_292087 exon_skip_292101 exon_skip_292100	57963444	57963591	57963473	57963473	Frame_Shift_Del	T	-	p.K97fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_292087 exon_skip_292101 exon_skip_292100	57963444	57963591	57963473	57963473	Frame_Shift_Del	T	-	p.K97fs
HNSC	TCGA-BA-A6DJ-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958381	57958382	Frame_Shift_Ins	-	A	p.Y137fs
BLCA	TCGA-XF-AAN7-01	exon_skip_292044 exon_skip_292042	57941025	57941208	57941183	57941183	Nonsense_Mutation	A	C	p.Y367*
HNSC	TCGA-BA-A6DJ-01	exon_skip_292077	57955464	57955695	57955640	57955640	Nonsense_Mutation	G	C	p.S198*
CESC	TCGA-C5-A1M6-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958298	57958298	Nonsense_Mutation	G	C	p.S165*
LUAD	TCGA-69-8255-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958311	57958311	Nonsense_Mutation	G	A	p.Q161*
LUAD	TCGA-17-Z014-01	exon_skip_292093 exon_skip_292094	57958255	57958471	57958410	57958410	Nonsense_Mutation	C	A	p.E128*

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-69-8255-01
	Cancer type: LUAD
	ESID: exon_skip_292094
	Skipped exon start: 57958255
	Skipped exon end: 57958471
	Mutation start: 57958311
	Mutation end: 57958311
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: A
	AAchange: p.Q161*
exon_skip_292094_LUAD_TCGA-69-8255-01.png
	Sample: TCGA-BA-A6DJ-01
	Cancer type: HNSC
	ESID: exon_skip_292094
	Skipped exon start: 57958255
	Skipped exon end: 57958471
	Mutation start: 57958381
	Mutation end: 57958382
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: A
	AAchange: p.Y137fs
	Sample: TCGA-BA-A6DJ-01
	Cancer type: HNSC
	ESID: exon_skip_292077
	Skipped exon start: 57955464
	Skipped exon end: 57955695
	Mutation start: 57955640
	Mutation end: 57955640
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S198*
exon_skip_292094_HNSC_TCGA-BA-A6DJ-01.png

- 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
SLR21_KIDNEY	57943970	57944110	57944004	57944008	Frame_Shift_Del	AATGA	-	p.VI346fs
CW2_LARGE_INTESTINE	57958255	57958471	57958358	57958358	Frame_Shift_Del	C	-	p.G145fs
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57941025	57941208	57941043	57941043	Missense_Mutation	C	A	p.W414L
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57941025	57941208	57941048	57941048	Missense_Mutation	C	A	p.K412N
NCIH2342_LUNG	57941025	57941208	57941149	57941149	Missense_Mutation	C	T	p.V379M
GP2D_LARGE_INTESTINE	57941025	57941208	57941185	57941185	Missense_Mutation	A	G	p.Y367H
ANGMCSS_CENTRAL_NERVOUS_SYSTEM	57941025	57941208	57941194	57941194	Missense_Mutation	G	A	p.P364S
OVCAR8_OVARY	57943970	57944110	57944003	57944003	Missense_Mutation	G	T	p.L348I
SNU520_STOMACH	57951900	57952064	57952058	57952058	Missense_Mutation	A	G	p.L259S
HEC251_ENDOMETRIUM	57955464	57955695	57955475	57955475	Missense_Mutation	C	T	p.R253Q
HMEL_BREAST	57955464	57955695	57955566	57955566	Missense_Mutation	A	C	p.S223A
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57955464	57955695	57955619	57955619	Missense_Mutation	T	A	p.E205V
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57955464	57955695	57955646	57955646	Missense_Mutation	C	T	p.R196Q
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57955464	57955695	57955667	57955667	Missense_Mutation	A	C	p.L189W
EN_ENDOMETRIUM	57958255	57958471	57958343	57958343	Missense_Mutation	A	G	p.L150S
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57958255	57958471	57958355	57958355	Missense_Mutation	G	A	p.T146I
U937_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57958255	57958471	57958403	57958403	Missense_Mutation	C	G	p.C130S
TUR_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	57958255	57958471	57958403	57958403	Missense_Mutation	C	G	p.C130S
HCC2108_LUNG	57963444	57963591	57963451	57963451	Missense_Mutation	C	A	p.A105S
HEC1_ENDOMETRIUM	57963444	57963591	57963555	57963555	Missense_Mutation	G	A	p.P70L
SNU1040_LARGE_INTESTINE	57963444	57963591	57963580	57963580	Missense_Mutation	G	A	p.R62W
MDAMB453_BREAST	57968192	57968402	57968222	57968222	Missense_Mutation	C	G	p.E48Q
NCIH1623_LUNG	57968192	57968402	57968222	57968222	Missense_Mutation	C	T	p.E48K
RL952_ENDOMETRIUM	57968192	57968402	57968234	57968234	Missense_Mutation	C	T	p.A44T
MDST8_LARGE_INTESTINE	57955464	57955695	57955515	57955515	Nonsense_Mutation	G	A	p.Q240*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TUBD1

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_292072	17	57943969:57944110:57951899:57952064:57955463:57955637	57951899:57952064	ENST00000539018.1,ENST00000394239.3,ENST00000325752.3,ENST00000592426.1	HNSC	rs2250526	chr17:57951973	G/A	1.78e-03
exon_skip_292105	17	57963443:57963591:57968191:57968402:57970057:57970076	57968191:57968402	ENST00000591611.1,ENST00000591548.1,ENST00000340993.6,ENST00000394239.3,ENST00000325752.3	LGG	rs143803908	chr17:57968398	AC/A	5.37e-04
exon_skip_292105	17	57963443:57963591:57968191:57968402:57970057:57970076	57968191:57968402	ENST00000591611.1,ENST00000591548.1,ENST00000340993.6,ENST00000394239.3,ENST00000325752.3	LUSC	rs143803908	chr17:57968398	AC/A	1.13e-06
exon_skip_292105	17	57963443:57963591:57968191:57968402:57970057:57970076	57968191:57968402	ENST00000591611.1,ENST00000591548.1,ENST00000340993.6,ENST00000394239.3,ENST00000325752.3	THCA	rs143803908	chr17:57968398	AC/A	7.14e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TUBD1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TUBD1

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RelatedDrugs for TUBD1

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

Gene	UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
	Q9UJT1	DB00570	Vinblastine	Tubulin delta chain	small molecule	approved

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RelatedDiseases for TUBD1

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 TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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