ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for KALRN

Gene summary

Gene information	Gene symbol	KALRN
	Gene ID	8997
	Gene name	kalirin RhoGEF kinase
	Synonyms	ARHGEF24\|CHD5\|CHDS5\|DUET\|DUO\|HAPIP\|TRAD
	Cytomap	3q21.1-q21.2
	Type of gene	protein-coding
	Description	kalirinhuntingtin-associated protein interacting protein (duo)serine/threonine-protein kinase with Dbl- and pleckstrin homology domain
	Modification date	20180519
	UniProtAcc	O60229
	Context	PubMed: KALRN [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 KALRN 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 KALRN

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 KALRN

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_377212	3	123813599:123813751:123881056:123881294:123881555:123882417	123881056:123881294	ENSG00000160145.11	ENST00000488825.1
exon_skip_377213	3	124065989:124066112:124103691:124103883:124113981:124114151	124103691:124103883	ENSG00000160145.11	ENST00000240874.3,ENST00000354186.4,ENST00000360013.3,ENST00000439170.2,ENST00000460856.1
exon_skip_377215	3	124153180:124153372:124157734:124157884:124160791:124160906	124157734:124157884	ENSG00000160145.11	ENST00000240874.3,ENST00000354186.4,ENST00000360013.3,ENST00000393501.1,ENST00000460856.1
exon_skip_377216	3	124165609:124165732:124174023:124174206:124175456:124175575	124174023:124174206	ENSG00000160145.11	ENST00000240874.3,ENST00000354186.4,ENST00000360013.3,ENST00000393501.1,ENST00000460856.1
exon_skip_377218	3	124215157:124215260:124281689:124281936:124351266:124351445	124281689:124281936	ENSG00000160145.11	ENST00000354186.4,ENST00000360013.3
exon_skip_377220	3	124351266:124351550:124352695:124352800:124369654:124369762	124352695:124352800	ENSG00000160145.11	ENST00000454902.1,ENST00000428018.2,ENST00000393496.1
exon_skip_377222	3	124352698:124352800:124356054:124356150:124369654:124369762	124356054:124356150	ENSG00000160145.11	ENST00000354186.4,ENST00000360013.3,ENST00000291478.5
exon_skip_377223	3	124369654:124369785:124374447:124374514:124376294:124376398	124374447:124374514	ENSG00000160145.11	ENST00000428018.2,ENST00000393496.1,ENST00000354186.4,ENST00000459915.1,ENST00000360013.3,ENST00000291478.5
exon_skip_377224	3	124378211:124378304:124379769:124379820:124380697:124380775	124379769:124379820	ENSG00000160145.11	ENST00000428018.2,ENST00000393496.1,ENST00000354186.4,ENST00000459915.1,ENST00000360013.3,ENST00000291478.5
exon_skip_377227	3	124397036:124397160:124398304:124398364:124412650:124412678	124398304:124398364	ENSG00000160145.11	ENST00000428018.2,ENST00000354186.4,ENST00000360013.3,ENST00000291478.5
exon_skip_377228	3	124431781:124431982:124436093:124436232:124437771:124440035	124436093:124436232	ENSG00000160145.11	ENST00000428018.2,ENST00000354186.4,ENST00000360013.3,ENST00000291478.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for KALRN

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_377213	3	124065989:124066112:124103691:124103883:124113981:124114151	124103691:124103883	ENSG00000160145.11	ENST00000460856.1,ENST00000240874.3,ENST00000360013.3,ENST00000354186.4,ENST00000439170.2
exon_skip_377215	3	124153180:124153372:124157734:124157884:124160791:124160906	124157734:124157884	ENSG00000160145.11	ENST00000460856.1,ENST00000240874.3,ENST00000360013.3,ENST00000354186.4,ENST00000393501.1
exon_skip_377216	3	124165609:124165732:124174023:124174206:124175456:124175575	124174023:124174206	ENSG00000160145.11	ENST00000460856.1,ENST00000240874.3,ENST00000360013.3,ENST00000354186.4,ENST00000393501.1
exon_skip_377218	3	124215157:124215260:124281689:124281936:124351266:124351445	124281689:124281936	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4
exon_skip_377220	3	124351266:124351550:124352695:124352800:124369654:124369762	124352695:124352800	ENSG00000160145.11	ENST00000393496.1,ENST00000454902.1,ENST00000428018.2
exon_skip_377222	3	124352698:124352800:124356054:124356150:124369654:124369762	124356054:124356150	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4,ENST00000291478.5
exon_skip_377223	3	124369654:124369785:124374447:124374514:124376294:124376398	124374447:124374514	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4,ENST00000393496.1,ENST00000291478.5,ENST00000428018.2,ENST00000459915.1
exon_skip_377224	3	124378211:124378304:124379769:124379820:124380697:124380775	124379769:124379820	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4,ENST00000393496.1,ENST00000291478.5,ENST00000428018.2,ENST00000459915.1
exon_skip_377227	3	124397036:124397160:124398304:124398364:124412650:124412678	124398304:124398364	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4,ENST00000291478.5,ENST00000428018.2
exon_skip_377228	3	124431781:124431982:124436093:124436232:124437771:124440035	124436093:124436232	ENSG00000160145.11	ENST00000360013.3,ENST00000354186.4,ENST00000291478.5,ENST00000428018.2

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 KALRN

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 KALRN

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 KALRN

- 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-A3A0-01	exon_skip_377215	124157735	124157884	124157840	124157840	Frame_Shift_Del	C	-	p.P1050fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_377215	124157735	124157884	124157852	124157852	Frame_Shift_Del	A	-	p.K1054fs
LIHC	TCGA-DD-A3A0-01	exon_skip_377215	124157735	124157884	124157862	124157862	Frame_Shift_Del	A	-	p.E1057fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_377216	124174024	124174206	124174076	124174076	Frame_Shift_Del	A	-	p.E1200fs
STAD	TCGA-F1-6177-01	exon_skip_377216	124174024	124174206	124174076	124174076	Frame_Shift_Del	A	-	p.E1200fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_377218	124281690	124281936	124281821	124281821	Frame_Shift_Del	G	-	p.L1687fs
LUAD	TCGA-17-Z053-01	exon_skip_377220	124352696	124352800	124352712	124352712	Frame_Shift_Del	G	-	p.W1826fs
STAD	TCGA-CD-A4MG-01	exon_skip_377220	124352696	124352800	124352739	124352740	Frame_Shift_Del	CA	-	p.1835_1835del
STAD	TCGA-CD-A4MG-01	exon_skip_377220	124352696	124352800	124352739	124352740	Frame_Shift_Del	CA	-	p.S1835fs
UCS	TCGA-NA-A4R1-01	exon_skip_377215	124157735	124157884	124157839	124157840	Frame_Shift_Ins	-	C	p.I1049fs
UCS	TCGA-NA-A4R1-01	exon_skip_377215	124157735	124157884	124157839	124157840	Frame_Shift_Ins	-	C	p.IP1049fs
HNSC	TCGA-DQ-7588-01	exon_skip_377213	124103692	124103883	124103785	124103785	Nonsense_Mutation	C	T	p.R620*
SKCM	TCGA-GN-A263-01	exon_skip_377213	124103692	124103883	124103806	124103806	Nonsense_Mutation	C	T	p.Q627*
SKCM	TCGA-GN-A263-01	exon_skip_377213	124103692	124103883	124103806	124103806	Nonsense_Mutation	C	T	p.Q627X
COAD	TCGA-A6-2676-01	exon_skip_377215	124157735	124157884	124157798	124157798	Nonsense_Mutation	C	T	p.R1036X
UCEC	TCGA-AX-A05Z-01	exon_skip_377216	124174024	124174206	124174168	124174168	Nonsense_Mutation	C	T	p.R1231*
LUSC	TCGA-60-2698-01	exon_skip_377218	124281690	124281936	124281801	124281801	Nonsense_Mutation	G	T	p.E1681*
UCEC	TCGA-AP-A059-01	exon_skip_377220	124352696	124352800	124352735	124352735	Nonsense_Mutation	G	T	p.E1834*
BLCA	TCGA-DK-A3IN-01	exon_skip_377222	124356055	124356150	124356151	124356151	Splice_Site	G	A	p.L1887_splice

- 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
EFO21_OVARY	124436094	124436232	124436112	124436121	Frame_Shift_Del	CTTAGACTAC	-	p.LLDY1068fs
CL34_LARGE_INTESTINE	124103692	124103883	124103865	124103866	Frame_Shift_Ins	-	CA	p.H647fs
IM95_STOMACH	124103692	124103883	124103767	124103767	Missense_Mutation	G	A	p.E614K
OVCAR4_OVARY	124103692	124103883	124103789	124103789	Missense_Mutation	A	C	p.H621P
CAL148_BREAST	124103692	124103883	124103848	124103848	Missense_Mutation	G	A	p.D641N
MDST8_LARGE_INTESTINE	124103692	124103883	124103861	124103861	Missense_Mutation	C	T	p.S645F
KYSE30_OESOPHAGUS	124157735	124157884	124157777	124157777	Missense_Mutation	G	A	p.D1029N
HH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124174024	124174206	124174063	124174063	Missense_Mutation	G	A	p.D1196N
RH28_SOFT_TISSUE	124174024	124174206	124174068	124174068	Missense_Mutation	C	A	p.S1197R
SNU308_BILIARY_TRACT	124174024	124174206	124174097	124174097	Missense_Mutation	C	T	p.T1207M
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124174024	124174206	124174097	124174097	Missense_Mutation	C	T	p.T1207M
OSC19_UPPER_AERODIGESTIVE_TRACT	124174024	124174206	124174106	124174106	Missense_Mutation	G	A	p.R1210K
HEC108_ENDOMETRIUM	124174024	124174206	124174171	124174171	Missense_Mutation	T	C	p.Y1232H
ALLPO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124281690	124281936	124281718	124281718	Missense_Mutation	T	C	p.V26A
NCIH835_LUNG	124281690	124281936	124281736	124281736	Missense_Mutation	C	T	p.A32V
RERFLCAD2_LUNG	124281690	124281936	124281736	124281736	Missense_Mutation	C	G	p.A32G
JHUEM2_ENDOMETRIUM	124281690	124281936	124281769	124281769	Missense_Mutation	G	A	p.G43E
VMCUB1_URINARY_TRACT	124281690	124281936	124281783	124281783	Missense_Mutation	C	A	p.L48M
TTC466_BONE	124281690	124281936	124281801	124281801	Missense_Mutation	G	A	p.E54K
KYSE140_OESOPHAGUS	124281690	124281936	124281851	124281852	Missense_Mutation	GG	AA	p.E71K
CP67MEL_SKIN	124352696	124352800	124352739	124352739	Missense_Mutation	C	T	p.S138L
HS939T_SKIN	124352696	124352800	124352756	124352756	Missense_Mutation	C	T	p.P144S
YD10B_UPPER_AERODIGESTIVE_TRACT	124352696	124352800	124352757	124352757	Missense_Mutation	C	A	p.P144Q
NCIH2052_PLEURA	124356055	124356150	124356070	124356070	Missense_Mutation	G	T	p.A164S
NCIBL2052_MATCHED_NORMAL_TISSUE	124356055	124356150	124356070	124356070	Missense_Mutation	G	T	p.A164S
MLMA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124374448	124374514	124374455	124374455	Missense_Mutation	C	G	p.L237V
DM3_FIBROBLAST	124398305	124398364	124398346	124398346	Missense_Mutation	C	A	p.D70E
NCIH23_LUNG	124398305	124398364	124398354	124398354	Missense_Mutation	C	G	p.T73S
NCIH2347_LUNG	124398305	124398364	124398364	124398364	Missense_Mutation	G	T	p.E76D
KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124436094	124436232	124436102	124436102	Missense_Mutation	A	G	p.D1065G
NCIH630_LARGE_INTESTINE	124436094	124436232	124436107	124436107	Missense_Mutation	C	T	p.R1067W
SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	124436094	124436232	124436118	124436118	Missense_Mutation	C	A	p.D1070E
NCIH1435_LUNG	124436094	124436232	124436122	124436122	Missense_Mutation	C	A	p.L1072I
JHUEM7_ENDOMETRIUM	124436094	124436232	124436162	124436162	Missense_Mutation	T	G	p.F1085C
YD15_SALIVARY_GLAND	124157735	124157884	124157798	124157798	Nonsense_Mutation	C	T	p.R1036*
RERFLCAD1_LUNG	124281690	124281936	124281689	124281690	Splice_Site	GC	TT	p.16_17QL>HF
COLO792_SKIN	124436094	124436232	124436094	124436094	Splice_Site	G	A	p.L1062L

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

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_377224	3	124378211:124378304:124379769:124379820:124380697:124380775	124379769:124379820	ENST00000428018.2,ENST00000393496.1,ENST00000354186.4,ENST00000459915.1,ENST00000360013.3,ENST00000291478.5	THCA	rs333289	chr3:124379817	T/C	1.66e-05
exon_skip_377224	3	124378211:124378304:124379769:124379820:124380697:124380775	124379769:124379820	ENST00000428018.2,ENST00000393496.1,ENST00000354186.4,ENST00000459915.1,ENST00000360013.3,ENST00000291478.5	THCA	rs333289	chr3:124379817	T/C	7.74e-05

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

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

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RelatedDrugs for KALRN

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 KALRN

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
KALRN	C0041696	Unipolar Depression	1	PSYGENET
KALRN	C1269683	Major Depressive Disorder	1	PSYGENET

	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 KALRN

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

Gene isoform structures and expression levels for KALRN

Exon skipping events with PSIs in TCGA for KALRN

Exon skipping events with PSIs in GTEx for KALRN

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

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

SNVs in the skipped exons for KALRN

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

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

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

RelatedDrugs for KALRN

RelatedDiseases for KALRN