ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for LZTFL1

Gene summary

Gene information	Gene symbol	LZTFL1
	Gene ID	54585
	Gene name	leucine zipper transcription factor like 1
	Synonyms	BBS17
	Cytomap	3p21.31
	Type of gene	protein-coding
	Description	leucine zipper transcription factor-like protein 1
	Modification date	20180519
	UniProtAcc	Q9NQ48
	Context	PubMed: LZTFL1 [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 LZTFL1 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 LZTFL1

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 LZTFL1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_382805	3	45867793:45867824:45868847:45868951:45869930:45870065	45868847:45868951	ENSG00000163818.12	ENST00000440576.2,ENST00000536047.1,ENST00000411866.1,ENST00000296135.6,ENST00000418700.1,ENST00000469874.1
exon_skip_382807	3	45869930:45870107:45872404:45872482:45872564:45872630	45872404:45872482	ENSG00000163818.12	ENST00000536047.1,ENST00000411866.1,ENST00000296135.6,ENST00000418700.1,ENST00000448111.1,ENST00000539217.1
exon_skip_382808	3	45872437:45872482:45872564:45872630:45874541:45874613	45872564:45872630	ENSG00000163818.12	ENST00000536047.1,ENST00000411866.1,ENST00000490463.1,ENST00000296135.6,ENST00000418700.1,ENST00000448111.1,ENST00000539217.1
exon_skip_382810	3	45877161:45877276:45879418:45879539:45883480:45883493	45879418:45879539	ENSG00000163818.12	ENST00000445698.1
exon_skip_382811	3	45877161:45877276:45879418:45879543:45883480:45883493	45879418:45879543	ENSG00000163818.12	ENST00000495864.1,ENST00000480156.1
exon_skip_382812	3	45877161:45877276:45879418:45879543:45896477:45896566	45879418:45879543	ENSG00000163818.12	ENST00000536047.1,ENST00000418700.1
exon_skip_382813	3	45879432:45879543:45896477:45896566:45954611:45954669	45896477:45896566	ENSG00000163818.12	ENST00000536047.1,ENST00000418700.1
exon_skip_382815	3	45896477:45896566:45900431:45900508:45954611:45954669	45900431:45900508	ENSG00000163818.12	ENST00000472635.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for LZTFL1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_382805	3	45867793:45867824:45868847:45868951:45869930:45870065	45868847:45868951	ENSG00000163818.12	ENST00000296135.6,ENST00000418700.1,ENST00000536047.1,ENST00000411866.1,ENST00000469874.1,ENST00000440576.2
exon_skip_382807	3	45869930:45870107:45872404:45872482:45872564:45872630	45872404:45872482	ENSG00000163818.12	ENST00000296135.6,ENST00000418700.1,ENST00000536047.1,ENST00000448111.1,ENST00000539217.1,ENST00000411866.1
exon_skip_382808	3	45872437:45872482:45872564:45872630:45874541:45874613	45872564:45872630	ENSG00000163818.12	ENST00000296135.6,ENST00000418700.1,ENST00000536047.1,ENST00000448111.1,ENST00000539217.1,ENST00000411866.1,ENST00000490463.1
exon_skip_382810	3	45877161:45877276:45879418:45879539:45883480:45883493	45879418:45879539	ENSG00000163818.12	ENST00000445698.1
exon_skip_382811	3	45877161:45877276:45879418:45879543:45883480:45883493	45879418:45879543	ENSG00000163818.12	ENST00000495864.1,ENST00000480156.1
exon_skip_382812	3	45877161:45877276:45879418:45879543:45896477:45896566	45879418:45879543	ENSG00000163818.12	ENST00000418700.1,ENST00000536047.1
exon_skip_382813	3	45879432:45879543:45896477:45896566:45954611:45954669	45896477:45896566	ENSG00000163818.12	ENST00000418700.1,ENST00000536047.1
exon_skip_382815	3	45896477:45896566:45900431:45900508:45954611:45954669	45900431:45900508	ENSG00000163818.12	ENST00000472635.1

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 LZTFL1

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
ENST00000296135	45868847	45868951	Frame-shift
ENST00000296135	45872404	45872482	In-frame
ENST00000296135	45872564	45872630	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
ENST00000296135	45868847	45868951	Frame-shift
ENST00000296135	45872404	45872482	In-frame
ENST00000296135	45872564	45872630	In-frame

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Infer the effects of exon skipping event on protein functional features for LZTFL1

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
ENST00000296135	4090	299	45872564	45872630	632	697	152	174
ENST00000296135	4090	299	45872404	45872482	698	775	174	200

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
ENST00000296135	4090	299	45872564	45872630	632	697	152	174
ENST00000296135	4090	299	45872404	45872482	698	775	174	200

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
Q9NQ48	152	174	1	299	Chain	ID=PRO_0000318757;Note=Leucine zipper transcription factor-like protein 1
Q9NQ48	152	174	96	296	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9NQ48	152	174	152	152	Natural variant	ID=VAR_038877;Note=K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15489334;Dbxref=dbSNP:rs17855512,PMID:15489334
Q9NQ48	152	174	145	299	Region	Note=Interaction with BSS9
Q9NQ48	174	200	1	299	Chain	ID=PRO_0000318757;Note=Leucine zipper transcription factor-like protein 1
Q9NQ48	174	200	96	296	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9NQ48	174	200	145	299	Region	Note=Interaction with BSS9

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
Q9NQ48	152	174	1	299	Chain	ID=PRO_0000318757;Note=Leucine zipper transcription factor-like protein 1
Q9NQ48	152	174	96	296	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9NQ48	152	174	152	152	Natural variant	ID=VAR_038877;Note=K->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15489334;Dbxref=dbSNP:rs17855512,PMID:15489334
Q9NQ48	152	174	145	299	Region	Note=Interaction with BSS9
Q9NQ48	174	200	1	299	Chain	ID=PRO_0000318757;Note=Leucine zipper transcription factor-like protein 1
Q9NQ48	174	200	96	296	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9NQ48	174	200	145	299	Region	Note=Interaction with BSS9

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SNVs in the skipped exons for LZTFL1

- 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.

LZTFL1_SKCM_exon_skip_382808_psi_boxplot.png
boxplot

LZTFL1_THYM_exon_skip_382813_psi_boxplot.png
boxplot

- 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-DD-A39Y-01	exon_skip_382807	45872405	45872482	45872444	45872444	Frame_Shift_Del	T	-	p.K187fs
SKCM	TCGA-DA-A1I8-06	exon_skip_382808	45872565	45872630	45872564	45872564	Splice_Site	C	G	.
BRCA	TCGA-D8-A1JJ-01	exon_skip_382810	45879419	45879539	45879417	45879417	Splice_Site	A	C	e2+2
BRCA	TCGA-D8-A1JJ-01	exon_skip_382811 exon_skip_382812	45879419	45879543	45879417	45879417	Splice_Site	A	C	e2+2
THYM	TCGA-XU-AAXX-01	exon_skip_382813	45896478	45896566	45896567	45896567	Splice_Site	C	A	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-XU-AAXX-01
	Cancer type: THYM
	ESID: exon_skip_382813
	Skipped exon start: 45896478
	Skipped exon end: 45896566
	Mutation start: 45896567
	Mutation end: 45896567
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: .
exon_skip_382813_THYM_TCGA-XU-AAXX-01.png
	Sample: TCGA-DA-A1I8-06
	Cancer type: SKCM
	ESID: exon_skip_382808
	Skipped exon start: 45872565
	Skipped exon end: 45872630
	Mutation start: 45872564
	Mutation end: 45872564
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: G
	AAchange: .
exon_skip_382808_SKCM_TCGA-DA-A1I8-06.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
NCIH661_LUNG	45868848	45868951	45868907	45868907	Missense_Mutation	C	A	p.M274I
EFO21_OVARY	45872405	45872482	45872412	45872412	Missense_Mutation	T	C	p.N198S
SKHEP1_LIVER	45872405	45872482	45872449	45872449	Missense_Mutation	C	T	p.E186K
TGBC24TKB_BILIARY_TRACT	45872405	45872482	45872472	45872472	Missense_Mutation	G	A	p.A178V
BICR18_UPPER_AERODIGESTIVE_TRACT	45872565	45872630	45872612	45872612	Missense_Mutation	C	G	p.E159Q
JHUEM7_ENDOMETRIUM	45872565	45872630	45872625	45872625	Missense_Mutation	A	C	p.I154M
U251MG_CENTRAL_NERVOUS_SYSTEM	45879419	45879543	45879435	45879435	Missense_Mutation	C	T	p.D38N
U251MG_CENTRAL_NERVOUS_SYSTEM	45879419	45879539	45879435	45879435	Missense_Mutation	C	T	p.D38N
KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879543	45879482	45879482	Missense_Mutation	C	T	p.R22H
KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879539	45879482	45879482	Missense_Mutation	C	T	p.R22H
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879543	45879482	45879482	Missense_Mutation	C	T	p.R22H
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879539	45879482	45879482	Missense_Mutation	C	T	p.R22H
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879543	45879492	45879492	Missense_Mutation	G	A	p.R19C
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	45879419	45879539	45879492	45879492	Missense_Mutation	G	A	p.R19C
OUMS23_LARGE_INTESTINE	45879419	45879543	45879534	45879534	Missense_Mutation	C	T	p.G5S
OUMS23_LARGE_INTESTINE	45879419	45879539	45879534	45879534	Missense_Mutation	C	T	p.G5S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LZTFL1

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

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LZTFL1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LZTFL1

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RelatedDrugs for LZTFL1

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 LZTFL1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
LZTFL1	C3714980	BARDET-BIEDL SYNDROME 17	1	UNIPROT

	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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