Bioinformatics Approach for Prediction of Functional Coding/Noncoding Simple Polymorphisms (SNPs/Indels) in Human BRAF Gene
Table 6
Predicted results of functional 3′ UTR SNPs/Indels.
dbSNP ID
Variant type
Ancestral allele
Allele
miR ID
Conservation
miRSite
Function class
Context + score change
rs114105685
SNP
G
A
hsa-miR-30a-5p
3
gTGTTTACAggtg
C
hsa-miR-30b-5p
3
gTGTTTACAggtg
C
hsa-miR-30c-5p
3
gTGTTTACAggtg
C
hsa-miR-30d-5p
3
gTGTTTACAggtg
C
hsa-miR-30e-5p
3
gTGTTTACAggtg
C
hsa-miR-3607-3p
4
gtgTTTACAGgtg
C
No change
rs184804021
SNP
T
T
hsa-miR-3908
4
tagaCATTGCTAa
D
hsa-miR-3942-5p
5
tagacATTGCTAa
D
hsa-miR-4703-5p
5
tagacATTGCTAa
D
hsa-miR-4766-3p
5
tagacATTGCTAA
D
C
hsa-miR-374b-3p
5
tagacaCTGCTAA
C
hsa-miR-4274
5
tagacACTGCTAa
C
hsa-miR-4519
4
tagaCACTGCTAa
C
hsa-miR-4524a-5p
5
tagacaCTGCTAA
C
hsa-miR-4524b-5p
5
tagacaCTGCTAA
C
hsa-miR-6499-3p
7
tagACACTGCtaa
C
hsa-miR-6733-3p
5
taGACACTGctaa
C
rs140083479
SNP
A
A
hsa-miR-3908
4
atagaCATTGCTA
D
hsa-miR-3942-5p
5
atagacATTGCTA
D
hsa-miR-4703-5p
5
atagacATTGCTA
D
hsa-miR-4766-3p
5
atagacATTGCTA
D
hsa-miR-4796-5p
3
ATAGACAttgcta
D
T
hsa-miR-548p
5
atagacTTTGCTA
C
rs200393520
Indel
—
—
hsa-miR-4311
2
acTCTCTTTtttt
O
0.004
T
rs143647707
SNP
A
A
hsa-miR-5580-3p
3
gaaCATATGTttg
D
T
hsa-miR-7-1-3p
4
gaacATTTGTTtg
C
hsa-miR-7-2-3p
4
gaacATTTGTTtg
C
rs202148822
SNP
G
G
hsa-miR-1976
3
tCAGGAGAgtagc
D
hsa-miR-6845-3p
3
tcAGGAGAGtagc
D
Conservation: occurrence of the miRNA site in other vertebrate genomes in addition to the query genome. miRSite: sequence context of the miRNA site: bases complementary to the seed region are in capital letters and SNPs are highlighted in bold font. Function class: D: the derived allele disrupts a conserved miRNA site (ancestral allele with support > 2); C: the derived allele creates a new miRNA site; O: the ancestral allele can not be determined. Context score: negative increase = increase in SNP functionality.