Secondary structure and small RNA-seq evidence for dme-mir-305

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:7425957-7426059 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droSim1	chr2L:7217527-7217627 +	GTAT--------CA-C-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droSec1	super_3:2941418-2941520 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droYak2	chr2L:5473614-5473716 -	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGC-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droEre2	scaffold_4929:16344683-16344785 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGT-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droAna3	scaffold_12916:15334141-15334251 +	GTATTTTTGAGAAATA-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCA-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAATGTCAA----------------AC
dp4	chr4_group1:4175881-4175974 +	G----------------------------------------------------TCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-CTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAAGTTCGT----------------GC
droPer1	super_5:1086315-1086408 -	G----------------------------------------------------TCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-CTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAAGTTCGT----------------GC
droWil1	scaffold_180772:5257378-5257513 -	GATT--------CT-CTTTTTTTTTTATTGGCATTTTTAATTTATTGTTGTTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCGTTTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGATCTTCAT------------------
droVir3	scaffold_12963:15419827-15419927 -	GTTT--------CA-------------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGAC-TTGTAACCCGGCACATGTTGAAGTACACTCAATATGCGTTGATTTGCAT----------------TT
droMoj3	scaffold_6500:18399247-18399346 -	GTGT--------C----------------------------------------TCCCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAG-TGGAAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGATTTGCAGTT--------------GC
droGri2	scaffold_15126:5008540-5008648 +	------------------------------------------------------CTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGATTGGCATTTGCTGCGTTTTAATTAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:7425957-7426059 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droSim1	chr2L:7217527-7217627 +	GTAT--------CA-C-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droSec1	super_3:2941418-2941520 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droYak2	chr2L:5473614-5473716 -	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGC-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droEre2	scaffold_4929:16344683-16344785 +	GTAT--------CAAC-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGT-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCAT----------------AC
droAna3	scaffold_12916:15334141-15334251 +	GTATTTTTGAGAAATA-----------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCA-CCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAATGTCAA----------------AC
dp4	chr4_group1:4175881-4175974 +	G----------------------------------------------------TCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-CTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAAGTTCGT----------------GC
droPer1	super_5:1086315-1086408 -	G----------------------------------------------------TCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTC-CTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAAGTTCGT----------------GC
droWil1	scaffold_180772:5257378-5257513 -	GATT--------CT-CTTTTTTTTTTATTGGCATTTTTAATTTATTGTTGTTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCGTTTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGATCTTCAT------------------
droVir3	scaffold_12963:15419827-15419927 -	GTTT--------CA-------------------------------------TGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGAC-TTGTAACCCGGCACATGTTGAAGTACACTCAATATGCGTTGATTTGCAT----------------TT
droMoj3	scaffold_6500:18399247-18399346 -	GTGT--------C----------------------------------------TCCCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAG-TGGAAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGATTTGCAGTT--------------GC
droGri2	scaffold_15126:5008540-5008648 +	------------------------------------------------------CTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAC-TCGTAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGATTGGCATTTGCTGCGTTTTAATTAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTATC-ACTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTCTCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGATTTGCATAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................ATTGTACTTCATCAGGTGCTCT...........................................................	22	2	514.50	1029	1029
......................ATTGTACTTCATCAGGTGCTCTGG.........................................................	24	2	167.50	335	335
......................ATTGTACTTCATCAGGTGCT.............................................................	20	2	129.00	258	258
......................ATTGTACTTCATCAGGTGCTCTG..........................................................	23	2	31.50	63	63
............................................................CGGCACATGTTGAAGTACACTC.....................	22	2	19.00	38	38
......................ATTGTACTTCATCAGGTGCTCTGGT........................................................	25	2	5.50	11	11
...........................................................CCGGCACATGTTGAAGTACACT......................	22	2	1.50	3	3
............................................................CGGCACATGTTGAAGTACA........................	19	2	1.50	3	3
...........................................................CCGGCACATGTTGAAGTACAC.......................	21	2	1.00	2	2
............................CTTCATCAGGTGCTCTGG.........................................................	18	2	0.50	1	1
.....................TATTGTACTTCATCAGGTGCTCT...........................................................	23	2	0.50	1	1
.........................GTACTTCATCAGGTGCTCTGG.........................................................	21	2	0.50	1	1

dp4

G---------TCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTCCTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAAGTTCGTGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
......................ATTGTACTTCATCAGGTGCTCT...........................................................	22	2	1722.50	3445	0	3445
......................ATTGTACTTCATCAGGTGCT.............................................................	20	2	1313.00	2626	315	2311
......................ATTGTACTTCATCAGGTGCTC............................................................	21	2	720.50	1441	1441	0
......................ATTGTACTTCATCAGGTGCTCTGG.........................................................	24	2	120.00	240	240	0
......................ATTGTACTTCATCAGGTGCTCTG..........................................................	23	2	44.50	89	89	0
...........................................................CCGGCACATGTTGAAGTACACT......................	22	2	9.00	18	3	15
......................ATTGTACTTCATCAGGTGC..............................................................	19	2	4.50	9	0	9
............................................................CGGCACATGTTGAAGTACA........................	19	2	3.50	7	5	2
.......................TTGTACTTCATCAGGTGCTCTGG.........................................................	23	2	3.00	6	6	0
...........................ACTTCATCAGGTGCTCTGG.........................................................	19	2	2.50	5	4	1
........................TGTACTTCATCAGGTGCTC............................................................	19	2	1.00	2	0	2

Secondary Structure

dm3

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droSim1

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droSec1

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droYak2

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droEre2

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droAna3

dG=-22.8, p-value=0.009901

dp4

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droPer1

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droWil1

dG=-22.7, p-value=0.009901

droVir3

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.3, p-value=0.009901

droMoj3

dG=-24.1, p-value=0.009901

droGri2

dG=-22.8, p-value=0.009901

Generated: 03/07/2013 at 05:11 PM