Secondary structure and small RNA-seq evidence for dme-mir-307a

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:5508741-5508858 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droSim1	chr2R:4140609-4140726 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAGC
droSec1	super_1:3126041-3126158 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAGC
droYak2	chr2L:18140631-18140748 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droEre2	scaffold_4929:8848869-8848986 +	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droAna3	scaffold_13266:12795467-12795585 -	AAGT---------TAG--CAGCCTTTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACAAGAC
dp4	chr3:14135687-14135806 -	AAGT---------TCGGGTCGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droPer1	super_4:1183061-1183180 +	AAGT---------TCGGGTCGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droWil1	scaffold_180701:3433650-3433765 -	---T---------TAA--CA-CA-TTTTGCCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTTATAATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGT
droVir3	scaffold_12875:5789441-5789560 -	AAAT---------AAACCGAACA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTAGTT-CGATTTGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAGTATCCACTAAGC
droMoj3	scaffold_6496:24271667-24271782 +	AAAC---------TA----AGAA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATTCGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droGri2	scaffold_15112:722942-723066 -	AAAATAAAAGAACT----AAACA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATTTGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAGAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:5508741-5508858 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droSim1	chr2R:4140609-4140726 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAGC
droSec1	super_1:3126041-3126158 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAGC
droYak2	chr2L:18140631-18140748 -	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droEre2	scaffold_4929:8848869-8848986 +	AAGT---------TAG--CAGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAAC
droAna3	scaffold_13266:12795467-12795585 -	AAGT---------TAG--CAGCCTTTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACAAGAC
dp4	chr3:14135687-14135806 -	AAGT---------TCGGGTCGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droPer1	super_4:1183061-1183180 +	AAGT---------TCGGGTCGCA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droWil1	scaffold_180701:3433650-3433765 -	---T---------TAA--CA-CA-TTTTGCCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTTATAATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGT
droVir3	scaffold_12875:5789441-5789560 -	AAAT---------AAACCGAACA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTAGTT-CGATTTGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAGTATCCACTAAGC
droMoj3	scaffold_6496:24271667-24271782 +	AAAC---------TA----AGAA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATTCGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC
droGri2	scaffold_15112:722942-723066 -	AAAATAAAAGAACT----AAACA-TTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTT-CGATTTGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAGAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGTTA--GCAGCATTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTTCGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGACAGAGTATCCACGAAGC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
........................................................................TCACAACCTCCTTGAGTGAGCGA.........................	23	2	40.50	81	81
........................................................................TCACAACCTCCTTGAGTGAGC...........................	21	2	25.00	50	50
..........................................................................ACAACCTCCTTGAGTGAGCGA.........................	21	2	3.00	6	6
..........................................................................ACAACCTCCTTGAGTGAGCG..........................	20	2	1.00	2	2
............................GACTCACTCAACCTGGGTGTGA......................................................................	22	2	0.50	1	1
.............................ACTCACTCAACCTGGGTGTGA......................................................................	21	2	0.50	1	1
.......................................................................ATCACAACCTCCTTGAGTGAGCGA.........................	24	2	0.50	1	1
.............................ACTCACTCAACCTGGGTGTGATG....................................................................	23	2	0.50	1	1
..........................................................................ACAACCTCCTTGAGTGAGC...........................	19	2	0.50	1	1
.............................ACTCACTCAACCTGGGTGTGATGT...................................................................	24	2	0.50	1	1
........................................................................TCACAACCTCCTTGAGTGAG............................	20	2	0.50	1	1
........................................................................TCACAACCTCCTTGAGTGAGCGAT........................	24	2	0.50	1	1

dp4

AAGTTCGGGTCGCATTTTGTCTTGCTTTGACTCACTCAACCTGGGTGTGATGTTATTTCGATATGGTATCCATCACAACCTCCTTGAGTGAGCGATAGCAGGATAGAATATCCACAAAGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
........................................................................TCACAACCTCCTTGAGTGAGCG..........................	22	2	7034.00	14068	0	14068
........................................................................TCACAACCTCCTTGAGTGAG............................	20	2	2238.50	4477	5	4472
.........................................................................CACAACCTCCTTGAGTGAGCGA.........................	22	2	548.00	1096	18	1078
.........................................................................CACAACCTCCTTGAGTGAGC...........................	20	2	435.00	870	2	868
........................................................................TCACAACCTCCTTGAGTGA.............................	19	2	164.50	329	3	326
..........................................................................ACAACCTCCTTGAGTGAGC...........................	19	2	69.00	138	0	138
.........................................................................CACAACCTCCTTGAGTGAGCGAT........................	23	2	53.00	106	0	106
.............................ACTCACTCAACCTGGGTGT........................................................................	19	2	24.50	49	0	49
.............................ACTCACTCAACCTGGGTGTGAT.....................................................................	22	2	17.50	35	0	35
............................GACTCACTCAACCTGGGTGT........................................................................	20	2	10.50	21	0	21
.............................ACTCACTCAACCTGGGTGTGATG....................................................................	23	2	10.00	20	0	20
.............................ACTCACTCAACCTGGGTGTGA......................................................................	21	2	8.00	16	1	15
.............................ACTCACTCAACCTGGGTGTGATGT...................................................................	24	2	1.00	2	2	0

Secondary Structure

dm3

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droSim1

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droSec1

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droYak2

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droEre2

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droAna3

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

dp4

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droPer1

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

droWil1

dG=-27.0, p-value=0.009901	dG=-27.0, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901

droVir3

dG=-24.8, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.6, p-value=0.009901

droMoj3

dG=-26.0, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.8, p-value=0.009901

droGri2

dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901

Generated: 03/07/2013 at 05:14 PM