ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for KLHL3

Gene summary

Gene information	Gene symbol	KLHL3
	Gene ID	26249
	Gene name	kelch like family member 3
	Synonyms	PHA2D
	Cytomap	5q31.2
	Type of gene	protein-coding
	Description	kelch-like protein 3
	Modification date	20180527
	UniProtAcc	Q9UH77
	Context	PubMed: KLHL3 [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
KLHL3	GO:0006511	ubiquitin-dependent protein catabolic process	23453970\|23576762
KLHL3	GO:0016567	protein ubiquitination	23453970
KLHL3	GO:0070936	protein K48-linked ubiquitination	23576762

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Exon skipping events across known transcript of Ensembl for KLHL3 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 KLHL3

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 KLHL3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_444438	5	136963985:136964126:136969725:136969854:136974641:136974839	136969725:136969854	ENSG00000146021.10	ENST00000506873.1
exon_skip_444440	5	136969732:136969854:136972982:136973084:136974641:136974839	136972982:136973084	ENSG00000146021.10	ENST00000309755.4,ENST00000506491.1,ENST00000508657.1
exon_skip_444441	5	137027973:137028136:137033975:137034097:137045438:137045545	137033975:137034097	ENSG00000146021.10	ENST00000309755.4,ENST00000394937.3,ENST00000505853.1,ENST00000508657.1
exon_skip_444443	5	137033975:137034097:137045438:137045545:137056153:137056273	137045438:137045545	ENSG00000146021.10	ENST00000309755.4,ENST00000394937.3,ENST00000508657.1
exon_skip_444444	5	137045438:137045545:137056153:137056273:137071321:137071431	137056153:137056273	ENSG00000146021.10	ENST00000309755.4,ENST00000512977.1,ENST00000394937.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for KLHL3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_444438	5	136963985:136964126:136969725:136969854:136974641:136974839	136969725:136969854	ENSG00000146021.10	ENST00000506873.1
exon_skip_444440	5	136969732:136969854:136972982:136973084:136974641:136974839	136972982:136973084	ENSG00000146021.10	ENST00000506491.1,ENST00000508657.1,ENST00000309755.4
exon_skip_444441	5	137027973:137028136:137033975:137034097:137045438:137045545	137033975:137034097	ENSG00000146021.10	ENST00000508657.1,ENST00000309755.4,ENST00000505853.1,ENST00000394937.3
exon_skip_444443	5	137033975:137034097:137045438:137045545:137056153:137056273	137045438:137045545	ENSG00000146021.10	ENST00000508657.1,ENST00000309755.4,ENST00000394937.3
exon_skip_444444	5	137045438:137045545:137056153:137056273:137071321:137071431	137056153:137056273	ENSG00000146021.10	ENST00000309755.4,ENST00000394937.3,ENST00000512977.1

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 KLHL3

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
ENST00000309755	137033975	137034097	Frame-shift
ENST00000309755	137045438	137045545	Frame-shift
ENST00000309755	136972982	136973084	In-frame
ENST00000309755	137056153	137056273	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
ENST00000309755	137033975	137034097	Frame-shift
ENST00000309755	137045438	137045545	Frame-shift
ENST00000309755	136972982	136973084	In-frame
ENST00000309755	137056153	137056273	In-frame

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Infer the effects of exon skipping event on protein functional features for KLHL3

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
ENST00000309755	6823	587	137056153	137056273	459	578	5	44
ENST00000309755	6823	587	136972982	136973084	1664	1765	406	440

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
ENST00000309755	6823	587	137056153	137056273	459	578	5	44
ENST00000309755	6823	587	136972982	136973084	1664	1765	406	440

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
Q9UH77	5	44	1	82	Alternative sequence	ID=VSP_002817;Note=In isoform C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10843806;Dbxref=PMID:10843806
Q9UH77	5	44	1	32	Alternative sequence	ID=VSP_002816;Note=In isoform B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10843806;Dbxref=PMID:10843806
Q9UH77	5	44	1	587	Chain	ID=PRO_0000119103;Note=Kelch-like protein 3
Q9UH77	5	44	10	10	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26435498;Dbxref=PMID:26435498
Q9UH77	406	440	404	407	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	411	415	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	420	424	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	435	439	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	1	587	Chain	ID=PRO_0000119103;Note=Kelch-like protein 3
Q9UH77	406	440	433	433	Modified residue	Note=Phosphoserine%3B by PKA;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:26435498,ECO:0000269\|PubMed:27727489;Dbxref=PMID:26435498,PMID:27727489
Q9UH77	406	440	433	433	Mutagenesis	Note=Phosphomimetic mutant that shows decreased interaction with WNK4. S->E%2CD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26435498;Dbxref=PMID:26435498
Q9UH77	406	440	410	410	Natural variant	ID=VAR_067516;Note=In PHA2D%3B impaired interaction with WNK1. S->L;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469641,PMID:22266938,PMID:
Q9UH77	406	440	426	426	Natural variant	ID=VAR_067517;Note=In PHA2D. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22406640;Dbxref=dbSNP:rs387907156,PMID:22406640
Q9UH77	406	440	427	427	Natural variant	ID=VAR_067518;Note=In PHA2D. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs199469642,PMID:22266938
Q9UH77	406	440	431	431	Natural variant	ID=VAR_067519;Note=In PHA2D. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs199469643,PMID:22266938
Q9UH77	406	440	432	432	Natural variant	ID=VAR_067520;Note=In PHA2D%3B impaired interaction with WNK1. S->N;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469631,PMID:22266938,PMID:
Q9UH77	406	440	433	433	Natural variant	ID=VAR_067521;Note=In PHA2D%3B decreased interaction with WNK4. S->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:26435498;Dbxref=PMID:22406640,PMID:26435498
Q9UH77	406	440	433	433	Natural variant	ID=VAR_067522;Note=In PHA2D. S->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469632,PMID:22266938,PMID:23387299
Q9UH77	406	440	438	438	Natural variant	ID=VAR_067523;Note=Found in a patient with hypertension%3B unknown pathological significance. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs907779058,PMID:22266938
Q9UH77	406	440	396	441	Repeat	Note=Kelch 3
Q9UH77	406	440	416	419	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9

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
Q9UH77	5	44	1	82	Alternative sequence	ID=VSP_002817;Note=In isoform C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10843806;Dbxref=PMID:10843806
Q9UH77	5	44	1	32	Alternative sequence	ID=VSP_002816;Note=In isoform B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10843806;Dbxref=PMID:10843806
Q9UH77	5	44	1	587	Chain	ID=PRO_0000119103;Note=Kelch-like protein 3
Q9UH77	5	44	10	10	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26435498;Dbxref=PMID:26435498
Q9UH77	406	440	404	407	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	411	415	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	420	424	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	435	439	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9
Q9UH77	406	440	1	587	Chain	ID=PRO_0000119103;Note=Kelch-like protein 3
Q9UH77	406	440	433	433	Modified residue	Note=Phosphoserine%3B by PKA;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:26435498,ECO:0000269\|PubMed:27727489;Dbxref=PMID:26435498,PMID:27727489
Q9UH77	406	440	433	433	Mutagenesis	Note=Phosphomimetic mutant that shows decreased interaction with WNK4. S->E%2CD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26435498;Dbxref=PMID:26435498
Q9UH77	406	440	410	410	Natural variant	ID=VAR_067516;Note=In PHA2D%3B impaired interaction with WNK1. S->L;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469641,PMID:22266938,PMID:
Q9UH77	406	440	426	426	Natural variant	ID=VAR_067517;Note=In PHA2D. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22406640;Dbxref=dbSNP:rs387907156,PMID:22406640
Q9UH77	406	440	427	427	Natural variant	ID=VAR_067518;Note=In PHA2D. M->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs199469642,PMID:22266938
Q9UH77	406	440	431	431	Natural variant	ID=VAR_067519;Note=In PHA2D. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs199469643,PMID:22266938
Q9UH77	406	440	432	432	Natural variant	ID=VAR_067520;Note=In PHA2D%3B impaired interaction with WNK1. S->N;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469631,PMID:22266938,PMID:
Q9UH77	406	440	433	433	Natural variant	ID=VAR_067521;Note=In PHA2D%3B decreased interaction with WNK4. S->G;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22406640,ECO:0000269\|PubMed:26435498;Dbxref=PMID:22406640,PMID:26435498
Q9UH77	406	440	433	433	Natural variant	ID=VAR_067522;Note=In PHA2D. S->N;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22266938,ECO:0000269\|PubMed:23387299;Dbxref=dbSNP:rs199469632,PMID:22266938,PMID:23387299
Q9UH77	406	440	438	438	Natural variant	ID=VAR_067523;Note=Found in a patient with hypertension%3B unknown pathological significance. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22266938;Dbxref=dbSNP:rs907779058,PMID:22266938
Q9UH77	406	440	396	441	Repeat	Note=Kelch 3
Q9UH77	406	440	416	419	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4CH9

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SNVs in the skipped exons for KLHL3

- 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
BRCA	TCGA-D8-A27N-01	exon_skip_444438	136969726	136969854	136969761	136969762	Frame_Shift_Del	TA	-	p.Y472fs
LIHC	TCGA-DD-A3A1-01	exon_skip_444438	136969726	136969854	136969813	136969813	Frame_Shift_Del	G	-	p.Q423fs
LIHC	TCGA-DD-A39Y-01	exon_skip_444443	137045439	137045545	137045490	137045490	Frame_Shift_Del	G	-	p.H32fs

- 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
HEC1_ENDOMETRIUM	136969726	136969854	136969729	136969729	Missense_Mutation	C	T	p.A483T
SNU1040_LARGE_INTESTINE	136969726	136969854	136969740	136969740	Missense_Mutation	C	T	p.R479H
MJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136969726	136969854	136969851	136969851	Missense_Mutation	T	C	p.K442R
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136972983	136973084	136972998	136972998	Missense_Mutation	C	T	p.V436M
SNU81_LARGE_INTESTINE	137033976	137034097	137034023	137034023	Missense_Mutation	C	A	p.D106Y
CHLA06ATRT_SOFT_TISSUE	137033976	137034097	137034088	137034088	Missense_Mutation	G	T	p.S84Y
NCIH1930_LUNG	137033976	137034097	137034090	137034090	Missense_Mutation	C	T	p.M83I
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	137045439	137045545	137045483	137045483	Missense_Mutation	A	T	p.V66E
DIFI_LARGE_INTESTINE	137045439	137045545	137045508	137045508	Missense_Mutation	C	T	p.D58N
NCIH2286_LUNG	137056154	137056273	137056239	137056239	Missense_Mutation	C	A	p.G17W

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for KLHL3

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 KLHL3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for KLHL3

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RelatedDrugs for KLHL3

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 KLHL3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
KLHL3	C3469605	PSEUDOHYPOALDOSTERONISM, TYPE IID	2	ORPHANET;UNIPROT
KLHL3	C0033805	Pseudohypoaldosteronism	1	CTD_human;HPO

	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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