SomamiR DB 2.0
Somatic mutations altering microRNA-ceRNA interactions
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PolymiRTS Database
Prediction criteria: TargetScan sites only     All 6mer or longer seed matches
RefSeq ID: NM_025208
Gene Symbol: PDGFD
Description: Homo sapiens platelet derived growth factor D (PDGFD), transcript variant 1, mRNA.
Gene Location: chr11(-):103777913-104035027
Browse Associations
Browse Pathways

Somatic mutations that impact miRNA target sites


Mutation Mutation ID Sample Name Cancer Type
chr11:g.103907486A>T COSN8729258 AOCS-064-3-3 [ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-130a-3p atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.213000 no TS No effect
hsa-miR-130b-3p atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.203000 no TS No effect
hsa-miR-19a-3p atctTTTGCACttctaaca
 1
 UGUGCAAA m7b Disrupted -0.182000 no TS 0.040000
hsa-miR-19b-3p atctTTTGCACttctaaca
 1
 UGUGCAAA m7b Disrupted -0.182000 no TS 0.030000
hsa-miR-301a-3p atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.203000 no TS No effect
hsa-miR-301b atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.213000 no TS 0.010000
hsa-miR-3666 atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.231000 no TS No effect
hsa-miR-4295 atcttTTGCACTtctaaca
 10
 CAGUGCAA m7b Disrupted -0.166000 no TS No effect
hsa-miR-454-3p atcttTTGCACTtctaaca
 10
 UAGUGCAA m7b Disrupted -0.194000 no TS 0.010000
hsa-miR-4795-5p atcttttgCACTTCTaaca
 0 AGAAGUGG m7a Disrupted NA NA -2.120000
hsa-miR-5197-3p atcttttgCTCTTCTaaca
 0 AAGAAGAG m7b Created no TS -0.234000 0.040000
hsa-miR-519a-3p atctttTGCACTTctaaca
 9
 AAAGUGCA m7b Disrupted -0.391000 -0.185000 No effect
hsa-miR-519b-3p atctttTGCACTTctaaca
 9
 AAAGUGCA m7b Disrupted -0.391000 -0.185000 No effect
hsa-miR-519c-3p atctttTGCACTTctaaca
 9
 AAAGUGCA m7b Disrupted -0.391000 -0.185000 No effect
hsa-miR-548aj-5p atCTTTTGCActtctaaca
 1
 UGCAAAAG m8a (m8a->m7b) -0.238000 -0.154000 0.010000
hsa-miR-548aw atcTTTTGCACttctaaca
 1
 GUGCAAAA m8a Disrupted -0.060000 0.007000 0.160000
hsa-miR-548g-5p atCTTTTGCActtctaaca
 1
 UGCAAAAG m8a (m8a->m7b) -0.238000 -0.154000 0.010000
hsa-miR-548p atcTTTTGCTcttctaaca
 9
 UAGCAAAA m7b (m6c->m7b) -0.040000 -0.125000 No effect
hsa-miR-548x-5p atCTTTTGCActtctaaca
 1
 UGCAAAAG m8a (m8a->m7b) -0.238000 -0.154000 0.010000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103907510C>A COSN1125551 HX15T [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-4434 aaaCTTCTCCcttggttac
 8
 AGGAGAAG m7b (m7b->m6c) -0.203000 no TS 2.030000
hsa-miR-4516 aaaCTTCTCCCttggttac
 8
 GGGAGAAG m8a Disrupted -0.166000 no TS 0.170000
hsa-miR-5703 aaaCTTCTCCcttggttac
 8
 AGGAGAAG m7b (m7b->m6c) -0.203000 no TS 3.840000
hsa-miR-4434 aaaCTTCTCCcttggttac
 0 AGGAGAAG m7b (m7b->m6c) -0.203 no TS 2.03
hsa-miR-4516 aaaCTTCTCCCttggttac
 0 GGGAGAAG m8a Disrupted -0.166 no TS 0.17
hsa-miR-5703 aaaCTTCTCCcttggttac
 0 AGGAGAAG m7b (m7b->m6c) -0.203 no TS 3.84

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103907515T>C COSN15114030 SM-4B296 [oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-4434 tattaaaaCTTCTCCcttg
 8
 AGGAGAAG m7b Disrupted -0.203000 no TS 2.100000
hsa-miR-4516 tattaaaaCTTCTCCCttg
 8
 GGGAGAAG m8a Disrupted -0.166000 no TS 0.170000
hsa-miR-5703 tattaaaaCTTCTCCcttg
 8
 AGGAGAAG m7b Disrupted -0.203000 no TS 4.420000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103908426G>A COSN1510295 RK137_C01 [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-376a-3p taaTCTATGAagcttgctt
 0 AUCAUAGA m7b (m6c->m7b) no TS -0.027000 -0.250000
hsa-miR-376b taaTCTATGAagcttgctt
 0 AUCAUAGA m7b (m6c->m7b) no TS -0.038000 -0.100000
hsa-miR-376a-3p taaTCTATGAagcttgctt
 0 AUCAUAGA m7b (m6c->m7b) no TS -0.027 -0.25
hsa-miR-376b taaTCTATGAagcttgctt
 0 AUCAUAGA m7b (m6c->m7b) no TS -0.038 -0.1

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103908754C>A COSN6606627 CHC433T [liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-33a-3p aaaagtgAACATTGaaaca
 0 CAAUGUUU m7a Disrupted NA NA 4.360000
hsa-miR-5096 aaaaGTGAAAattgaaaca
 0 GUUUCACC m6b Created 0.016000 0.024000 -0.220000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103908836A>G COSN15109689 SM-4B296 [oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-1200 atccttTCAGGAatggcat
 0 CUCCUGAG m6b Created no TS -0.029000 No effect
hsa-miR-3140-5p atcctTTCAGGaatggcat
 0 ACCUGAAU m6b Created no TS -0.023000 -0.170000
hsa-miR-378a-5p atccttTCAGGAatggcat
 0 CUCCUGAC m6b Created no TS -0.032000 -2.840000
hsa-miR-4635 atcctTTCAAGAatggcat
 6
 UCUUGAAG m7a Disrupted 0.042000 no TS No effect
hsa-miR-4766-5p atcCTTTCAGgaatggcat
 0 UCUGAAAG m7b (m6c->m7b) no TS -0.006000 -0.120000
hsa-miR-488-3p atCCTTTCAAgaatggcat
 3
 UUGAAAGG m8a (m8a->m7b) -0.135000 -0.066000 0.010000
hsa-miR-526b-5p atccttTCAAGAatggcat
 1
 CUCUUGAG m6b Disrupted -0.093000 -0.096000 0.230000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103909394->TTT ICGC_ssm_v2_17278 HX5T [liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-3613-3p aatgttTTTTTTGgtatatataa
 0 ACAAAAAA m7b Disrupted 0.126000 0.094000 -0.750000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103909545G>T COSN1125553 BN31T [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-330-3p cctTGCTTTGttaatgcca
 1
 GCAAAGCA m7b (m7b->m6c) -0.209000 -0.056000 0.050000
hsa-miR-495 ccttgcTTTGTTaatgcca
 0 AAACAAAC m6b Disrupted 0.029000 no TS 0.020000
hsa-miR-5688 ccttgcTTTGTTAatgcca
 0 UAACAAAC m7a Disrupted 0.032000 no TS 0.507000
hsa-miR-7-1-3p ccttgcTTTGTTaatgcca
 0 CAACAAAU m6b Disrupted 0.030000 no TS 1.400000
hsa-miR-7-2-3p ccttgcTTTGTTaatgcca
 0 CAACAAAU m6b Disrupted 0.033000 no TS 0.350000
hsa-miR-330-3p cctTGCTTTGttaatgcca
 0 GCAAAGCA m7b (m7b->m6c) -0.209 -0.056 0.05
hsa-miR-495 ccttgcTTTGTTaatgcca
 0 AAACAAAC m6b Disrupted 0.029 no TS 0.02
hsa-miR-5688 ccttgcTTTGTTAatgcca
 0 UAACAAAC m7a Disrupted 0.032 no TS 0.507
hsa-miR-7-1-3p ccttgcTTTGTTaatgcca
 0 CAACAAAU m6b Disrupted 0.03 no TS 1.4
hsa-miR-7-2-3p ccttgcTTTGTTaatgcca
 0 CAACAAAU m6b Disrupted 0.033 no TS 0.35

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103909562A>T COSN8729259 AOCS-001-1-7 [ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-3120-3p tggTTGCTGTGtctcagcc
 0 CACAGCAA m8a Created no TS -0.067000 -0.750000
hsa-miR-3672 tggttgctgAGTCTCAgcc
 3
 AUGAGACU m7b (m7b->m6b) -0.096000 no TS 3.860000
hsa-miR-512-5p tggttGCTGAGTctcagcc
 7
 CACUCAGC m7b Disrupted -0.200000 no TS 2.560000
hsa-miR-873-3p tggttgctgAGTCTCagcc
 3
 GGAGACUG m6b Disrupted -0.096000 no TS No effect

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103909612C>T COSN15450165 AOCS-164-1-7 [ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-138-5p tcctACCAGCaaccaaact
 2
 AGCUGGUG m6b Disrupted -0.302000 -0.138000 0.110000
hsa-miR-409-5p tcctaccaGTAACCaaact
 0 AGGUUACC m6b Created no TS -0.146000 -0.010000

Mutation Mutation ID Sample Name Cancer Type
chr11:g.103909666C>A COSN8863128 SNUH_G16_S1 [haematopoietic_and_lymphoid_tissue][NS][haematopoietic_neoplasm][acute_myeloid_leukaemia]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-30a-3p acattaagcCTGAAAGaac
 0 CUUUCAGU m7a (m7a->m6a) NA NA 0.080000
hsa-miR-30d-3p acattaagcCTGAAAGaac
 0 CUUUCAGU m7a (m7a->m6a) NA NA No effect
hsa-miR-30e-3p acattaagcCTGAAAGaac
 0 CUUUCAGU m7a (m7a->m6a) NA NA 0.180000
hsa-miR-3155a acattaAGCCTGaaagaac
 2
 CCAGGCUC m6b Disrupted -0.196000 no TS 0.090000
hsa-miR-3155b acattaAGCCTGaaagaac
 2
 CCAGGCUC m6b Disrupted -0.196000 no TS 0.140000
hsa-miR-484 acattaAGCCTGAaagaac
 2
 UCAGGCUC m7a Disrupted -0.189000 no TS 0.020000

*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
103909392 rs199962975 G
T hsa-miR-410-3p
hsa-miR-495-3p
hsa-miR-5688
hsa-miR-7-1-3p
hsa-miR-7-2-3p
2
2
2
2
2
 tttttGTTATATA
ttTTTGTTAtata
ttTTTGTTAtata
ttTTTGTTAtata
ttTTTGTTAtata
 Created
Created
Created
Created
Created
N
N
N
N
N
 -0.148
-0.015
-0.015
-0.008
-0.004
103909393 rs202088609 - - hsa-miR-3613-3p
1
 ttTTTTTTGgtatatat
 Unknown
N
 0.032
TTT
103909394 rs60621493 - - hsa-miR-3613-3p
1
 gttTTTTTTGgtatata
 Unknown
N
 0.032
TTT
103909614 rs75277266 A A hsa-miR-133a-5p
hsa-miR-138-5p
hsa-miR-6131
1
6
6
 ccTACCAGCAacc
cctACCAGCAacc
cctACCAGCAacc
 Disrupted
Disrupted
Disrupted
N
N
N
 -0.403
-0.164
-0.162
G hsa-miR-656-5p
10
 cctaccGGCAACC
 Created
N
 -0.302
103909666 rs147740543 C C hsa-miR-3155a
hsa-miR-3155b
hsa-miR-484
2
2
2
 ttaAGCCTGAaag
ttaAGCCTGAaag
ttaAGCCTGAaag
 Disrupted
Disrupted
Disrupted
N
N
N
 -0.196
-0.196
-0.189
A hsa-miR-4720-3p
hsa-miR-4804-3p
2
2
 TTAAGCAtgaaag
TTAAGCAtgaaag
 Created
Created
N
N
 -0.108
-0.099

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