ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TTLL1

Gene summary

Gene information	Gene symbol	TTLL1
	Gene ID	25809
	Gene name	tubulin tyrosine ligase like 1
	Synonyms	C22orf7\|HS323M22B
	Cytomap	22q13.2
	Type of gene	protein-coding
	Description	probable tubulin polyglutamylase TTLL1PGs3catalytic subunit of neural tubulin polyglutamylasetubulin polyglutamylase complex subunit 3tubulin tyrosine ligase-like family, member 1tubulin--tyrosine ligase-like protein 1tubulin-tyrosine ligase
	Modification date	20180519
	UniProtAcc	O95922
	Context	PubMed: TTLL1 [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 TTLL1 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 TTLL1

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 TTLL1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_370201	22	43435674:43435911:43442415:43442579:43447806:43447893	43442415:43442579	ENSG00000100271.12	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7
exon_skip_370203	22	43442415:43442579:43447806:43447893:43455389:43455533	43447806:43447893	ENSG00000100271.12	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENSG00000100271.12	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7
exon_skip_370205	22	43459818:43459927:43460195:43460330:43464415:43464596	43460195:43460330	ENSG00000100271.12	ENST00000331018.7,ENST00000439248.1,ENST00000440761.1,ENST00000266254.7
exon_skip_370208	22	43464415:43464596:43465641:43465850:43471479:43471596	43465641:43465850	ENSG00000100271.12	ENST00000331018.7,ENST00000266254.7
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENSG00000100271.12	ENST00000439248.1,ENST00000440761.1
exon_skip_370214	22	43465641:43465850:43471479:43471596:43475907:43475992	43471479:43471596	ENSG00000100271.12	ENST00000331018.7,ENST00000266254.7
exon_skip_370217	22	43471479:43471596:43475907:43475992:43485282:43485344	43475907:43475992	ENSG00000100271.12	ENST00000445824.1,ENST00000439248.1,ENST00000440761.1,ENST00000266254.7

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TTLL1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_370201	22	43435674:43435911:43442415:43442579:43447806:43447893	43442415:43442579	ENSG00000100271.12	ENST00000439248.1,ENST00000266254.7,ENST00000440761.1
exon_skip_370203	22	43442415:43442579:43447806:43447893:43455389:43455533	43447806:43447893	ENSG00000100271.12	ENST00000439248.1,ENST00000266254.7,ENST00000440761.1
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENSG00000100271.12	ENST00000439248.1,ENST00000266254.7,ENST00000440761.1
exon_skip_370205	22	43459818:43459927:43460195:43460330:43464415:43464596	43460195:43460330	ENSG00000100271.12	ENST00000331018.7,ENST00000439248.1,ENST00000266254.7,ENST00000440761.1
exon_skip_370208	22	43464415:43464596:43465641:43465850:43471479:43471596	43465641:43465850	ENSG00000100271.12	ENST00000331018.7,ENST00000266254.7
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENSG00000100271.12	ENST00000439248.1,ENST00000440761.1
exon_skip_370214	22	43465641:43465850:43471479:43471596:43475907:43475992	43471479:43471596	ENSG00000100271.12	ENST00000331018.7,ENST00000266254.7
exon_skip_370217	22	43471479:43471596:43475907:43475992:43485282:43485344	43475907:43475992	ENSG00000100271.12	ENST00000439248.1,ENST00000266254.7,ENST00000440761.1,ENST00000445824.1

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 TTLL1

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
ENST00000266254	43471479	43471596	3UTR-3CDS
ENST00000266254	43475907	43475992	3UTR-3UTR
ENST00000266254	43442415	43442579	Frame-shift
ENST00000266254	43465641	43465850	Frame-shift
ENST00000266254	43447806	43447893	In-frame
ENST00000266254	43455389	43455533	In-frame
ENST00000266254	43460195	43460330	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
ENST00000266254	43471479	43471596	3UTR-3CDS
ENST00000266254	43475907	43475992	3UTR-3UTR
ENST00000266254	43442415	43442579	Frame-shift
ENST00000266254	43465641	43465850	Frame-shift
ENST00000266254	43447806	43447893	In-frame
ENST00000266254	43455389	43455533	In-frame
ENST00000266254	43460195	43460330	In-frame

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Infer the effects of exon skipping event on protein functional features for TTLL1

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
ENST00000266254	1662	423	43460195	43460330	745	879	168	212
ENST00000266254	1662	423	43455389	43455533	989	1132	249	297
ENST00000266254	1662	423	43447806	43447893	1133	1219	297	326

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
ENST00000266254	1662	423	43460195	43460330	745	879	168	212
ENST00000266254	1662	423	43455389	43455533	989	1132	249	297
ENST00000266254	1662	423	43447806	43447893	1133	1219	297	326

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
O95922	168	212	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	168	212	194	194	Binding site	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	168	212	196	196	Binding site	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	168	212	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	168	212	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568
O95922	168	212	168	168	Natural variant	ID=VAR_052409;Note=S->L;Dbxref=dbSNP:rs6003030
O95922	168	212	181	184	Nucleotide binding	Note=ATP binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	249	297	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	249	297	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	249	297	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568
O95922	297	326	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	297	326	298	326	Alternative sequence	ID=VSP_011825;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12529303;Dbxref=PMID:12529303
O95922	297	326	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	297	326	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568

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
O95922	168	212	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	168	212	194	194	Binding site	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	168	212	196	196	Binding site	Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	168	212	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	168	212	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568
O95922	168	212	168	168	Natural variant	ID=VAR_052409;Note=S->L;Dbxref=dbSNP:rs6003030
O95922	168	212	181	184	Nucleotide binding	Note=ATP binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6ZT98
O95922	249	297	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	249	297	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	249	297	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568
O95922	297	326	60	423	Alternative sequence	ID=VSP_006672;Note=In isoform B. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11054573,ECO:0000303\|PubMed:12529303;Dbxref=PMID:11054573,PMID:12529303
O95922	297	326	298	326	Alternative sequence	ID=VSP_011825;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12529303;Dbxref=PMID:12529303
O95922	297	326	1	423	Chain	ID=PRO_0000212438;Note=Probable tubulin polyglutamylase TTLL1
O95922	297	326	1	367	Domain	Note=TTL;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00568

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SNVs in the skipped exons for TTLL1

- 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
LUSC	TCGA-37-5819-01	exon_skip_370208	43465642	43465850	43465699	43465699	Frame_Shift_Del	C	-	p.E89fs
LIHC	TCGA-DD-A3A0-01	exon_skip_370208	43465642	43465850	43465717	43465717	Frame_Shift_Del	T	-	p.R83fs
LIHC	TCGA-DD-A39Y-01	exon_skip_370208	43465642	43465850	43465728	43465728	Frame_Shift_Del	T	-	p.K79fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_370208	43465642	43465850	43465769	43465769	Frame_Shift_Del	A	-	p.F65fs
LIHC	TCGA-DD-A1EG-01	exon_skip_370214	43471480	43471596	43471484	43471484	Frame_Shift_Del	A	-	p.Y37fs
THYM	TCGA-ZB-A96B-01	exon_skip_370205	43460196	43460330	43460216	43460216	Nonsense_Mutation	G	T	p.Y206X

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

Depth of coverage in three exons

Mutation description

- 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
NCIH2066_LUNG	43442416	43442579	43442453	43442453	Missense_Mutation	A	T	p.S369T
HEC6_ENDOMETRIUM	43442416	43442579	43442488	43442488	Missense_Mutation	G	A	p.P357L
HS683_CENTRAL_NERVOUS_SYSTEM	43442416	43442579	43442501	43442501	Missense_Mutation	T	C	p.N353D
JHUEM1_ENDOMETRIUM	43442416	43442579	43442533	43442533	Missense_Mutation	A	T	p.I342N
RERFLCAD2_LUNG	43455390	43455533	43455424	43455424	Missense_Mutation	T	G	p.H286P
HEC108_ENDOMETRIUM	43455390	43455533	43455446	43455446	Missense_Mutation	T	C	p.S279G
FTC238_THYROID	43455390	43455533	43455460	43455460	Missense_Mutation	C	T	p.G274D
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	43455390	43455533	43455463	43455463	Missense_Mutation	C	T	p.R273H
DSH1_URINARY_TRACT	43455390	43455533	43455485	43455485	Missense_Mutation	G	A	p.R266W
OVMIU_OVARY	43455390	43455533	43455485	43455485	Missense_Mutation	G	A	p.R266W
YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	43455390	43455533	43455485	43455485	Missense_Mutation	G	A	p.R266W
LNCAPCLONEFGC_PROSTATE	43455390	43455533	43455497	43455497	Missense_Mutation	C	T	p.V262M
SNU1040_LARGE_INTESTINE	43460196	43460330	43460241	43460241	Missense_Mutation	C	T	p.R198H
NCIH838_LUNG	43465642	43465850	43465653	43465653	Missense_Mutation	T	C	p.Y104C
HCC2450_LUNG	43465642	43465850	43465659	43465659	Missense_Mutation	C	A	p.G102V
NCIH1770_LUNG	43471480	43471596	43471580	43471580	Missense_Mutation	C	A	p.V5L
NCIH2106_LUNG	43471480	43471596	43471580	43471580	Missense_Mutation	C	A	p.V5L
MDAPCA2B_PROSTATE	43455390	43455533	43455391	43455391	Splice_Site	G	A	p.A297V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TTLL1

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_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	GBM	rs5759125	chr22:43455432	G/A	1.68e-05
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	BRCA	rs1132079	chr22:43455531	A/G	1.64e-05
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	LGG	rs5759125	chr22:43455432	G/A	6.01e-19
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	LGG	rs1132079	chr22:43455531	A/G	4.82e-09
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	THYM	rs5759125	chr22:43455432	G/A	4.37e-04
exon_skip_370204	22	43447806:43447893:43455389:43455533:43459818:43459927	43455389:43455533	ENST00000439248.1,ENST00000440761.1,ENST00000266254.7	THCA	rs1132079	chr22:43455531	A/G	2.10e-03
exon_skip_370208	22	43464415:43464596:43465641:43465850:43471479:43471596	43465641:43465850	ENST00000331018.7,ENST00000266254.7	LGG	rs2076155	chr22:43465814	A/G	2.58e-05
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	GBM	rs2076161	chr22:43466247	G/C	7.81e-09
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	LGG	rs2076156	chr22:43466217	A/G	2.08e-09
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	PRAD	rs2076161	chr22:43466247	G/C	3.47e-11
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	SARC	rs2076161	chr22:43466247	G/C	9.10e-06
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	SARC	rs2076156	chr22:43466217	A/G	1.66e-04
exon_skip_370211	22	43465641:43465850:43466176:43466248:43471479:43471596	43466176:43466248	ENST00000439248.1,ENST00000440761.1	THYM	rs2076161	chr22:43466247	G/C	1.27e-05

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTLL1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTLL1

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RelatedDrugs for TTLL1

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

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RelatedDiseases for TTLL1

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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Gene summary for TTLL1

Exon skipping events across known transcript of Ensembl for TTLL1 from UCSC genome browser

Gene isoform structures and expression levels for TTLL1

Exon skipping events with PSIs in TCGA for TTLL1

Exon skipping events with PSIs in GTEx for TTLL1

Open reading frame (ORF) annotation in the exon skipping event for TTLL1

Infer the effects of exon skipping event on protein functional features for TTLL1

SNVs in the skipped exons for TTLL1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TTLL1

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTLL1

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTLL1

RelatedDrugs for TTLL1

RelatedDiseases for TTLL1