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

Secondary Structure

dm3

-23.9	-23.5	-23.0	-23.0

droSim1

-25.4	-25.0	-24.5

droSec1

-25.4	-25.0	-24.5

droYak2

-25.7	-25.3	-24.8

droEre2

-25.4	-25.0	-24.5

droAna3

-25.4	-25.0	-24.5

dp4

-23.4	-23.0	-22.8	-22.5	-22.4

droPer1

-23.4	-23.0	-22.8	-22.5	-22.4

droWil1

-25.7	-25.3	-24.8

droVir3

-24.4	-24.2	-24.0	-23.8	-23.5

droMoj3

-25.0	-24.6	-24.1

droGri2

-25.0	-24.6	-24.1

Generated: 01/05/2013 at 05:05 PM