ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for FERMT2

Gene summary

Gene information	Gene symbol	FERMT2
	Gene ID	10979
	Gene name	fermitin family member 2
	Synonyms	KIND2\|MIG2\|PLEKHC1\|UNC112\|UNC112B\|mig-2
	Cytomap	14q22.1
	Type of gene	protein-coding
	Description	fermitin family homolog 2PH domain-containing family C member 1kindlin 2mitogen inducible gene 2 proteinpleckstrin homology domain containing, family C (with FERM domain) member 1pleckstrin homology domain containing, family C member 1
	Modification date	20180519
	UniProtAcc	Q96AC1
	Context	PubMed: FERMT2 [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 FERMT2 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 FERMT2

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 FERMT2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_113383	14	53327058:53327183:53327731:53327752:53331118:53331239	53327731:53327752	ENSG00000073712.9	ENST00000554152.1,ENST00000553768.1,ENST00000399304.3,ENST00000343279.4,ENST00000553373.1
exon_skip_113386	14	53331464:53331571:53339516:53339641:53340894:53340944	53339516:53339641	ENSG00000073712.9	ENST00000395631.2,ENST00000554152.1,ENST00000341590.3,ENST00000399304.3,ENST00000343279.4,ENST00000553373.1
exon_skip_113388	14	53340894:53340944:53341940:53342075:53345299:53345407	53341940:53342075	ENSG00000073712.9	ENST00000395631.2,ENST00000554152.1,ENST00000341590.3,ENST00000399304.3,ENST00000343279.4,ENST00000553373.1
exon_skip_113393	14	53347961:53348187:53348513:53348546:53360010:53360145	53348513:53348546	ENSG00000073712.9	ENST00000554152.1
exon_skip_113394	14	53347961:53348187:53360010:53360145:53385840:53386057	53360010:53360145	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000554288.1,ENST00000399304.3,ENST00000343279.4,ENST00000553373.1
exon_skip_113395	14	53360093:53360145:53385840:53386074:53417129:53417286	53385840:53386074	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000554712.1,ENST00000399304.3,ENST00000343279.4,ENST00000553373.1
exon_skip_113396	14	53385840:53386074:53415279:53415298:53417129:53417286	53415279:53415298	ENSG00000073712.9	ENST00000557562.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for FERMT2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_113383	14	53327058:53327183:53327731:53327752:53331118:53331239	53327731:53327752	ENSG00000073712.9	ENST00000554152.1,ENST00000343279.4,ENST00000553373.1,ENST00000399304.3,ENST00000553768.1
exon_skip_113386	14	53331464:53331571:53339516:53339641:53340894:53340944	53339516:53339641	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000554152.1,ENST00000343279.4,ENST00000553373.1,ENST00000399304.3
exon_skip_113388	14	53340894:53340944:53341940:53342075:53345299:53345407	53341940:53342075	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000554152.1,ENST00000343279.4,ENST00000553373.1,ENST00000399304.3
exon_skip_113393	14	53347961:53348187:53348513:53348546:53360010:53360145	53348513:53348546	ENSG00000073712.9	ENST00000554152.1
exon_skip_113394	14	53347961:53348187:53360010:53360145:53385840:53386057	53360010:53360145	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000343279.4,ENST00000553373.1,ENST00000399304.3,ENST00000554288.1
exon_skip_113395	14	53360093:53360145:53385840:53386074:53417129:53417286	53385840:53386074	ENSG00000073712.9	ENST00000395631.2,ENST00000341590.3,ENST00000343279.4,ENST00000553373.1,ENST00000399304.3,ENST00000554712.1
exon_skip_113396	14	53385840:53386074:53415279:53415298:53417129:53417286	53415279:53415298	ENSG00000073712.9	ENST00000557562.1

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 FERMT2

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
ENST00000341590	53339516	53339641	Frame-shift
ENST00000395631	53339516	53339641	Frame-shift
ENST00000341590	53341940	53342075	In-frame
ENST00000395631	53341940	53342075	In-frame
ENST00000341590	53360010	53360145	In-frame
ENST00000395631	53360010	53360145	In-frame
ENST00000341590	53385840	53386074	In-frame
ENST00000395631	53385840	53386074	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
ENST00000341590	53339516	53339641	Frame-shift
ENST00000395631	53339516	53339641	Frame-shift
ENST00000341590	53341940	53342075	In-frame
ENST00000395631	53341940	53342075	In-frame
ENST00000341590	53360010	53360145	In-frame
ENST00000395631	53360010	53360145	In-frame
ENST00000341590	53385840	53386074	In-frame
ENST00000395631	53385840	53386074	In-frame

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Infer the effects of exon skipping event on protein functional features for FERMT2

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
ENST00000341590	3355	680	53385840	53386074	344	577	52	130
ENST00000395631	3386	680	53385840	53386074	375	608	52	130
ENST00000341590	3355	680	53360010	53360145	578	712	130	175
ENST00000395631	3386	680	53360010	53360145	609	743	130	175
ENST00000341590	3355	680	53341940	53342075	1150	1284	321	366
ENST00000395631	3386	680	53341940	53342075	1181	1315	321	366

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
ENST00000341590	3355	680	53385840	53386074	344	577	52	130
ENST00000395631	3386	680	53385840	53386074	375	608	52	130
ENST00000341590	3355	680	53360010	53360145	578	712	130	175
ENST00000395631	3386	680	53360010	53360145	609	743	130	175
ENST00000341590	3355	680	53341940	53342075	1150	1284	321	366
ENST00000395631	3386	680	53341940	53342075	1181	1315	321	366

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
Q96AC1	52	130	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	52	130	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	52	130	79	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	79	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	74	81	Mutagenesis	Note=Abolishes lipid-binding via the N-terminus%3B when associated with A-40. KTHWTLDK->ATAATLDA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22078565;Dbxref=PMID:22078565
Q96AC1	52	130	74	81	Mutagenesis	Note=Abolishes lipid-binding via the N-terminus%3B when associated with A-40. KTHWTLDK->ATAATLDA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22078565;Dbxref=PMID:22078565
Q96AC1	52	130	40	81	Region	Note=Interaction with membranes containing phosphatidylinositol phosphate
Q96AC1	52	130	40	81	Region	Note=Interaction with membranes containing phosphatidylinositol phosphate
Q96AC1	52	130	66	68	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	66	68	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	130	175	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	130	175	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	130	175	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q96AC1	130	175	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q96AC1	321	366	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	321	366	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	321	366	189	661	Domain	Note=FERM
Q96AC1	321	366	189	661	Domain	Note=FERM
Q96AC1	321	366	354	357	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	354	357	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	339	339	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q96AC1	321	366	339	339	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q96AC1	321	366	351	351	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:20068231,PMID:21406692,PMID:24275569
Q96AC1	321	366	351	351	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:20068231,PMID:21406692,PMID:24275569
Q96AC1	321	366	347	353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	347	353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU

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
Q96AC1	52	130	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	58	65	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	52	130	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	52	130	79	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	79	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	74	81	Mutagenesis	Note=Abolishes lipid-binding via the N-terminus%3B when associated with A-40. KTHWTLDK->ATAATLDA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22078565;Dbxref=PMID:22078565
Q96AC1	52	130	74	81	Mutagenesis	Note=Abolishes lipid-binding via the N-terminus%3B when associated with A-40. KTHWTLDK->ATAATLDA;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22078565;Dbxref=PMID:22078565
Q96AC1	52	130	40	81	Region	Note=Interaction with membranes containing phosphatidylinositol phosphate
Q96AC1	52	130	40	81	Region	Note=Interaction with membranes containing phosphatidylinositol phosphate
Q96AC1	52	130	66	68	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	52	130	66	68	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LGX
Q96AC1	130	175	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	130	175	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	130	175	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q96AC1	130	175	159	159	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:18669648,ECO:0000244\|PubMed:19690332,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:1
Q96AC1	321	366	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	321	366	1	680	Chain	ID=PRO_0000219456;Note=Fermitin family homolog 2
Q96AC1	321	366	189	661	Domain	Note=FERM
Q96AC1	321	366	189	661	Domain	Note=FERM
Q96AC1	321	366	354	357	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	354	357	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	339	339	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q96AC1	321	366	339	339	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:20068231;Dbxref=PMID:20068231
Q96AC1	321	366	351	351	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:20068231,PMID:21406692,PMID:24275569
Q96AC1	321	366	351	351	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692,ECO:0000244\|PubMed:24275569;Dbxref=PMID:20068231,PMID:21406692,PMID:24275569
Q96AC1	321	366	347	353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU
Q96AC1	321	366	347	353	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2MSU

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SNVs in the skipped exons for FERMT2

- 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
KIRC	TCGA-B2-3924-01	exon_skip_113394	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K152fs
LIHC	TCGA-G3-A25T-01	exon_skip_113394	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K154fs
STAD	TCGA-BR-8487-01	exon_skip_113394	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K152fs
STAD	TCGA-BR-8591-01	exon_skip_113394	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K152fs
STAD	TCGA-BR-A4QL-01	exon_skip_113394	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K152fs
KIRC	TCGA-CW-5580-01	exon_skip_113395	53385841	53386074	53385912	53385912	Frame_Shift_Del	T	-	p.K107fs
STAD	TCGA-BR-4363-01	exon_skip_113395	53385841	53386074	53386064	53386064	Frame_Shift_Del	T	-	p.D57fs
STAD	TCGA-BR-4363-01	exon_skip_113395	53385841	53386074	53386064	53386064	Frame_Shift_Del	T	-	p.K56fs
STAD	TCGA-VQ-A8P2-01	exon_skip_113395	53385841	53386074	53386064	53386064	Frame_Shift_Del	T	-	p.D57fs
STAD	TCGA-VQ-A8P2-01	exon_skip_113395	53385841	53386074	53386064	53386064	Frame_Shift_Del	T	-	p.K56fs
ESCA	TCGA-L5-A4OI-01	exon_skip_113394	53360011	53360145	53360081	53360082	Frame_Shift_Ins	-	T	p.K152fs
ESCA	TCGA-L5-A4OI-01	exon_skip_113394	53360011	53360145	53360081	53360082	Frame_Shift_Ins	-	T	p.K153fs
STAD	TCGA-BR-8361-01	exon_skip_113395	53385841	53386074	53386063	53386064	Frame_Shift_Ins	-	T	p.D57fs
STAD	TCGA-BR-8361-01	exon_skip_113395	53385841	53386074	53386064	53386065	Frame_Shift_Ins	-	T	p.K56fs
BLCA	TCGA-XF-AAMG-01	exon_skip_113395	53385841	53386074	53386038	53386038	Nonsense_Mutation	C	T	p.W65*

- 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
HEC6_ENDOMETRIUM	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K154fs
NUGC3_STOMACH	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K154fs
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	53360011	53360145	53360082	53360082	Frame_Shift_Del	T	-	p.K154fs
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	53339517	53339641	53339525	53339525	Missense_Mutation	T	C	p.N422S
SNU1066_UPPER_AERODIGESTIVE_TRACT	53360011	53360145	53360038	53360038	Missense_Mutation	C	G	p.E167Q
BC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	53360011	53360145	53360068	53360068	Missense_Mutation	C	T	p.D157N
LB771PBL_MATCHED_NORMAL_TISSUE	53360011	53360145	53360100	53360100	Missense_Mutation	T	C	p.D146G
A431_SKIN	53360011	53360145	53360103	53360103	Missense_Mutation	C	T	p.R145K
CCK81_LARGE_INTESTINE	53385841	53386074	53385847	53385847	Missense_Mutation	T	G	p.T129P
COLO783_SKIN	53385841	53386074	53386045	53386045	Missense_Mutation	G	A	p.L63F
NCIH322_LUNG	53385841	53386074	53386054	53386054	Missense_Mutation	C	T	p.D60N
JSC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	53385841	53386074	53386063	53386063	Missense_Mutation	C	A	p.D57Y
KS1_CENTRAL_NERVOUS_SYSTEM	53385841	53386074	53386064	53386064	Missense_Mutation	T	A	p.K56N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FERMT2

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 FERMT2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for FERMT2

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RelatedDrugs for FERMT2

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 FERMT2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
FERMT2	C0005695	Bladder Neoplasm	1	CTD_human
FERMT2	C0017605	Angle Closure Glaucoma	1	CTD_human

	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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