Secondary structure and small RNA-seq evidence for dme-mir-2b-2

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:19570167-19570279 -	ATCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droSim1	chr2L:19258228-19258340 -	ATCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droSec1	super_7:3184520-3184632 -	ACCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droYak2	chr2R:6067209-6067321 -	ATCGAAGC-----------------------------------------AAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTCTGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGACAAAA--------------A
droEre2	scaffold_4845:4719511-4719623 +	ATCGAAGT-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGACAAAA--------------A
droAna3	scaffold_12916:12013302-12013412 +	CC----AC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCAATG-CTCAAGACAAAA-------------AA
dp4	chr4_group5:1152145-1152298 +	ACCCAAAGAACCCAAAGCCTCGGGTCTCGGGGCCCCCGTGTCCGGGCCAAGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAAGACAAAA--------------G
droPer1	super_5:5559630-5559783 +	ACCCAAAGAACCCAAAGCCTCGGGTCTCGGGGCCCCCGTGTCCGGGCCAAGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAAGACAAAA--------------G
droWil1	scaffold_180708:4283205-4283312 +	---GAGGC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCAATGGCTCAAGTTA------------------
droVir3	scaffold_12723:2961084-2961203 -	AGCGAGAGA----------------------------------GAGAGAAAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAGCACAAAA--------------A
droMoj3	scaffold_6500:6907804-6907929 +	GACCAAGA-----------------------------------------GAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGC-TTTTTCTGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAGTACAAAATTCAAAACATGAAAA
droGri2	scaffold_15126:521314-521426 +	GAGAGAGA-----------------------------------------GAGAGAATTGTGTCCTTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAACACAAAA--------------A

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:19570167-19570279 -	ATCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droSim1	chr2L:19258228-19258340 -	ATCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droSec1	super_7:3184520-3184632 -	ACCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGGCAAAA--------------A
droYak2	chr2R:6067209-6067321 -	ATCGAAGC-----------------------------------------AAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTCTGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGACAAAA--------------A
droEre2	scaffold_4845:4719511-4719623 +	ATCGAAGT-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATG-CTCAAGACAAAA--------------A
droAna3	scaffold_12916:12013302-12013412 +	CC----AC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCAATG-CTCAAGACAAAA-------------AA
dp4	chr4_group5:1152145-1152298 +	ACCCAAAGAACCCAAAGCCTCGGGTCTCGGGGCCCCCGTGTCCGGGCCAAGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAAGACAAAA--------------G
droPer1	super_5:5559630-5559783 +	ACCCAAAGAACCCAAAGCCTCGGGTCTCGGGGCCCCCGTGTCCGGGCCAAGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAAGACAAAA--------------G
droWil1	scaffold_180708:4283205-4283312 +	---GAGGC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCAATGGCTCAAGTTA------------------
droVir3	scaffold_12723:2961084-2961203 -	AGCGAGAGA----------------------------------GAGAGAAAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAGCACAAAA--------------A
droMoj3	scaffold_6500:6907804-6907929 +	GACCAAGA-----------------------------------------GAGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGC-TTTTTCTGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAGTACAAAATTCAAAACATGAAAA
droGri2	scaffold_15126:521314-521426 +	GAGAGAGA-----------------------------------------GAGAGAATTGTGTCCTTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTACTCATATCACAGCCAGCTTTGAGGAGCGACACGATG-CTCAACACAAAA--------------A

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATCGAAAC-----------------------------------------AGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGATGCTCAAGGCAAAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................................................................................................TATCACAGCCAGCTTTGAGGAGCG.....................	24	2	62522.00	125044	125044
.............................................................................................................TATCACAGCCAGCTTTGAGGAG.......................	22	2	18546.50	37093	37093
.............................................................................................................TATCACAGCCAGCTTTGAGGAGCGA....................	25	1	1481.00	1481	1481
.............................................................................................................TATCACAGCCAGCTTTGAGGA........................	21	2	1283.00	2566	2566
................................................................TTCTTCAAAGTGGTTGTGAAATG...................................................................	23	1	821.00	821	821
...............................................................................................................TCACAGCCAGCTTTGAGGAGCG.....................	22	2	323.50	647	647
................................................................TTCTTCAAAGTGGTTGTGAAAT....................................................................	22	1	126.00	126	126
.................................................................................................................ACAGCCAGCTTTGAGGAGC......................	19	2	105.00	210	210
...............................................................................................................TCACAGCCAGCTTTGAGGAG.......................	20	2	80.50	161	161
.................................................................TCTTCAAAGTGGTTGTGAAATG...................................................................	22	1	71.00	71	71
..............................................................................................................ATCACAGCCAGCTTTGAGGAGCG.....................	23	2	47.50	95	95
...............................................................................................................TCACAGCCAGCTTTGAGGAGCGA....................	23	1	42.00	42	42
................................................................TTCTTCAAAGTGGTTGTGAAA.....................................................................	21	1	27.00	27	27
....AAAC-----------------------------------------AGGAGAATTGTGTCA..........................................................................................	19	1	22.00	22	22
.................................................................................................................ACAGCCAGCTTTGAGGAGCGA....................	21	1	10.00	10	10
.................................................................TCTTCAAAGTGGTTGTGAAAT....................................................................	21	1	8.00	8	8
...................................................................................................................AGCCAGCTTTGAGGAGCG.....................	18	2	6.50	13	13
.......................................................................................TTTGCCTTTTTATGCCTATTCA.............................................	22	1	6.00	6	6
.............................................................................................................TATCACAGCCAGCTTTGAGGAGCGAC...................	26	1	4.00	4	4
..............................................................................................................ATCACAGCCAGCTTTGAGGAGCGA....................	24	1	4.00	4	4
................................................................TTCTTCAAAGTGGTTGTGAA......................................................................	20	1	3.00	3	3
................................................................TTCTTCAAAGTGGTTGTGA.......................................................................	19	1	3.00	3	3
.............................................................................................................TATCACAGCCAGCTTTGA...........................	18	5	2.60	13	13

dp4

ACCCAAAGAACCCAAAGCCTCGGGTCTCGGGGCCCCCGTGTCCGGGCCAAGGAGAATTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACACGATGCTCAAGACAAAAG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................................................................................TATCACAGCCAGCTTTGAGGAG.......................	22	2	23091.50	46183	0	46183
.............................................................................................................TATCACAGCCAGCTTTGAGGAGC......................	23	2	20982.50	41965	41965	0
.............................................................................................................TATCACAGCCAGCTTTGAGGA........................	21	2	1456.00	2912	0	2912
................................................................TTCTTCAAAGTGGTTGTGAAATG...................................................................	23	1	669.00	669	524	145
.............................................................................................................TATCACAGCCAGCTTTGAGGAGCGA....................	25	1	598.00	598	491	107
.................................................................................................................ACAGCCAGCTTTGAGGAGCG.....................	20	2	401.00	802	696	106
.................................................................................................................ACAGCCAGCTTTGAGGAGC......................	19	2	206.50	413	319	94
.................................................................TCTTCAAAGTGGTTGTGAAATG...................................................................	22	1	64.00	64	56	8
...............................................................................................................TCACAGCCAGCTTTGAGGAG.......................	20	2	58.50	117	0	117
................................................................TTCTTCAAAGTGGTTGTGAAA.....................................................................	21	1	30.00	30	10	20
.............................................................................................................TATCACAGCCAGCTTTGAGG.........................	20	2	28.00	56	6	50
...............................................................................................................TCACAGCCAGCTTTGAGGAGC......................	21	2	23.00	46	0	46
................................................................TTCTTCAAAGTGGTTGTGAAAT....................................................................	22	1	22.00	22	15	7
................................................................TTCTTCAAAGTGGTTGTGA.......................................................................	19	1	18.00	18	0	18
.............................................................................................................TATCACAGCCAGCTTTGAG..........................	19	2	17.00	34	7	27
.......................................................................................TTTGCCTTTTTATGCCTATTCA.............................................	22	1	10.00	10	9	1
...............................................................................................................TCACAGCCAGCTTTGAGGAGCGA....................	23	1	10.00	10	10	0
................................................................TTCTTCAAAGTGGTTGTGAA......................................................................	20	1	9.00	9	2	7
..............................................................................................................ATCACAGCCAGCTTTGAGGAGC......................	22	2	8.50	17	0	17
.............................................GCCAAGGAGAATTGTGTCA..........................................................................................	19	1	8.00	8	8	0
..............................................................................................................ATCACAGCCAGCTTTGAGGAG.......................	21	2	7.50	15	0	15
.................................................................................................................ACAGCCAGCTTTGAGGAGCGA....................	21	1	6.00	6	5	1
................................................................................................................CACAGCCAGCTTTGAGGAGCG.....................	21	2	3.50	7	7	0

Secondary Structure

dm3

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droSim1

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droSec1

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droYak2

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droEre2

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droAna3

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

dp4

dG=-32.6, p-value=0.009901	dG=-32.2, p-value=0.009901	dG=-32.1, p-value=0.009901	dG=-31.7, p-value=0.009901

droPer1

dG=-32.6, p-value=0.009901	dG=-32.2, p-value=0.009901	dG=-32.1, p-value=0.009901	dG=-31.7, p-value=0.009901

droWil1

dG=-32.1, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.5, p-value=0.009901

droVir3

dG=-32.6, p-value=0.009901	dG=-32.2, p-value=0.009901	dG=-32.1, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.6, p-value=0.009901

droMoj3

dG=-33.4, p-value=0.009901	dG=-33.0, p-value=0.009901	dG=-32.9, p-value=0.009901	dG=-32.5, p-value=0.009901	dG=-32.4, p-value=0.009901

droGri2

dG=-31.9, p-value=0.009901	dG=-31.5, p-value=0.009901	dG=-31.4, p-value=0.009901	dG=-31.0, p-value=0.009901	dG=-30.9, p-value=0.009901

Generated: 03/07/2013 at 05:09 PM