SomamiR DB

SomamiR DB 2.0 Somatic mutations altering microRNA-ceRNA interactions
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Prediction criteria:	TargetScan sites only All 6mer or longer seed matches

PolymiRTS Database

RefSeq ID:	NM_014916
Gene Symbol:	LMTK2
Description:	Homo sapiens lemur tyrosine kinase 2 (LMTK2), mRNA.
Gene Location:	chr7(+):97736196-97838944
Browse Associations

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98206520G>A			COSN8807484		SS6003314		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4746-3p	caccGCACCGCTtccctcc	1	AGCGGUGC	m8a	Disrupted	-0.844000	-0.743000	-0.740000
hsa-miR-4795-5p	caccgcaCCACTTCcctcc	3	AGAAGUGG	m7b	Created	0.060000	0.124000	No effect
hsa-miR-675-5p	caCCGCACCActtccctcc	2	UGGUGCGG	m8a	(m7a->m8a)	-0.116000	-0.279000	-2.100000

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98206665C>T			COSN8049487		8034291		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-224-5p	gggaccgttTGACTTGatg	2	CAAGUCAC	m7a	(m6b->m7a)	-0.081000	-0.081000	No effect
hsa-miR-553	gggACCGTTTgacttgatg	0	AAAACGGU	m7b	(m6b->m7b)	no TS	0.038000	-0.060000

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98206935C>T			COSN5229966		SS6003302		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98207192T>A			COSN9518132		AOCS-106-1-1		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4282	cacccaacAAATTTTccgg	0	UAAAAUUU	m7b	Created	no TS	0.336000	-0.090000
hsa-miR-4781-3p	cacCCAACATattttccgg	1	AAUGUUGG	m7b	(m7b->m6b)	0.099000	no TS	0.170000

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98207264C>T			COSN1356056		HCC33T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3937	caggggCCGCCTGgggtac	2	ACAGGCGG	m7b	Disrupted	-0.001000	no TS	2.360000
hsa-miR-3937	caggggCCGCCTGgggtac	2	ACAGGCGG	m7b	Disrupted	-0.001000	no TS	2.360000
hsa-miR-3937	caggggCCGCCTGgggtac	2	ACAGGCGG	m7b	Disrupted	-0.001	no TS	2.36

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98207344C>T			COSN8049488		8015259		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3974	aaTGACCTTTattgccagt	10	AAAGGUCA	m8a	(m7a->m8a)	0.032000	0.005000	-0.250000
hsa-miR-493-3p	aatGACCTTCAttgccagt	3	UGAAGGUC	m8a	Disrupted	-0.047000	no TS	1.200000
hsa-miR-548m	aatgACCTTTattgccagt	0	CAAAGGUA	m6b	Created	no TS	0.079000	-0.200000

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98208246C>T			9_30570		CRC-4-Tumor		Colorectal adenocarcinoma
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1229	atggaggGGTGAGAtttta	4	CUCUCACC	m7b	Created	no TS	-0.051	No effect
hsa-miR-1285-5p	atggagggGTGAGATttta	4	GAUCUCAC	m7b	Created	0.07	0.063	0.09
hsa-miR-4749-3p	atgGAGGGGCGagatttta	4	CGCCCCUC	m8a	Disrupted	-0.258	-0.14	1.65

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98208937G>T			COSN5105668		HX27T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr7:g.98208984G>C			COSN8049490		8034061		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4655-5p	cagggCCCCGGTGgaagga	2	CACCGGGG	m8a	Disrupted	-0.175000	no TS	0.760000

**Germline mutations in target sites of miRNAs in somatic mutation table**
Location	SNP ID	Ancestral Allele	Allele	miR ID	Conservation	miRSite	FuncClass	Validation	context+ score change
98205820	rs140980138	C	C	hsa-miR-4746-3p hsa-miR-8064	1 1	tgtgtGCACCGCA tGTGTGCAccgca	Disrupted Disrupted	N N	-0.509 -0.07
98205820	rs140980138	C	T	hsa-miR-329-3p hsa-miR-362-3p hsa-miR-3941 hsa-miR-603	1 1 1 1	tGTGTGTAccgca tGTGTGTAccgca tGTGTGTAccgca tGTGTGTAccgca	Created Created Created Created	N N N N	-0.022 -0.022 -0.011 -0.018
98206495	rs185085102	T	T	hsa-miR-1301-3p hsa-miR-3944-5p hsa-miR-4660 hsa-miR-5047	2 1 2 2	gagAGCTGCAccc gagaGCTGCACcc gaGAGCTGCAccc gagAGCTGCAccc	Disrupted Disrupted Disrupted Disrupted	N N N N	0.02 -0.04 -0.143 0.039
98206495	rs185085102	T	C	hsa-miR-4466 hsa-miR-6741-3p hsa-miR-675-5p	1 2 1	gagagCCGCACCc gAGAGCCGcaccc gagagCCGCACCc	Created Created Created	N N N	-0.092 -0.047 -0.092
98207262	rs146744242	C	C	hsa-miR-3937	2	aggggCCGCCTGg	Disrupted	N	-0.001
98207262	rs146744242	C	T	hsa-miR-4514 hsa-miR-4645-5p hsa-miR-4673 hsa-miR-4692 hsa-miR-6769a-3p	2 2 2 2 2	aggggCTGCCTGg aggggcTGCCTGG aggggcTGCCTGG aggggCTGCCTGg AGGGGCTgcctgg	Created Created Created Created Created	N N N N N	0.123 0.124 0.097 0.132 0.053
98207264	rs35215639	-	C	hsa-miR-3937	2	gggCCGCCTGggg	Unknown	N	-0.001
98207264	rs35215639	-	-
98207505	rs200445166	T	T	hsa-miR-10a-3p	2	cgCGAATTTtttt	Disrupted	N	0.121
98207505	rs200445166	T	A	hsa-miR-3606-3p hsa-miR-4282 hsa-miR-513a-3p hsa-miR-513c-3p	2 2 2 2	cgcGAAATTTttt cgcgAAATTTTtt cgcGAAATTTttt cgcGAAATTTttt	Created Created Created Created	N N N N	0.209 0.237 0.2 0.2
98208120	rs200702089	-	C		0
98208120	rs200702089	-	-	hsa-miR-4282	0	aaaaaAAATTTT	Unknown	N	0.152
98208120	rs74617349	-
98208120	rs74617349	-	A	hsa-miR-4282	0	aaaaaaAAATTTT	Unknown	N	0.159
98208246	rs180844153	C	C	hsa-miR-4749-3p	2	GAGGGGCgagatt	Disrupted	N	-0.118
98208246	rs180844153	C	T	hsa-miR-1229-3p hsa-miR-1285-5p hsa-miR-216a-5p hsa-miR-6511a-3p hsa-miR-6511b-3p hsa-miR-6784-3p hsa-miR-6802-3p hsa-miR-6862-3p	2 2 2 2 2 2 2 2	gaggGGTGAGAtt gagggGTGAGATt gaggggTGAGATT gaggGGTGAGAtt gaggGGTGAGAtt gagGGGTGAGAtt gaGGGGTGAgatt gagGGGTGAGAtt	Created Created Created Created Created Created Created Created	N N N N N N N N	-0.051 -0.007 0.047 -0.044 -0.044 -0.149 -0.116 -0.138
98208984	rs3735255	G	G	hsa-miR-181d-3p hsa-miR-4655-5p hsa-miR-6784-5p	3 2 3	ggcCCCGGTGgaa ggCCCCGGTggaa gGCCCCGGtggaa	Disrupted Disrupted Disrupted	N N N	-0.145 -0.175 -0.208
98208984	rs3735255	G	A	hsa-miR-1227-5p hsa-miR-1273g-3p hsa-miR-128-1-5p hsa-miR-128-2-5p hsa-miR-181a-2-3p hsa-miR-4436b-5p hsa-miR-6509-3p hsa-miR-6762-5p hsa-miR-6845-5p	3 3 3 3 3 15 2 3 3	GGCCCCAgtggaa ggcccCAGTGGAa GGCCCCAgtggaa GGCCCCAgtggaa ggcccCAGTGGAa ggccccAGTGGAA ggcccCAGTGGAA GGCCCCAgtggaa GGCCCCAgtggaa	Created Created Created Created Created Created Created Created Created	N N N N N N N N N	-0.131 -0.013 -0.157 -0.157 -0.031 -0.013 -0.101 -0.153 -0.146
98209147	rs116450388	G	G	hsa-miR-224-5p hsa-miR-6890-3p	2 1	cgcaGTGACTTcc cGCAGTGActtcc	Disrupted Disrupted	N N	-0.081 -0.115
98209147	rs116450388	G	A	hsa-miR-4670-3p	3	cgcagTAACTTCc	Created	N	-0.018

**Genome Browser**
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Somatic mutations that impact miRNA target sites

Germline mutations in target sites of miRNAs in somatic mutation table

Genome Browser