Secondary structure and small RNA-seq evidence for dme-mir-7

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:16493557-16493674 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droSim1	chr2R:15154934-15155051 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droSec1	super_1:14047859-14047976 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droYak2	chr2R:12702727-12702844 -	GACTGGTC-CTCC-TGGGAGTGCATTTCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droEre2	scaffold_4845:10640174-10640291 +	GATTGGTC-CTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droAna3	scaffold_13266:4109353-4109468 -	TGGGAGTC-CT-G-TGGAAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTTTATGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTCG--GCTCATCACTCT----------A
dp4	chr3:8655644-8655762 -	GATTGGCCTCTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCT----------A
droPer1	super_4:2540080-2540198 -	GATTGGCCTCTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCT----------A
droWil1	scaffold_180700:3423572-3423692 -	AAATTGTGTGTGG-T-GGAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTAATAAAATTAACAATAAATCCCTTGTCTTCTTATGGCGTGTATTTAAAGCTCTTCATT-T----------G
droVir3	scaffold_12823:2295157-2295274 -	G--TCGT-----C-TCCAAATGCTTTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCGCGCAT-TC-TGCTCTTCATTTATAATA--A-TT
droMoj3	scaffold_6496:1650020-1650148 -	TAACCGTTCGTCGTATCGAGTGCTTGCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCTCGCAT-TG-AGCTCTTCATTTCAAATCTCGTTA
droGri2	scaffold_15245:15782213-15782323 +	GTTT-------------AAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGTTAA---TAACAATAAATCCCTTGTCTCCTAACGGCGCGCAT-TG-TGCTCTTCATTAT----TTC-TTA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:16493557-16493674 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droSim1	chr2R:15154934-15155051 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droSec1	super_1:14047859-14047976 +	GATTGGTC-CTCC-TGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droYak2	chr2R:12702727-12702844 -	GACTGGTC-CTCC-TGGGAGTGCATTTCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droEre2	scaffold_4845:10640174-10640291 +	GATTGGTC-CTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCT----------A
droAna3	scaffold_13266:4109353-4109468 -	TGGGAGTC-CT-G-TGGAAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTTTATGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTCG--GCTCATCACTCT----------A
dp4	chr3:8655644-8655762 -	GATTGGCCTCTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCT----------A
droPer1	super_4:2540080-2540198 -	GATTGGCCTCTCC-TGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCT----------A
droWil1	scaffold_180700:3423572-3423692 -	AAATTGTGTGTGG-T-GGAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTAATAAAATTAACAATAAATCCCTTGTCTTCTTATGGCGTGTATTTAAAGCTCTTCATT-T----------G
droVir3	scaffold_12823:2295157-2295274 -	G--TCGT-----C-TCCAAATGCTTTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCGCGCAT-TC-TGCTCTTCATTTATAATA--A-TT
droMoj3	scaffold_6496:1650020-1650148 -	TAACCGTTCGTCGTATCGAGTGCTTGCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCTCGCAT-TG-AGCTCTTCATTTCAAATCTCGTTA
droGri2	scaffold_15245:15782213-15782323 +	GTTT-------------AAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGTTAA---TAACAATAAATCCCTTGTCTCCTAACGGCGCGCAT-TG-TGCTCTTCATTAT----TTC-TTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GATTGGTC-CTCCTGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTGTGCTCTTCATTCTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................TGGAAGACTAGTGATTTTGTTGTT.................................................................	24	1	2878.00	2878	2878
..............................TGGAAGACTAGTGATTTTGTTG...................................................................	22	1	1061.00	1061	1061
..............................TGGAAGACTAGTGATTTTGTTGT..................................................................	23	1	563.00	563	563
......................................................................CAATAAATCCCTTGTCTTCTTA...........................	22	1	490.00	490	490
..............................TGGAAGACTAGTGATTTTGTT....................................................................	21	1	183.00	183	183
..............................TGGAAGACTAGTGATTTTGTTGTTT................................................................	25	1	40.00	40	40
..............................TGGAAGACTAGTGATTTTGT.....................................................................	20	1	31.00	31	31
.......................................................................AATAAATCCCTTGTCTTCTTA...........................	21	1	29.00	29	29
......................................................................CAATAAATCCCTTGTCTTCTT............................	21	1	12.00	12	12
..................................AGACTAGTGATTTTGTTGTT.................................................................	20	1	3.00	3	3
.......................................................................AATAAATCCCTTGTCTTCTT............................	20	1	3.00	3	3
....................................ACTAGTGATTTTGTTGTT.................................................................	18	1	2.00	2	2
.................................AAGACTAGTGATTTTGTTGT..................................................................	20	1	1.00	1	1
...................................GACTAGTGATTTTGTTGTT.................................................................	19	1	1.00	1	1
.......C-CTCCTGGGAGTGCATTCCGTA.........................................................................................	22	1	1.00	1	1

dp4

GATTGGCCTCTCCTGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTGTGCTCTTCATTCTA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................TGGAAGACTAGTGATTTTGTTG...................................................................	22	1	5273.00	5273	920	4353
..............................TGGAAGACTAGTGATTTTGTT....................................................................	21	1	2114.00	2114	177	1937
..............................TGGAAGACTAGTGATTTTGTTGTT.................................................................	24	1	1880.00	1880	1031	849
..............................TGGAAGACTAGTGATTTTGTTGT..................................................................	23	1	1212.00	1212	587	625
......................................................................CAATAAATCCCTTGTCTTCTTA...........................	22	1	773.00	773	768	5
..............................TGGAAGACTAGTGATTTTGT.....................................................................	20	1	449.00	449	24	425
..............................TGGAAGACTAGTGATTTTGTTGTTT................................................................	25	1	61.00	61	40	21
.......................................................................AATAAATCCCTTGTCTTCTTA...........................	21	1	36.00	36	36	0
..............................TGGAAGACTAGTGATTTTG......................................................................	19	1	33.00	33	1	32
..............................TGGAAGACTAGTGATTTT.......................................................................	18	1	10.00	10	0	10
......................................................................CAATAAATCCCTTGTCTTCTT............................	21	1	6.00	6	6	0
.......................................................................AATAAATCCCTTGTCTTCTT............................	20	1	4.00	4	4	0
.................................AAGACTAGTGATTTTGTTG...................................................................	19	1	2.00	2	0	2
...................................GACTAGTGATTTTGTTGTT.................................................................	19	1	1.00	1	1	0
......................................................................CAATAAATCCCTTGTCTTC..............................	19	1	1.00	1	0	1
......................ATTCCGTATGGAAGACTAGT.............................................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901

droSim1

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901

droSec1

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901

droYak2

dG=-20.5, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.2, p-value=0.009901

droEre2

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901

droAna3

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901

dp4

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

droPer1

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

droWil1

dG=-21.2, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-20.8, p-value=0.009901

droVir3

dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901

droMoj3

dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901

droGri2

dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-19.8, p-value=0.009901

Generated: 03/07/2013 at 07:01 PM