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

RefSeq ID:	NM_001039535
Gene Symbol:	SKA1
Description:	Homo sapiens spindle and kinetochore associated complex subunit 1 (SKA1), transcript variant 1, mRNA.
Gene Location:	chr18(+):47901391-47920538
Browse Associations

Somatic mutations that impact miRNA target sites

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392347G>T			COSN1206889		HCC109T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3148	atctttttTTTTTCCtttt	0	UGGAAAAA	m7b	Created	no TS	-0.156000	-0.010000
hsa-miR-3613-3p	atcTTTTTTGTttcctttt	1	ACAAAAAA	m8a	Disrupted	0.041000	0.093000	-0.290000
hsa-miR-4261	atctttttTGTTTCCTttt	0	AGGAAACA	m8a	Disrupted	-0.254000	no TS	0.450000
hsa-miR-4496	atcttttttGTTTCCTttt	0	GAGGAAAC	m7b	(m7b->m6c)	-0.270000	no TS	2.770000
hsa-miR-3148	atctttttTTTTTCCtttt	0	UGGAAAAA	m7b	Created	no TS	-0.156	-0.01
hsa-miR-3613-3p	atcTTTTTTGTttcctttt	0	ACAAAAAA	m8a	Disrupted	0.041	0.093	0.28
hsa-miR-4261	atctttttTGTTTCCTttt	0	AGGAAACA	m8a	Disrupted	-0.254	no TS	0.45
hsa-miR-4496	atcttttttGTTTCCTttt	0	GAGGAAAC	m7b	(m7b->m6c)	-0.27	no TS	2.77

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392367G>T			COSN6416503		HCC117T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3613-3p	tttTTTTTTGagacaggat	1	ACAAAAAA	m7b	(m7b->m6b)	0.041000	0.103000	-0.300000
hsa-miR-371a-5p	ttttttTTTGAGacaggat	2	ACUCAAAC	m6b	Disrupted	-0.040000	0.006000	1.250000
hsa-miR-371b-5p	tttttTTTTGAGacaggat	2	ACUCAAAA	m7b	Disrupted	-0.244000	-0.061000	3.760000
hsa-miR-373-5p	tttttTTTTGAGacaggat	2	ACUCAAAA	m7b	Disrupted	-0.223000	-0.061000	3.660000
hsa-miR-616-5p	tttttTTTTGAGacaggat	2	ACUCAAAA	m7b	Disrupted	-0.276000	-0.082000	1.030000

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392619T>A			COSN7361598		8066452		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3929	ccaccctccTCAGCCTCcc	1	GAGGCUGA	m8a	(m8a->m7b)	-0.082000	-0.016000	0.030000
hsa-miR-4419b	ccaccctccTCAGCCTCcc	1	GAGGCUGA	m8a	(m8a->m7b)	-0.100000	-0.034000	No effect
hsa-miR-4478	ccaccctccTCAGCCTCcc	1	GAGGCUGA	m8a	(m8a->m7b)	-0.137000	-0.053000	No effect
hsa-miR-4689	ccaccCTCCTCAgcctccc	1	UUGAGGAG	m7b	Disrupted	-0.092000	no TS	No effect
hsa-miR-4779	ccaCCCTCCTcagcctccc	1	UAGGAGGG	m7b	(m7b->m6b)	-0.160000	no TS	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392852C>T			COSN8343444		0007_CRUK_PC_0007_T3_DNA		[prostate][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3154	cctcagCCTTCTGagtagc	0	CAGAAGGG	m7a	Created	NA	NA	-0.710000
hsa-miR-3664-3p	cctcagccTCCTGAGtagc	0	UCUCAGGA	m7b	Disrupted	-0.160000	-0.135000	0.770000
hsa-miR-3929	ccTCAGCCTCctgagtagc	1	GAGGCUGA	m8a	(m8a->m7a)	-0.082000	-0.109000	0.010000
hsa-miR-4419b	ccTCAGCCTCctgagtagc	1	GAGGCUGA	m8a	(m8a->m7a)	-0.100000	-0.127000	0.240000
hsa-miR-4433-3p	cctcagcCTCCTGagtagc	1	ACAGGAGU	m6b	Disrupted	-0.113000	-0.085000	0.130000
hsa-miR-4459	cctcagCCTCCTGagtagc	1	CCAGGAGG	m7b	Disrupted	-0.357000	-0.164000	0.600000
hsa-miR-4478	ccTCAGCCTCctgagtagc	1	GAGGCUGA	m8a	(m8a->m7a)	-0.137000	-0.164000	0.230000
hsa-miR-4695-5p	cctcaGCCTCCTGagtagc	0	CAGGAGGC	m8a	Disrupted	-0.140000	no TS	0.020000
hsa-miR-4768-3p	cctcagcCTCCTGagtagc	1	CCAGGAGA	m6b	Disrupted	-0.258000	-0.233000	0.010000
hsa-miR-485-5p	cctCAGCCTCctgagtagc	1	AGAGGCUG	m7b	(m7b->m6b)	-0.537000	-0.447000	0.020000
hsa-miR-510	cctcagcctCCTGAGTAgc	0	UACUCAGG	m8a	(m8a->m7b)	-0.198000	-0.020000	2.720000

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392867C>T			ICGC_8D9BC1C0-2A78-11E2-96E7-04FD496BB9B8		CPCG_0102_Pr_P_P1		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-20b-3p	tagctgggACTACAGgcac	0	ACUGUAGU	m7b	Disrupted	0.022	no TS	No effect
hsa-miR-4733-5p	tagcTGGGATTacaggcac	0	AAUCCCAA	m7a	Created	NA	NA	No effect
hsa-miR-5588-3p	tagcTGGGACTacaggcac	1	AAGUCCCA	m7b	Disrupted	-0.451	-0.271	0.02

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50392981G>A			ICGC_B0A40A60-2A78-11E2-8335-12FD496BB9B8		CPCG_0102_Pr_P_P2		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3929	gcccaccTCAGCCTCccaa	0	GAGGCUGA	m8a	Created	-0.082	-0.066	-3.28
hsa-miR-4419b	gcccaccTCAGCCTCccaa	0	GAGGCUGA	m8a	Created	-0.1	-0.103	No effect
hsa-miR-4478	gcccaccTCAGCCTCccaa	0	GAGGCUGA	m8a	Created	-0.137	-0.149	-0.06
hsa-miR-485-5p	gcccacctCAGCCTCccaa	0	AGAGGCUG	m7b	Created	-0.537	-0.609	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50393005A>T			COSN1745671		RK184_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

No TargetScan sites are altered. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50393282T>C			ICGC_8D9BC698-2A78-11E2-96E7-04FD496BB9B8		CPCG_0102_Pr_P_P1		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3135b	gcaCTCCAGCCtgggcaac	0	GGCUGGAG	m8a	Created	-0.23	-0.333	No effect
hsa-miR-3652	gcacTCCAGCCtgggcaac	0	CGGCUGGA	m7b	Created	no TS	-0.039	No effect
hsa-miR-4430	gcacTCCAGCCTgggcaac	0	AGGCUGGA	m8a	Created	no TS	-0.029	No effect
hsa-miR-4463	gcactCCAGTCTgggcaac	1	GAGACUGG	m7b	Disrupted	-0.292	-0.243	No effect
hsa-miR-4494	gcactcCAGTCTGGgcaac	1	CCAGACUG	m8a	Disrupted	-0.135	-0.146	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50393807G>A			COSN14959567		LP6005409-DNA_G03		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

No TargetScan sites are altered. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.50394003G>T			COSN6125865		RK205_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-345-3p	agcTTCAGGGttggcaaac	2	GCCCUGAA	m7b	(m7b->m6b)	-0.423000	-0.302000	No effect

*By default, only target sites identified by TargetScan are displayed. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.

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
50392366	rs79038584	T	T	hsa-miR-3613-3p hsa-miR-371a-5p hsa-miR-371b-5p hsa-miR-372-5p hsa-miR-373-5p hsa-miR-616-5p	1 1 21 21 21 21	tTTTTTTGAgaca ttttTTTGAGAca tttTTTTGAGAca ttttTTTGAGAca tttTTTTGAGAca tttTTTTGAGAca	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	-0.027 -0.046 -0.183 -0.04 -0.162 -0.194
			G	hsa-miR-515-5p hsa-miR-519d-5p hsa-miR-519e-5p hsa-miR-5695	21 21 21 21	ttttTTGGAGAca tttTTTGGAGAca ttttTTGGAGAca ttttTTGGAGAca	Created Created Created Created	N N N N	-0.215 -0.309 -0.187 -0.119
50392367	rs78433683	G	G	hsa-miR-3613-3p hsa-miR-371a-5p hsa-miR-371b-5p hsa-miR-372-5p hsa-miR-373-5p hsa-miR-616-5p	1 12 12 12 12 12	TTTTTTGAgacag tttTTTGAGAcag ttTTTTGAGAcag tttTTTGAGAcag ttTTTTGAGAcag ttTTTTGAGAcag	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	-0.062 -0.046 -0.183 -0.04 -0.162 -0.194
50392451	rs144560688	-	CTCAA	hsa-miR-1304-5p hsa-miR-2467-5p hsa-miR-3188 hsa-miR-3975 hsa-miR-485-5p hsa-miR-6765-5p hsa-miR-6884-5p	2 2 2 2 2 2 2	tcactgcaGCCTCAAcctccc tcactgcAGCCTCAacctccc tcactgcAGCCTCAacctccc tcactgcAGCCTCAacctccc tcactgCAGCCTCAacctccc tcactgcaGCCTCAAcctccc tcactgCAGCCTCAacctccc	Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N	-0.19 -0.134 -0.122 -0.124 -0.318 -0.131 -0.307
			-	hsa-miR-149-3p hsa-miR-4446-3p hsa-miR-4721 hsa-miR-4728-5p hsa-miR-6785-5p hsa-miR-6829-5p hsa-miR-6883-5p	2 2 2 2 2 2 2	tcactgcagCCCTCCC tcactgCAGCCCTccc tcactgcAGCCCTCcc tcactgcagCCCTCCC tcactgcagCCCTCCC tcactGCAGCCCtccc tcactgcagCCCTCCC	Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N	-0.184 -0.172 -0.171 -0.215 -0.219 -0.218 -0.211
50392749	rs199503473	T	T	hsa-miR-3613-3p hsa-miR-371a-5p hsa-miR-371b-5p hsa-miR-372-5p hsa-miR-373-5p hsa-miR-616-5p	1 2 2 2 2 2	tTTTTTTGAgaca ttttTTTGAGAca tttTTTTGAGAca ttttTTTGAGAca tttTTTTGAGAca tttTTTTGAGAca	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	0.008 0.006 -0.061 0.009 -0.061 -0.082
			G	hsa-miR-515-5p hsa-miR-519d-5p hsa-miR-519e-5p hsa-miR-5695	2 2 2 2	ttttTTGGAGAca tttTTTGGAGAca ttttTTGGAGAca ttttTTGGAGAca	Created Created Created Created	N N N N	-0.157 -0.208 -0.129 -0.074
50392836	rs60621976	C	C	hsa-miR-2392 hsa-miR-3605-5p hsa-miR-4459 hsa-miR-6894-5p	1 1 1 1	cgCCATCCTcctg cgcCATCCTCctg cgccatCCTCCTG cgccATCCTCCtg	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.041 -0.023 -0.085 -0.041
			T	hsa-miR-4768-3p	1	cgccatTCTCCTG	Created	N	-0.055
50392854	rs9952721	C	T	hsa-miR-3664-3p hsa-miR-4433-3p hsa-miR-4459 hsa-miR-4695-5p hsa-miR-4768-3p hsa-miR-510-5p hsa-miR-512-5p	0	gccTCCTGAGtag gcCTCCTGAgtag gCCTCCTGAgtag GCCTCCTgagtag gcCTCCTGAgtag gcctCCTGAGTAg gcctcCTGAGTAg	Created Created Created Created Created Created Created	N N N N N N N	-0.025 -0.028 -0.203 -0.14 -0.025 -0.198 -0.027
			C	hsa-miR-6746-5p hsa-miR-6771-5p	0	gcCTCCCGAgtag gcCTCCCGAgtag	Disrupted Disrupted	N N	-0.131 -0.135
50393440	rs181560821	G	G	hsa-miR-151a-3p hsa-miR-4463 hsa-miR-4499	5 5 5	atttCAGTCTAta atttCAGTCTAta attTCAGTCTAta	Disrupted Disrupted Disrupted	N N N	-0.154 -0.077 -0.22
50393444	rs186280753	A	A	hsa-miR-151a-3p hsa-miR-4463 hsa-miR-4499	5 5 5	CAGTCTAtaggta CAGTCTAtaggta CAGTCTAtaggta	Disrupted Disrupted Disrupted	N N N	-0.154 -0.077 -0.11
			G	hsa-miR-4494	5	CAGTCTGtaggta	Created	N	-0.155
50394044	rs74730636	A	A	hsa-miR-122-5p hsa-miR-3135b hsa-miR-320a hsa-miR-320b hsa-miR-320c hsa-miR-320d hsa-miR-320e hsa-miR-4429 hsa-miR-504-3p hsa-miR-9-3p	2 2 2 2 2 2 2 2 2 2	CACTCCAgcttta caCTCCAGCttta cactcCAGCTTTA cactcCAGCTTTA cactcCAGCTTTA cactcCAGCTTTA cactCCAGCTTta cactcCAGCTTTA CACTCCAgcttta cactccAGCTTTA	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N N N	-0.122 -0.23 -0.206 -0.206 -0.206 -0.206 -0.19 -0.206 -0.179 -0.039
			T	hsa-miR-4422 hsa-miR-4433-3p hsa-miR-4433b-3p hsa-miR-4722-5p hsa-miR-6165 hsa-miR-6835-3p	2 2 2 2 2 2	cactccTGCTTTA cACTCCTGcttta CACTCCTgcttta caCTCCTGCttta cacTCCTGCTtta cactccTGCTTTA	Created Created Created Created Created Created	N N N N N N	-0.031 -0.126 -0.137 -0.228 -0.178 -0.036

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