Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

Hazra, Anjan; Dasgupta, Nirjhar; Sengupta, Chandan; Das, Sauren

doi:10.1186/s13104-017-2577-x

BMC Research Notes

Table 1 List of predicted microRNAs and occurrence of SSR motifs with designed primer

From: Extrapolative microRNA precursor based SSR mining from tea EST database in respect to agronomic traits

Predicted miRNA	Precusor id	MFE (−kCal)	References	SSR start	SSR end	SSR motif	SSR length	Primer F	Primer R	Product size
miR164	CV013669	20	[21]
miR169	GE650220	7.8	[21]	81	93	CGC	3	GGAGTGAAGGAGGGAAGA	CCGAGAGAATAATAAGGAGGA	205
miR1846	DN976181	40.5	[21]
miR1863	GH623864	19.2	[21]	224	236	GAG	3	AGTGATTATTGGTGGTGGTC	TCTCAACCAATTCAACAAGTC	152
miR 408	GD254786.1	120.1	[22]	519	541	TA	2	CTGTTACTGCAGCTTAACCAA	AAATATGCTGCTCATTCAAAC	152
				142	154	GGC	3	AGAAGATGTCTCAGGGAAGAG	ACACAAGTATGTCACCAGCTC	177
csi-miR1171	FE943069.1	45.97	[22]	280	295	GTGGA	5	GAACCTTTCCTCCAGAATTTA	TCACATTTAGCTTTTCACTCC	162
csi-miR414a	GD254734.1	63.18	[22]
csi-miR414d	GW342817.1	37.72	[22]	170	188	GATGAC	6	ACGATGGTGGTTATGAATATG	GGGTTTTTGTTAAGTTGTTCA	139
csi-miR414f	GE651542.1	18.5	[22]	99	111	TTC	3	AGACAAAAACCAAGGCTAGAT	CATCTTGTGCAGATCTCAGTT	149
				121	139	ATC	3	AGACAAAAACCAAGGCTAGAT	CATCTTGTGCAGATCTCAGTT	149
cas-miR1122	EU849076.1	91.23	[22]
csi-miR414 g	CV013826.1	25.2	[22]	504	519	CTC	3	TGATGATGAGGAAGGAGATAA	TTGCTTTAGTGAAACAACTCC	136
csi-miRf10132-akr	CV014169.1	69.5	[22]
cja-miR2910	U42815.1	−91	[22]
csi-miR2914	AB120309.1	20.9	[22]
cas-miRf10185-akr	GH623933.1	51.1	[22]
cas-miR11590-akr	GE651674.1	23.8	[22]
csi-miR414 h	GW863581.1	86.83	[22]
miR156	HS396956.1	45.8	[23]	113	125	AAC	3	CGTTAGGCTATTTTGTTTCAA	TTCTGTCAATCATCCAATTTC	159
miR171a	FS948108.1	39.2	[23]	115	127	TC	2	TACTTCCAACCAAACACAAGT	TAGCTTACCACCTCAATCAAA	168
miR171b	FS948109.1	40.4	[23]
miR397	CV699725.1	39.2	[23]
miR399	FS958856.1	52.8	[23]
miR2863	FS950435.1	21.5	[23]	57	69	TCTA	4	CTCCTGTACACTCTCTCTCTCC	GATGAACAGCATAGGTATCCA	127
miR2911a	JK476023.1	65.4	[23]
miR2911b	FS953337.1	69.2	[23]
miR5021a	GW690847.1	71.9	[23]	72	84	GGA	3	AGACACAGGCAGACATAGAGA	AAGATGCGATGAGATCAGATA	165
				239	254	TTC	3	AGATACACATTGGGAAGAAGG	TAGAACTTGCAGAGAGAAACG	149
				252	264	TC	2	AGATACACATTGGGAAGAAGG	TAGAACTTGCAGAGAGAAACG	149
miR5021b	GE651759.1	72.2	[23]	60	78	GA	2	TAGAACTTGCAGAGAGAATCG	TACACATTGGGAAGAAGAAGA	152
				75	90	AGA	3	TAGAACTTGCAGAGAGAATCG	TACACATTGGGAAGAAGAAGA	152
miR5368a	GE653011.1	76.1	[23]
miR5368b	FS945766.1	68.5	[23]
miR6483a	HS398296.1	29.8	[23]
miR6483b	JK714410.1	30	[23]
miR1533	JK478587.1	89.99	Reported	403	419	AC	2
miR8002-3p	FS955851.1	155.67	Reported

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ISSN: 1756-0500

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