Secondary structure and small RNA-seq evidence for dme-mir-5

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548648-15548746 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTT----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTTTAAA---GTCCAC
droSim1	chr2R:14254083-14254180 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTC----CC-AACATATCACAGTGATTTTCCTTTATATCGCATGTTAAAA---GTCCAC
droSec1	super_1:13063377-13063475 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTC----CCGAACATATCACAGTGATTTTCCTTTATAACGCATGTTTAAA---GTCCAC
droYak2	chr2R:13624045-13624143 +	TTT----------AA-CGGGCCGTTCGCTAAAAGGAACGATCGTTGTGATATGCGTTA-TTC----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTACAAA---GTCCAC
droEre2	scaffold_4845:9748899-9748997 -	TTT----------GA-CGGGCCGTTCGCTAAAAGGAACGATCGTTGTGATATGCGTTG-TTC----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTAAAAA---GTCCAA
droAna3	scaffold_13266:9731665-9731765 +	TTC----------TA-AGGACCATTCGCTAAAAGGAACGATCGTTGTGATATGCGTTT-ATCC-CTCGTTACATATCACAGTGATTTTCCTTTATAACGCATGCAG-TT---GTCCAA
dp4	chr3:12677226-12677327 -	TTC----------CTAGGGGCCATACGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATTC-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCATGTCT-GC---GCCCAC
droPer1	super_2:8906345-8906446 +	TTC----------CTAGGGGCCATACGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATTC-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCATGTCT-GC---GCCCAC
droWil1	scaffold_180701:1651453-1651556 -	TTT----------TTCTGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGCGTTAGATTC-ACCGTTATATATCACAGTGATTTTCCTTTATAGCGCATGCAT-GTTCTGTC--C
droVir3	scaffold_12875:4112452-4112549 +	TAA----------AT-TGGGTCATGCTCTAAAAGGAACGATCGTTGTGATATGCGTTC-ATTA-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGC----A---GCCCGT
droMoj3	scaffold_6496:20936453-20936560 -	TGCAAACTCGATGAA-TGGGCCATGCGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATCG-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGC----A---GTCCCC
droGri2	scaffold_15112:2108518-2108620 -	GTC------G---TTATGGGTCACTCGCTAAAAGGAACGATCGTTGTGATATGCGTTC-ATTAAATCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGCTC--T---GCCCAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548648-15548746 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTT----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTTTAAA---GTCCAC
droSim1	chr2R:14254083-14254180 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTC----CC-AACATATCACAGTGATTTTCCTTTATATCGCATGTTAAAA---GTCCAC
droSec1	super_1:13063377-13063475 -	TTC----------AT-CGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTC----CCGAACATATCACAGTGATTTTCCTTTATAACGCATGTTTAAA---GTCCAC
droYak2	chr2R:13624045-13624143 +	TTT----------AA-CGGGCCGTTCGCTAAAAGGAACGATCGTTGTGATATGCGTTA-TTC----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTACAAA---GTCCAC
droEre2	scaffold_4845:9748899-9748997 -	TTT----------GA-CGGGCCGTTCGCTAAAAGGAACGATCGTTGTGATATGCGTTG-TTC----CCTAACATATCACAGTGATTTTCCTTTATAACGCATGTAAAAA---GTCCAA
droAna3	scaffold_13266:9731665-9731765 +	TTC----------TA-AGGACCATTCGCTAAAAGGAACGATCGTTGTGATATGCGTTT-ATCC-CTCGTTACATATCACAGTGATTTTCCTTTATAACGCATGCAG-TT---GTCCAA
dp4	chr3:12677226-12677327 -	TTC----------CTAGGGGCCATACGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATTC-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCATGTCT-GC---GCCCAC
droPer1	super_2:8906345-8906446 +	TTC----------CTAGGGGCCATACGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATTC-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCATGTCT-GC---GCCCAC
droWil1	scaffold_180701:1651453-1651556 -	TTT----------TTCTGGGCCATTCGCTAAAAGGAACGATCGTTGTGATATGCGTTAGATTC-ACCGTTATATATCACAGTGATTTTCCTTTATAGCGCATGCAT-GTTCTGTC--C
droVir3	scaffold_12875:4112452-4112549 +	TAA----------AT-TGGGTCATGCTCTAAAAGGAACGATCGTTGTGATATGCGTTC-ATTA-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGC----A---GCCCGT
droMoj3	scaffold_6496:20936453-20936560 -	TGCAAACTCGATGAA-TGGGCCATGCGCTAAAAGGAACGATCGTTGTGATATGCGTTA-ATCG-ACCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGC----A---GTCCCC
droGri2	scaffold_15112:2108518-2108620 -	GTC------G---TTATGGGTCACTCGCTAAAAGGAACGATCGTTGTGATATGCGTTC-ATTAAATCGTTACATATCACAGTGATTTTCCTTTATAGCGCGTGCTC--T---GCCCAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTCATCG-GGCCATTCGCTAAAAGGAACGATCGTTGTGATATGAGTTG-TTCCC---AACATATCACAGTGATTTTCCTTTATATCGCATGTTAAAAGTCCAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................AAAGGAACGATCGTTGTGATATG............................................................	23	1	5824.00	5824	5824
.............................................................TATCACAGTGATTTTCCTTTAT....................	22	1	2377.00	2377	2377
....................AAAGGAACGATCGTTGTGATAT.............................................................	22	1	1991.00	1991	1991
.............................................................TATCACAGTGATTTTCCTTTATA...................	23	1	1451.00	1451	1451
....................AAAGGAACGATCGTTGTGAT...............................................................	20	1	318.00	318	318
..............................................................ATCACAGTGATTTTCCTTTAT....................	21	1	309.00	309	309
....................AAAGGAACGATCGTTGTGATA..............................................................	21	1	239.00	239	239
..............................................................ATCACAGTGATTTTCCTTTATA...................	22	1	124.00	124	124
.............................................................TATCACAGTGATTTTCCTTT......................	20	1	41.00	41	41
.............................................................TATCACAGTGATTTTCCTTTA.....................	21	1	30.00	30	30
....................AAAGGAACGATCGTTGTGATATGA...........................................................	24	1	24.00	24	24
.................................................................ACAGTGATTTTCCTTTAT....................	18	1	18.00	18	18
.................................................................ACAGTGATTTTCCTTTATA...................	19	1	17.00	17	17
....................AAAGGAACGATCGTTGTGA................................................................	19	1	11.00	11	11
...............................................................TCACAGTGATTTTCCTTTAT....................	20	1	7.00	7	7
TTCATCG-GGCCATTCGCTA...................................................................................	19	1	7.00	7	7
.............................................................TATCACAGTGATTTTCCT........................	18	1	6.00	6	6
..................TAAAAGGAACGATCGTTGTGAT...............................................................	22	1	6.00	6	6
...............................................................TCACAGTGATTTTCCTTTATA...................	21	1	6.00	6	6
.............................................................TATCACAGTGATTTTCCTTTATAT..................	24	1	4.00	4	4
..............................................................ATCACAGTGATTTTCCTTTA.....................	20	1	3.00	3	3
.............................................................TATCACAGTGATTTTCCTT.......................	19	1	2.00	2	2

dp4

TTCCTAGGGGCCATACGCTAAAAGGAACGATCGTTGTGATATGCGTTAATTCACCGTTACATATCACAGTGATTTTCCTTTATAGCGCATGTCT-GCGCCCAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................AAAGGAACGATCGTTGTGATATG............................................................	23	1	7316.00	7316	7312	4
.............................................................TATCACAGTGATTTTCCTTTAT....................	22	1	3041.00	3041	3041	0
.............................................................TATCACAGTGATTTTCCTTTATA...................	23	1	1872.00	1872	1872	0
....................AAAGGAACGATCGTTGTGATAT.............................................................	22	1	1796.00	1796	1796	0
....................AAAGGAACGATCGTTGTGATA..............................................................	21	1	454.00	454	454	0
....................AAAGGAACGATCGTTGTGAT...............................................................	20	1	266.00	266	265	1
..............................................................ATCACAGTGATTTTCCTTTAT....................	21	1	196.00	196	196	0
..............................................................ATCACAGTGATTTTCCTTTATA...................	22	1	138.00	138	138	0
.............................................................TATCACAGTGATTTTCCTTT......................	20	1	50.00	50	50	0
.................................................................ACAGTGATTTTCCTTTAT....................	18	1	36.00	36	36	0
..................TAAAAGGAACGATCGTTGTGAT...............................................................	22	1	33.00	33	33	0
.TCCTAGGGGCCATACGCTA...................................................................................	19	1	32.00	32	32	0
.............................................................TATCACAGTGATTTTCCTTTA.....................	21	1	32.00	32	32	0
.................................................................ACAGTGATTTTCCTTTATA...................	19	1	22.00	22	22	0
....................AAAGGAACGATCGTTGTGATATGC...........................................................	24	1	17.00	17	17	0
...............................................................TCACAGTGATTTTCCTTTAT....................	20	1	15.00	15	15	0
TTCCTAGGGGCCATACGCTA...................................................................................	20	1	14.00	14	14	0
..................TAAAAGGAACGATCGTTGTGATA..............................................................	23	1	13.00	13	13	0
...............................................................TCACAGTGATTTTCCTTTATA...................	21	1	13.00	13	13	0
....................AAAGGAACGATCGTTGTGA................................................................	19	1	13.00	13	13	0
.............................................................TATCACAGTGATTTTCCT........................	18	1	5.00	5	5	0
.........................................TGCGTTAATTCACCGTTACATA........................................	22	1	4.00	4	4	0
................................................................CACAGTGATTTTCCTTTAT....................	19	1	4.00	4	4	0
....................AAAGGAACGATCGTTGTG.................................................................	18	1	4.00	4	4	0
.....................AAGGAACGATCGTTGTGATATG............................................................	22	1	3.00	3	3	0
...............................................................TCACAGTGATTTTCCTTTATAGC.................	23	1	3.00	3	3	0
.............................................................TATCACAGTGATTTTCCTT.......................	19	1	2.00	2	2	0

Secondary Structure

dm3

dG=-21.9, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-21.3, p-value=0.009901

droSim1

dG=-22.8, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.3, p-value=0.009901

droSec1

dG=-22.7, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-21.9, p-value=0.009901

droYak2

dG=-21.9, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.2, p-value=0.009901

droEre2

dG=-21.9, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.1, p-value=0.009901

droAna3

dG=-22.0, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.7, p-value=0.009901	dG=-21.6, p-value=0.009901	dG=-21.5, p-value=0.009901

dp4

dG=-28.6, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.1, p-value=0.009901

droPer1

dG=-28.6, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.1, p-value=0.009901

droWil1

dG=-27.4, p-value=0.009901	dG=-26.4, p-value=0.009901

droVir3

dG=-23.2, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-22.2, p-value=0.009901

droMoj3

dG=-28.6, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.1, p-value=0.009901	dG=-28.1, p-value=0.009901	dG=-28.0, p-value=0.009901

droGri2

dG=-28.6, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.0, p-value=0.009901

Generated: 03/07/2013 at 06:57 PM