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.