ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for IFT140

Gene summary

Gene information	Gene symbol	IFT140
	Gene ID	9742
	Gene name	intraflagellar transport 140
	Synonyms	MZSDS\|RP80\|SRTD9\|WDTC2\|c305C8.4\|c380F5.1\|gs114
	Cytomap	16p13.3
	Type of gene	protein-coding
	Description	intraflagellar transport protein 140 homologWD and tetratricopeptide repeats protein 2intraflagellar transport 140 homolog
	Modification date	20180527
	UniProtAcc	Q96RY7
	Context	PubMed: IFT140 [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 IFT140 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 IFT140

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 IFT140

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_140677	16	1560430:1561151:1568216:1568358:1569881:1570039	1568216:1568358	ENSG00000187535.9	ENST00000397417.2,ENST00000565298.1,ENST00000426508.2,ENST00000361339.5
exon_skip_140682	16	1575887:1576078:1576619:1576797:1607935:1608135	1576619:1576797	ENSG00000187535.9	ENST00000426508.2
exon_skip_140683	16	1575887:1576078:1576733:1576797:1607935:1608135	1576733:1576797	ENSG00000187535.9	ENST00000397417.2
exon_skip_140684	16	1613997:1614163:1616161:1616292:1618217:1618335	1616161:1616292	ENSG00000187535.9	ENST00000397417.2,ENST00000565298.1,ENST00000439987.2,ENST00000426508.2
exon_skip_140687	16	1616161:1616292:1618217:1618335:1621407:1621535	1618217:1618335	ENSG00000187535.9	ENST00000397417.2,ENST00000565298.1,ENST00000439987.2,ENST00000426508.2
exon_skip_140694	16	1618217:1618335:1621407:1621535:1630759:1630851	1621407:1621535	ENSG00000187535.9	ENST00000397417.2,ENST00000565298.1,ENST00000439987.2,ENST00000426508.2
exon_skip_140698	16	1630759:1630851:1633314:1633387:1634217:1634264	1633314:1633387	ENSG00000187535.9	ENST00000397417.2,ENST00000565298.1,ENST00000439987.2,ENST00000426508.2
exon_skip_140700	16	1637198:1637305:1637933:1638025:1639605:1639781	1637933:1638025	ENSG00000187535.9	ENST00000439987.2,ENST00000426508.2
exon_skip_140703	16	1637933:1638025:1639605:1639781:1642176:1642319	1639605:1639781	ENSG00000187535.9	ENST00000439987.2,ENST00000426508.2
exon_skip_140704	16	1639605:1639781:1642176:1642319:1642467:1642589	1642176:1642319	ENSG00000187535.9	ENST00000439987.2,ENST00000426508.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for IFT140

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_140677	16	1560430:1561151:1568216:1568358:1569881:1570039	1568216:1568358	ENSG00000187535.9	ENST00000361339.5,ENST00000426508.2,ENST00000565298.1,ENST00000397417.2
exon_skip_140682	16	1575887:1576078:1576619:1576797:1607935:1608135	1576619:1576797	ENSG00000187535.9	ENST00000426508.2
exon_skip_140683	16	1575887:1576078:1576733:1576797:1607935:1608135	1576733:1576797	ENSG00000187535.9	ENST00000397417.2
exon_skip_140684	16	1613997:1614163:1616161:1616292:1618217:1618335	1616161:1616292	ENSG00000187535.9	ENST00000426508.2,ENST00000565298.1,ENST00000397417.2,ENST00000439987.2
exon_skip_140687	16	1616161:1616292:1618217:1618335:1621407:1621535	1618217:1618335	ENSG00000187535.9	ENST00000426508.2,ENST00000565298.1,ENST00000397417.2,ENST00000439987.2
exon_skip_140694	16	1618217:1618335:1621407:1621535:1630759:1630851	1621407:1621535	ENSG00000187535.9	ENST00000426508.2,ENST00000565298.1,ENST00000397417.2,ENST00000439987.2
exon_skip_140698	16	1630759:1630851:1633314:1633387:1634217:1634264	1633314:1633387	ENSG00000187535.9	ENST00000426508.2,ENST00000565298.1,ENST00000397417.2,ENST00000439987.2
exon_skip_140700	16	1637198:1637305:1637933:1638025:1639605:1639781	1637933:1638025	ENSG00000187535.9	ENST00000426508.2,ENST00000439987.2
exon_skip_140703	16	1637933:1638025:1639605:1639781:1642176:1642319	1639605:1639781	ENSG00000187535.9	ENST00000426508.2,ENST00000439987.2
exon_skip_140704	16	1639605:1639781:1642176:1642319:1642467:1642589	1642176:1642319	ENSG00000187535.9	ENST00000426508.2,ENST00000439987.2

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 IFT140

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
ENST00000426508	1568216	1568358	Frame-shift
ENST00000426508	1576619	1576797	Frame-shift
ENST00000426508	1616161	1616292	Frame-shift
ENST00000426508	1618217	1618335	Frame-shift
ENST00000426508	1621407	1621535	Frame-shift
ENST00000426508	1633314	1633387	Frame-shift
ENST00000426508	1637933	1638025	Frame-shift
ENST00000426508	1639605	1639781	Frame-shift
ENST00000426508	1642176	1642319	Frame-shift

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
ENST00000426508	1568216	1568358	Frame-shift
ENST00000426508	1576619	1576797	Frame-shift
ENST00000426508	1616161	1616292	Frame-shift
ENST00000426508	1618217	1618335	Frame-shift
ENST00000426508	1621407	1621535	Frame-shift
ENST00000426508	1633314	1633387	Frame-shift
ENST00000426508	1637933	1638025	Frame-shift
ENST00000426508	1639605	1639781	Frame-shift
ENST00000426508	1642176	1642319	Frame-shift

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Infer the effects of exon skipping event on protein functional features for IFT140

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

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

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 IFT140

- 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-DD-A1EG-01	exon_skip_140682	1576620	1576797	1576722	1576722	Frame_Shift_Del	C	-	p.G825fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_140682	1576620	1576797	1576754	1576754	Frame_Shift_Del	G	-	p.Q815fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_140683	1576734	1576797	1576754	1576754	Frame_Shift_Del	G	-	p.Q815fs
BRCA	TCGA-BH-A0AY-01	exon_skip_140684	1616162	1616292	1616239	1616240	Frame_Shift_Del	TG	-	p.T608fs
LIHC	TCGA-DD-A1EG-01	exon_skip_140687	1618218	1618335	1618276	1618276	Frame_Shift_Del	C	-	p.G571fs
UCEC	TCGA-B5-A11R-01	exon_skip_140703	1639606	1639781	1639743	1639743	Nonsense_Mutation	G	A	p.Q225*
ACC	TCGA-OR-A5KZ-01	exon_skip_140704	1642177	1642319	1642210	1642210	Nonsense_Mutation	C	A	p.E201*
ESCA	TCGA-JY-A6FG-01	exon_skip_140694	1621408	1621535	1621406	1621406	Splice_Site	A	G	.
ESCA	TCGA-JY-A6FG-01	exon_skip_140694	1621408	1621535	1621406	1621406	Splice_Site	A	G	e12+2

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-JY-A6FG-01
	Cancer type: ESCA
	ESID: exon_skip_140694
	Skipped exon start: 1621408
	Skipped exon end: 1621535
	Mutation start: 1621406
	Mutation end: 1621406
	Mutation type: Splice_Site
	Reference seq: A
	Mutation seq: G
	AAchange: .
	Sample: TCGA-JY-A6FG-01
	Cancer type: ESCA
	ESID: exon_skip_140694
	Skipped exon start: 1621408
	Skipped exon end: 1621535
	Mutation start: 1621406
	Mutation end: 1621406
	Mutation type: Splice_Site
	Reference seq: A
	Mutation seq: G
	AAchange: e12+2
exon_skip_140694_ESCA_TCGA-JY-A6FG-01.png
exon_skip_384278_ESCA_TCGA-JY-A6FG-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
SNU1040_LARGE_INTESTINE	1568217	1568358	1568273	1568273	Missense_Mutation	C	T	p.G1376R
SNU1040_LARGE_INTESTINE	1568217	1568358	1568279	1568279	Missense_Mutation	G	A	p.R1374C
HCT116_LARGE_INTESTINE	1568217	1568358	1568332	1568332	Missense_Mutation	G	A	p.S1356F
SNU1040_LARGE_INTESTINE	1568217	1568358	1568338	1568338	Missense_Mutation	T	C	p.K1354R
QIMRWIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1576620	1576797	1576681	1576681	Missense_Mutation	G	A	p.A839V
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1576620	1576797	1576709	1576709	Missense_Mutation	C	T	p.A830T
HEC59_ENDOMETRIUM	1576620	1576797	1576734	1576734	Missense_Mutation	C	A	p.K821N
HEC59_ENDOMETRIUM	1576734	1576797	1576734	1576734	Missense_Mutation	C	A	p.K821N
NCIH1105_LUNG	1576620	1576797	1576771	1576771	Missense_Mutation	C	A	p.R809L
NCIH1105_LUNG	1576734	1576797	1576771	1576771	Missense_Mutation	C	A	p.R809L
SNU175_LARGE_INTESTINE	1576620	1576797	1576774	1576774	Missense_Mutation	G	A	p.A808V
SNU175_LARGE_INTESTINE	1576734	1576797	1576774	1576774	Missense_Mutation	G	A	p.A808V
SNU1040_LARGE_INTESTINE	1616162	1616292	1616241	1616241	Missense_Mutation	T	C	p.T608A
LIM1215_LARGE_INTESTINE	1618218	1618335	1618235	1618235	Missense_Mutation	T	C	p.S585G
MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1618218	1618335	1618261	1618261	Missense_Mutation	C	T	p.R576Q
L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1618218	1618335	1618271	1618271	Missense_Mutation	C	A	p.A573S
M1203273_SKIN	1618218	1618335	1618280	1618281	Missense_Mutation	CC	TT	p.G570R
HCC4006_LUNG	1618218	1618335	1618282	1618282	Missense_Mutation	A	G	p.V569A
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1618218	1618335	1618289	1618289	Missense_Mutation	G	A	p.P567S
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1618218	1618335	1618325	1618325	Missense_Mutation	C	T	p.A555T
WIL2NS_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1621408	1621535	1621411	1621411	Missense_Mutation	C	T	p.R550Q
SNUC2A_LARGE_INTESTINE	1621408	1621535	1621465	1621465	Missense_Mutation	T	C	p.N532S
SNUC2B_LARGE_INTESTINE	1621408	1621535	1621465	1621465	Missense_Mutation	T	C	p.N532S
SQ1_LUNG	1633315	1633387	1633342	1633342	Missense_Mutation	G	T	p.L469I
TCYIK_CERVIX	1633315	1633387	1633342	1633342	Missense_Mutation	G	T	p.L469I
CAL12T_LUNG	1633315	1633387	1633345	1633345	Missense_Mutation	C	T	p.E468K
WM88_SKIN	1637934	1638025	1638004	1638004	Missense_Mutation	C	T	p.G278S
SCMCRM2_SOFT_TISSUE	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
JHOC5_OVARY	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
MCAS_OVARY	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
SNU308_BILIARY_TRACT	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
TM31_CENTRAL_NERVOUS_SYSTEM	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
LC1F_LUNG	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
LC1SQSF_LUNG	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
CAR1_LARGE_INTESTINE	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
LC1SQ_LUNG	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
NO10_CENTRAL_NERVOUS_SYSTEM	1639606	1639781	1639644	1639644	Missense_Mutation	T	A	p.T258S
HEC59_ENDOMETRIUM	1639606	1639781	1639761	1639761	Missense_Mutation	C	T	p.E219K
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1642177	1642319	1642286	1642286	Missense_Mutation	G	C	p.S175R

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for IFT140

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 IFT140

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for IFT140

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RelatedDrugs for IFT140

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 IFT140

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
IFT140	C1849437	Mainzer-Saldino Disease	2	ORPHANET;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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Gene summary for IFT140

Exon skipping events across known transcript of Ensembl for IFT140 from UCSC genome browser

Gene isoform structures and expression levels for IFT140

Exon skipping events with PSIs in TCGA for IFT140

Exon skipping events with PSIs in GTEx for IFT140

Open reading frame (ORF) annotation in the exon skipping event for IFT140

Infer the effects of exon skipping event on protein functional features for IFT140

SNVs in the skipped exons for IFT140

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for IFT140

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for IFT140

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for IFT140

RelatedDrugs for IFT140

RelatedDiseases for IFT140