ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for LRRC41

Gene summary

Gene information	Gene symbol	LRRC41
	Gene ID	10489
	Gene name	leucine rich repeat containing 41
	Synonyms	MUF1\|PP7759
	Cytomap	1p34.1-p33
	Type of gene	protein-coding
	Description	leucine-rich repeat-containing protein 41MUF1 protein (MUF1)elongin BC-interacting leucine-rich repeat proteinprotein Muf1
	Modification date	20180523
	UniProtAcc	Q15345
	Context	PubMed: LRRC41 [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 LRRC41 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 LRRC41

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 LRRC41

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_26344	1	46744853:46744929:46745163:46745286:46745863:46745962	46745163:46745286	ENSG00000132128.12	ENST00000496156.1,ENST00000343304.6
exon_skip_26349	1	46745163:46745286:46745863:46745962:46746067:46746232	46745863:46745962	ENSG00000132128.12	ENST00000472710.1,ENST00000496156.1,ENST00000343304.6
exon_skip_26353	1	46745863:46745962:46746067:46746232:46746796:46746833	46746067:46746232	ENSG00000132128.12	ENST00000472710.1,ENST00000343304.6
exon_skip_26357	1	46746067:46746232:46746796:46747057:46751033:46752171	46746796:46747057	ENSG00000132128.12	ENST00000472710.1,ENST00000343304.6
exon_skip_26359	1	46746796:46747057:46751033:46752171:46763234:46763305	46751033:46752171	ENSG00000132128.12	ENST00000472710.1,ENST00000343304.6
exon_skip_26362	1	46751033:46752171:46763234:46763305:46763955:46764042	46763234:46763305	ENSG00000132128.12	ENST00000498402.1,ENST00000472710.1,ENST00000343304.6

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for LRRC41

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_26344	1	46744853:46744929:46745163:46745286:46745863:46745962	46745163:46745286	ENSG00000132128.12	ENST00000496156.1,ENST00000343304.6
exon_skip_26349	1	46745163:46745286:46745863:46745962:46746067:46746232	46745863:46745962	ENSG00000132128.12	ENST00000496156.1,ENST00000343304.6,ENST00000472710.1
exon_skip_26353	1	46745863:46745962:46746067:46746232:46746796:46746833	46746067:46746232	ENSG00000132128.12	ENST00000343304.6,ENST00000472710.1
exon_skip_26357	1	46746067:46746232:46746796:46747057:46751033:46752171	46746796:46747057	ENSG00000132128.12	ENST00000343304.6,ENST00000472710.1
exon_skip_26359	1	46746796:46747057:46751033:46752171:46763234:46763305	46751033:46752171	ENSG00000132128.12	ENST00000343304.6,ENST00000472710.1
exon_skip_26362	1	46751033:46752171:46763234:46763305:46763955:46764042	46763234:46763305	ENSG00000132128.12	ENST00000343304.6,ENST00000472710.1,ENST00000498402.1

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 LRRC41

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

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

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Infer the effects of exon skipping event on protein functional features for LRRC41

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 LRRC41

- 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.

LRRC41_KIRC_exon_skip_26359_psi_boxplot.png
boxplot

LRRC41_LGG_exon_skip_26359_psi_boxplot.png
boxplot

LRRC41_LIHC_exon_skip_26359_psi_boxplot.png
boxplot

LRRC41_PRAD_exon_skip_26359_psi_boxplot.png
boxplot

LRRC41_STAD_exon_skip_26359_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-A1EG-01	exon_skip_26349	46745864	46745962	46745887	46745887	Frame_Shift_Del	A	-	p.L667fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_26349	46745864	46745962	46745887	46745887	Frame_Shift_Del	A	-	p.L667fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_26357	46746797	46747057	46746829	46746829	Frame_Shift_Del	G	-	p.P575fs
BRCA	TCGA-AR-A1AQ-01	exon_skip_26357	46746797	46747057	46746855	46746855	Frame_Shift_Del	A	-	p.G567fs
COAD	TCGA-A6-6141-01	exon_skip_26357	46746797	46747057	46746971	46746972	Frame_Shift_Del	TG	-	p.528_528del
PRAD	TCGA-HC-7077-01	exon_skip_26359	46751034	46752171	46751117	46751117	Frame_Shift_Del	G	-	p.P471fs
LIHC	TCGA-DD-A39Y-01	exon_skip_26359	46751034	46752171	46751210	46751210	Frame_Shift_Del	A	-	p.L440fs
LIHC	TCGA-DD-A3A0-01	exon_skip_26359	46751034	46752171	46751381	46751381	Frame_Shift_Del	G	-	p.P383fs
LIHC	TCGA-DD-A3A0-01	exon_skip_26359	46751034	46752171	46752129	46752129	Frame_Shift_Del	A	-	p.S134fs
COAD	TCGA-A6-5660-01	exon_skip_26359	46751034	46752171	46751228	46751229	Frame_Shift_Ins	-	C	p.E434fs
KIRC	TCGA-A3-3308-01	exon_skip_26359	46751034	46752171	46751494	46751495	Frame_Shift_Ins	-	G	p.R345fs
LGG	TCGA-DU-6392-01	exon_skip_26359	46751034	46752171	46751494	46751495	Frame_Shift_Ins	-	G	p.R345fs
STAD	TCGA-BR-8081-01	exon_skip_26359	46751034	46752171	46751495	46751496	Frame_Shift_Ins	-	G	p.P345fs
BLCA	TCGA-FD-A62O-01	exon_skip_26357	46746797	46747057	46747009	46747009	Nonsense_Mutation	G	C	p.S515*
BLCA	TCGA-GU-A42R-01	exon_skip_26359	46751034	46752171	46751604	46751604	Nonsense_Mutation	C	A	p.E309*
BLCA	TCGA-BT-A20U-01	exon_skip_26362	46763235	46763305	46763283	46763283	Nonsense_Mutation	C	T	p.W103*
BLCA	TCGA-GU-A42R-01	exon_skip_26344	46745164	46745286	46745288	46745288	Splice_Site	T	C	p.E674_splice
SKCM	TCGA-D3-A51G-06	exon_skip_26362	46763235	46763305	46763234	46763234	Splice_Site	C	T	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-A3-3308-01
	Cancer type: KIRC
	ESID: exon_skip_26359
	Skipped exon start: 46751034
	Skipped exon end: 46752171
	Mutation start: 46751494
	Mutation end: 46751495
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: G
	AAchange: p.R345fs
exon_skip_10918_KIRC_TCGA-A3-3308-01.png
exon_skip_26359_KIRC_TCGA-A3-3308-01.png
exon_skip_348822_KIRC_TCGA-A3-3308-01.png
exon_skip_43714_KIRC_TCGA-A3-3308-01.png
exon_skip_93534_KIRC_TCGA-A3-3308-01.png
	Sample: TCGA-DU-6392-01
	Cancer type: LGG
	ESID: exon_skip_26359
	Skipped exon start: 46751034
	Skipped exon end: 46752171
	Mutation start: 46751494
	Mutation end: 46751495
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: G
	AAchange: p.R345fs
exon_skip_106946_LGG_TCGA-DU-6392-01.png
exon_skip_114879_LGG_TCGA-DU-6392-01.png
exon_skip_120606_LGG_TCGA-DU-6392-01.png
exon_skip_130417_LGG_TCGA-DU-6392-01.png
exon_skip_138304_LGG_TCGA-DU-6392-01.png
exon_skip_143841_LGG_TCGA-DU-6392-01.png
exon_skip_143843_LGG_TCGA-DU-6392-01.png
exon_skip_145922_LGG_TCGA-DU-6392-01.png
exon_skip_155098_LGG_TCGA-DU-6392-01.png
exon_skip_26359_LGG_TCGA-DU-6392-01.png
exon_skip_290929_LGG_TCGA-DU-6392-01.png
exon_skip_297109_LGG_TCGA-DU-6392-01.png
exon_skip_33957_LGG_TCGA-DU-6392-01.png
exon_skip_343170_LGG_TCGA-DU-6392-01.png
exon_skip_354191_LGG_TCGA-DU-6392-01.png
exon_skip_367235_LGG_TCGA-DU-6392-01.png
exon_skip_423495_LGG_TCGA-DU-6392-01.png
exon_skip_423582_LGG_TCGA-DU-6392-01.png
exon_skip_430528_LGG_TCGA-DU-6392-01.png
exon_skip_432953_LGG_TCGA-DU-6392-01.png
exon_skip_436589_LGG_TCGA-DU-6392-01.png
exon_skip_438105_LGG_TCGA-DU-6392-01.png
exon_skip_438310_LGG_TCGA-DU-6392-01.png
exon_skip_442085_LGG_TCGA-DU-6392-01.png
exon_skip_481046_LGG_TCGA-DU-6392-01.png
exon_skip_484517_LGG_TCGA-DU-6392-01.png
exon_skip_502736_LGG_TCGA-DU-6392-01.png
exon_skip_512614_LGG_TCGA-DU-6392-01.png
exon_skip_7508_LGG_TCGA-DU-6392-01.png
exon_skip_7509_LGG_TCGA-DU-6392-01.png
exon_skip_79467_LGG_TCGA-DU-6392-01.png
exon_skip_85050_LGG_TCGA-DU-6392-01.png
exon_skip_95050_LGG_TCGA-DU-6392-01.png
exon_skip_95053_LGG_TCGA-DU-6392-01.png
	Sample: TCGA-HC-7077-01
	Cancer type: PRAD
	ESID: exon_skip_26359
	Skipped exon start: 46751034
	Skipped exon end: 46752171
	Mutation start: 46751117
	Mutation end: 46751117
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P471fs
exon_skip_135418_PRAD_TCGA-HC-7077-01.png
exon_skip_26359_PRAD_TCGA-HC-7077-01.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
SKUT1_SOFT_TISSUE	46751034	46752171	46751495	46751495	Frame_Shift_Del	G	-	p.P345fs
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46751034	46752171	46752129	46752129	Frame_Shift_Del	A	-	p.S134fs
SNU349_KIDNEY	46751034	46752171	46752129	46752129	Frame_Shift_Del	A	-	p.S134fs
RKO_LARGE_INTESTINE	46751034	46752171	46752129	46752129	Frame_Shift_Del	A	-	p.S134fs
MFE319_ENDOMETRIUM	46751034	46752171	46752129	46752129	Frame_Shift_Del	A	-	p.S134fs
NK92MI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46745164	46745286	46745206	46745206	Missense_Mutation	T	C	p.N701D
BICR18_UPPER_AERODIGESTIVE_TRACT	46745164	46745286	46745244	46745244	Missense_Mutation	G	A	p.A688V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46745164	46745286	46745244	46745244	Missense_Mutation	G	A	p.A688V
HEC6_ENDOMETRIUM	46745864	46745962	46745915	46745915	Missense_Mutation	C	T	p.A657T
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46746068	46746232	46746191	46746191	Missense_Mutation	C	T	p.A600T
NCIH835_LUNG	46746797	46747057	46746835	46746836	Missense_Mutation	CC	AA	p.G573L
SNU1040_LARGE_INTESTINE	46746797	46747057	46746935	46746935	Missense_Mutation	T	C	p.T540A
EW16_BONE	46746797	46747057	46746985	46746985	Missense_Mutation	C	T	p.R523H
SF295_CENTRAL_NERVOUS_SYSTEM	46746797	46747057	46746992	46746992	Missense_Mutation	G	A	p.R521C
NK92MI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46746797	46747057	46747018	46747018	Missense_Mutation	C	T	p.R512Q
VMCUB1_URINARY_TRACT	46746797	46747057	46747048	46747048	Missense_Mutation	G	C	p.S502C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46751034	46752171	46751108	46751108	Missense_Mutation	G	A	p.T474I
RXF393_KIDNEY	46751034	46752171	46751118	46751119	Missense_Mutation	GA	AC	p.P471S
NCIH1651_LUNG	46751034	46752171	46751322	46751322	Missense_Mutation	G	A	p.R403C
NB5_AUTONOMIC_GANGLIA	46751034	46752171	46751327	46751327	Missense_Mutation	C	T	p.R401H
NY_BONE	46751034	46752171	46751327	46751327	Missense_Mutation	C	T	p.R401H
EFO21_OVARY	46751034	46752171	46751328	46751328	Missense_Mutation	G	A	p.R401C
LS411N_LARGE_INTESTINE	46751034	46752171	46751328	46751328	Missense_Mutation	G	A	p.R401C
SNU1040_LARGE_INTESTINE	46751034	46752171	46751361	46751361	Missense_Mutation	G	A	p.R390C
CHLA15_AUTONOMIC_GANGLIA	46751034	46752171	46751418	46751418	Missense_Mutation	T	C	p.T371A
NCIH1648_LUNG	46751034	46752171	46751444	46751444	Missense_Mutation	G	A	p.A362V
HGC27_STOMACH	46751034	46752171	46751447	46751447	Missense_Mutation	G	T	p.P361Q
LS123_LARGE_INTESTINE	46751034	46752171	46751634	46751634	Missense_Mutation	C	A	p.A299S
RL952_ENDOMETRIUM	46751034	46752171	46751711	46751711	Missense_Mutation	C	A	p.R273L
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46751034	46752171	46751777	46751777	Missense_Mutation	G	A	p.A251V
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46751034	46752171	46751804	46751804	Missense_Mutation	A	C	p.L242R
UBLC1_URINARY_TRACT	46751034	46752171	46751871	46751871	Missense_Mutation	G	C	p.Q220E
UBLC1_URINARY_TRACT	46751034	46752171	46751929	46751929	Missense_Mutation	G	T	p.F200L
SNU1040_LARGE_INTESTINE	46751034	46752171	46751975	46751975	Missense_Mutation	C	T	p.R185H
HEC108_ENDOMETRIUM	46751034	46752171	46752074	46752074	Missense_Mutation	T	C	p.Q152R
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	46751034	46752171	46752080	46752080	Missense_Mutation	C	T	p.C150Y
HEC108_ENDOMETRIUM	46751034	46752171	46752113	46752113	Missense_Mutation	C	A	p.G139V
GP2D_LARGE_INTESTINE	46751034	46752171	46752152	46752152	Missense_Mutation	G	A	p.A126V
GP5D_LARGE_INTESTINE	46751034	46752171	46752152	46752152	Missense_Mutation	G	A	p.A126V
MDAPCA2B_PROSTATE	46745864	46745962	46745867	46745867	Nonsense_Mutation	G	A	p.Q673*
UBLC1_URINARY_TRACT	46751034	46752171	46751810	46751810	Nonsense_Mutation	G	T	p.S240*
HEC59_ENDOMETRIUM	46751034	46752171	46752075	46752075	Nonsense_Mutation	G	A	p.Q152*
BICR18_UPPER_AERODIGESTIVE_TRACT	46763235	46763305	46763235	46763235	Splice_Site	T	C	p.E119E
BICR18_UPPER_AERODIGESTIVE_TRACT	46763235	46763305	46763304	46763304	Splice_Site	G	A	p.G96G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRRC41

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 LRRC41

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRC41

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RelatedDrugs for LRRC41

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 LRRC41

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 LRRC41

Exon skipping events across known transcript of Ensembl for LRRC41 from UCSC genome browser

Gene isoform structures and expression levels for LRRC41

Exon skipping events with PSIs in TCGA for LRRC41

Exon skipping events with PSIs in GTEx for LRRC41

Open reading frame (ORF) annotation in the exon skipping event for LRRC41

Infer the effects of exon skipping event on protein functional features for LRRC41

SNVs in the skipped exons for LRRC41

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRRC41

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRC41

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRC41

RelatedDrugs for LRRC41

RelatedDiseases for LRRC41