Secondary structure and small RNA-seq evidence for dme-mir-1010

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:18118586-18118686 +	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAA----TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droSim1	chr3R:17925969-17926072 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droSec1	super_0:18476145-18476248 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droYak2	chr3R:18962287-18962391 +	GTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droEre2	scaffold_4820:9960766-9960869 -	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTCGA
droAna3	scaffold_13340:9102978-9103081 +	GTTCGTGCTTAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTATGAGGACCTGGA
dp4	chr2:12275938-12276041 +	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTT-ATTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATCTCGA
droPer1	super_0:8195066-8195169 -	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTT-ATTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATCTCGA
droWil1	scaffold_181130:12259759-12259863 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGATACGAGGATCTCGA
droVir3	scaffold_13047:8363181-8363284 -	GTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAAT-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGATCTGGA
droMoj3	scaffold_6540:27812506-27812608 +	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAT--TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATTTGGA
droGri2	scaffold_15074:1256125-1256227 +	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAAACTCTCAACAAT--TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGATCTGGA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:18118586-18118686 +	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAA----TTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droSim1	chr3R:17925969-17926072 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droSec1	super_0:18476145-18476248 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droYak2	chr3R:18962287-18962391 +	GTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA
droEre2	scaffold_4820:9960766-9960869 -	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTCGA
droAna3	scaffold_13340:9102978-9103081 +	GTTCGTGCTTAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATA-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTATGAGGACCTGGA
dp4	chr2:12275938-12276041 +	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTT-ATTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATCTCGA
droPer1	super_0:8195066-8195169 -	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTT-ATTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATCTCGA
droWil1	scaffold_181130:12259759-12259863 +	ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGATACGAGGATCTCGA
droVir3	scaffold_13047:8363181-8363284 -	GTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAAT-TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGATCTGGA
droMoj3	scaffold_6540:27812506-27812608 +	CTTTGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTCACAACAAT--TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATTTGGA
droGri2	scaffold_15074:1256125-1256227 +	GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAAACTCTCAACAAT--TTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGATCTGGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTTACCAACAATATTTTTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGCTACGAGGACCTGGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.................................................................TTTCACCTATCGTTCCATTTGC.................	22	1	529.00	529	529
.................................................................TTTCACCTATCGTTCCATTTGCAG...............	24	1	253.00	253	253
...............GTAAGTGGTGTAGATGAAACA....................................................................	21	1	207.00	207	207
.................................................................TTTCACCTATCGTTCCATTTGCA................	23	1	104.00	104	104
.................................................................TTTCACCTATCGTTCCATTTG..................	21	1	38.00	38	38
...............GTAAGTGGTGTAGATGAAAC.....................................................................	20	1	32.00	32	32
.................................................................TTTCACCTATCGTTCCATTTGCAGC..............	25	1	18.00	18	18
...............GTAAGTGGTGTAGATGAAA......................................................................	19	1	4.00	4	4
.................................................................TTTCACCTATCGTTCCATTT...................	20	1	4.00	4	4
..................................................................TTCACCTATCGTTCCATTTGC.................	21	1	1.00	1	1
..................................................................TTCACCTATCGTTCCATTTGCA................	22	1	1.00	1	1

dp4

GTTCGTGCTCAACGGGTAAGTGGTGTAGATGAAACAAATTAACCAACCTTTATTGTGTTGGATTGTTTCACCTATCGTTCCATTTGCAGGTACGAGGATCTCGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.................................................................TTTCACCTATCGTTCCATTTGC.................	22	1	1161.00	1161	595	566
.................................................................TTTCACCTATCGTTCCATTTGCAG...............	24	1	917.00	917	416	501
.................................................................TTTCACCTATCGTTCCATTTGCA................	23	1	426.00	426	128	298
...............GTAAGTGGTGTAGATGAAACA....................................................................	21	1	116.00	116	105	11
.................................................................TTTCACCTATCGTTCCATTTG..................	21	1	60.00	60	15	45
...............GTAAGTGGTGTAGATGAAAC.....................................................................	20	1	22.00	22	18	4
.................................................................TTTCACCTATCGTTCCATTT...................	20	1	7.00	7	4	3
..................................................................TTCACCTATCGTTCCATTTGC.................	21	1	6.00	6	4	2
...............GTAAGTGGTGTAGATGAAA......................................................................	19	1	5.00	5	3	2
..................................................................TTCACCTATCGTTCCATTTGCAG...............	23	1	3.00	3	1	2
.................................................................TTTCACCTATCGTTCCATT....................	19	1	2.00	2	0	2
.................AAGTGGTGTAGATGAAACA....................................................................	19	1	2.00	2	2	0
.................................................................TTTCACCTATCGTTCCATTTGCAGG..............	25	1	2.00	2	2	0
...............GTAAGTGGTGTAGATGAA.......................................................................	18	1	2.00	2	1	1
..................................................................TTCACCTATCGTTCCATTTG..................	20	1	1.00	1	1	0
..................AGTGGTGTAGATGAAACA....................................................................	18	1	1.00	1	1	0
................TAAGTGGTGTAGATGAAACA....................................................................	20	1	1.00	1	1	0
..................................................................TTCACCTATCGTTCCATTTGCA................	22	1	1.00	1	0	1
...............GTAAGTGGTGTAGATGAAACAA...................................................................	22	1	1.00	1	1	0
...............GTAAGTGGTGTAGATGAAACAAAT.................................................................	24	1	1.00	1	1	0

Secondary Structure

dm3

dG=-23.9, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-23.0, p-value=0.009901

droSim1

dG=-25.4, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.5, p-value=0.009901

droSec1

dG=-25.4, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.5, p-value=0.009901

droYak2

dG=-25.7, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-24.8, p-value=0.009901

droEre2

dG=-25.4, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.5, p-value=0.009901

droAna3

dG=-25.4, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.5, p-value=0.009901

dp4

dG=-23.4, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.4, p-value=0.009901

droPer1

dG=-23.4, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.4, p-value=0.009901

droWil1

dG=-25.7, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-24.8, p-value=0.009901

droVir3

dG=-24.4, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.5, p-value=0.009901

droMoj3

dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.1, p-value=0.009901

droGri2

dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.1, p-value=0.009901

Generated: 03/07/2013 at 04:47 PM