Secondary structure and small RNA-seq evidence for dme-mir-2a-1

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:19569882-19569987 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droSim1	chr2L:19257947-19258052 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droSec1	super_7:3184244-3184349 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droYak2	chr2R:6066940-6067043 -	--TTGG-CGCATTCACGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droEre2	scaffold_4845:4719792-4719897 +	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATA-TC----AGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droAna3	scaffold_12916:12013650-12013754 +	TATTGG-CACATTCCTGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TC----CATTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTTATGTATCGTACA
dp4	chr4_group5:1152486-1152589 +	TATTGG-CACATTCATGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TT-----GCTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTCGGCGTAATGTATCGTACA
droPer1	super_5:5559971-5560074 +	TATTGG-CACATTCATGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TT-----GCTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTCGGCGTAATGTATCGTACA
droWil1	scaffold_180708:4284676-4284781 +	CA-CGA-CACATTCATGCTGAGCTCACAAAGTGGTTGTGAAATGCATTATT----TGCTTTATCCAGCATATCACAGCCAGCTTTGATGAGCTCTGCGTAATGTGAATTGCA
droVir3	scaffold_12723:2960768-2960874 -	GATTGG-CACATTCATGCTGCGCTCTCAAAGTGGTTGTGAAATGCATT-TG--AAAGCTTTGCGC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTCACGTACA
droMoj3	scaffold_6500:6908308-6908415 +	-ATTGGCCACATTCATGCTGAGCTCTCAAAGAGGCTGTGAAATGCATT-TT-GAAAGCTTTGCGA-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTAACGTACA
droGri2	scaffold_15126:521642-521748 +	--TTGG-CACATTCATGCTGCGCTCTCAAAGTGGTTGTGAAATGCATT-TTTGAAAGCTTTGCGC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTAAACTACt

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:19569882-19569987 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droSim1	chr2L:19257947-19258052 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droSec1	super_7:3184244-3184349 -	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droYak2	chr2R:6066940-6067043 -	--TTGG-CGCATTCACGCTGGGCTCTCAAAGTGGTTGTGAAATGCATT-TC----CGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droEre2	scaffold_4845:4719792-4719897 +	TATTGG-CGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATA-TC----AGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA
droAna3	scaffold_12916:12013650-12013754 +	TATTGG-CACATTCCTGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TC----CATTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTTATGTATCGTACA
dp4	chr4_group5:1152486-1152589 +	TATTGG-CACATTCATGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TT-----GCTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTCGGCGTAATGTATCGTACA
droPer1	super_5:5559971-5560074 +	TATTGG-CACATTCATGCTGGGCTCACAAAGTGGTTGTGAAATGCATT-TT-----GCTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTCGGCGTAATGTATCGTACA
droWil1	scaffold_180708:4284676-4284781 +	CA-CGA-CACATTCATGCTGAGCTCACAAAGTGGTTGTGAAATGCATTATT----TGCTTTATCCAGCATATCACAGCCAGCTTTGATGAGCTCTGCGTAATGTGAATTGCA
droVir3	scaffold_12723:2960768-2960874 -	GATTGG-CACATTCATGCTGCGCTCTCAAAGTGGTTGTGAAATGCATT-TG--AAAGCTTTGCGC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTCACGTACA
droMoj3	scaffold_6500:6908308-6908415 +	-ATTGGCCACATTCATGCTGAGCTCTCAAAGAGGCTGTGAAATGCATT-TT-GAAAGCTTTGCGA-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTAACGTACA
droGri2	scaffold_15126:521642-521748 +	--TTGG-CACATTCATGCTGCGCTCTCAAAGTGGTTGTGAAATGCATT-TTTGAAAGCTTTGCGC-GCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTAAACTACt

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TATTGGCGCATTCATGCTGGGCTCTCAAAGTGGTTGTGAAATGCATTTCCGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGCGTAATGTATCGTACA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................................................TATCACAGCCAGCTTTGATGAGCT...................	24	2	80214.00	160428	160428
...............................................................TATCACAGCCAGCTTTGATGAGC....................	23	2	7352.00	14704	14704
...............................................................TATCACAGCCAGCTTTGATGAG.....................	22	2	4475.50	8951	8951
...............................................................TATCACAGCCAGCTTTGATGAGCTT..................	25	1	3648.00	3648	3648
.................................................................TCACAGCCAGCTTTGATGAGCTT..................	23	1	1535.00	1535	1535
................................................................ATCACAGCCAGCTTTGATGAGCT...................	23	2	303.00	606	606
.....................CTCTCAAAGTGGTTGTGAAATG...............................................................	22	1	191.00	191	191
...............................................................TATCACAGCCAGCTTTGATG.......................	20	3	39.00	117	117
...................................................................ACAGCCAGCTTTGATGAGCTT..................	21	1	34.00	34	34
................................................................ATCACAGCCAGCTTTGATGAGCTT..................	24	1	31.00	31	31
.....................................................................AGCCAGCTTTGATGAGCT...................	18	2	19.00	38	38
.................................................................TCACAGCCAGCTTTGATGAGCTTA.................	24	1	18.00	18	18
.ATTGGCGCATTCATGCTGGG.....................................................................................	20	1	10.00	10	10
....................................................................CAGCCAGCTTTGATGAGCT...................	19	2	9.00	18	18
...............................................................TATCACAGCCAGCTTTGATGAGCTTA.................	26	1	9.00	9	9
.....................CTCTCAAAGTGGTTGTGAAAT................................................................	21	1	9.00	9	9
..................................................................CACAGCCAGCTTTGATGAGC....................	20	2	7.00	14	14
................................................................ATCACAGCCAGCTTTGATGAG.....................	21	2	5.00	10	10
.....................CTCTCAAAGTGGTTGTGAAA.................................................................	20	1	5.00	5	5
..TTGGCGCATTCATGCTGGG.....................................................................................	19	1	4.00	4	4
....................................................................CAGCCAGCTTTGATGAGC....................	18	2	4.00	8	8
TATTGGCGCATTCATGCTGGG.....................................................................................	21	1	4.00	4	4

dp4

TATTGGCACATTCATGCTGGGCTCACAAAGTGGTTGTGAAATGCATTT-TGCTTTGCCC-GCATATCACAGCCAGCTTTGATGAGCTCGGCGTAATGTATCGTACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............................................................TATCACAGCCAGCTTTGATGAGCT...................	24	2	90936.50	181873	181873	0
...............................................................TATCACAGCCAGCTTTGATGAGC....................	23	2	16103.00	32206	32206	0
...............................................................TATCACAGCCAGCTTTGATGAG.....................	22	2	3970.00	7940	0	7940
...................................................................ACAGCCAGCTTTGATGAGCT...................	20	2	1178.50	2357	1885	472
.................................................................TCACAGCCAGCTTTGATGAGCTC..................	23	1	570.00	570	483	87
...............................................................TATCACAGCCAGCTTTGATGA......................	21	2	361.50	723	723	0
...............................................................TATCACAGCCAGCTTTGATG.......................	20	3	247.33	742	0	742
...............................................................TATCACAGCCAGCTTTGATGAGCTC..................	25	1	140.00	140	118	22
................................................................ATCACAGCCAGCTTTGATGAGCT...................	23	2	137.00	274	0	274
...................................................................ACAGCCAGCTTTGATGAG.....................	18	2	112.00	224	224	0
.................................................................TCACAGCCAGCTTTGATGA......................	19	2	101.50	203	0	203
...................................................................ACAGCCAGCTTTGATGAGC....................	19	2	56.00	112	0	112
................................................................ATCACAGCCAGCTTTGATGAGC....................	22	2	55.50	111	83	28
.....................CTCACAAAGTGGTTGTGAAATG...............................................................	22	1	43.00	43	36	7
................................................................ATCACAGCCAGCTTTGATGAG.....................	21	2	34.50	69	27	42
..................................................................CACAGCCAGCTTTGATGAGCT...................	21	2	29.50	59	0	59
.....................................................................AGCCAGCTTTGATGAGCT...................	18	2	25.00	50	41	9
....................................................................CAGCCAGCTTTGATGAGC....................	18	2	24.50	49	48	1
.................................................................TCACAGCCAGCTTTGATGAGCTCG.................	24	1	18.00	18	17	1
....................................................................CAGCCAGCTTTGATGAGCT...................	19	2	16.00	32	32	0
..............................................................ATATCACAGCCAGCTTTGATGAGCT...................	25	2	14.00	28	28	0
.....................CTCACAAAGTGGTTGTGAAA.................................................................	20	1	11.00	11	7	4
...........................................CATTT-TGCTTTGCCC-GCA...........................................	18	1	7.00	7	7	0
..................................................................CACAGCCAGCTTTGATGAG.....................	19	2	7.00	14	8	6

Secondary Structure

dm3

dG=-39.0, p-value=0.009901	dG=-38.9, p-value=0.009901	dG=-38.8, p-value=0.009901	dG=-38.6, p-value=0.009901	dG=-38.5, p-value=0.009901

droSim1

dG=-39.0, p-value=0.009901	dG=-38.9, p-value=0.009901	dG=-38.8, p-value=0.009901	dG=-38.6, p-value=0.009901	dG=-38.5, p-value=0.009901

droSec1

dG=-39.0, p-value=0.009901	dG=-38.9, p-value=0.009901	dG=-38.8, p-value=0.009901	dG=-38.6, p-value=0.009901	dG=-38.5, p-value=0.009901

droYak2

dG=-39.0, p-value=0.009901	dG=-38.9, p-value=0.009901	dG=-38.8, p-value=0.009901	dG=-38.6, p-value=0.009901	dG=-38.5, p-value=0.009901

droEre2

dG=-37.1, p-value=0.009901	dG=-37.0, p-value=0.009901	dG=-36.7, p-value=0.009901	dG=-36.6, p-value=0.009901

droAna3

dG=-35.9, p-value=0.009901	dG=-35.5, p-value=0.009901

dp4

dG=-37.3, p-value=0.009901	dG=-36.9, p-value=0.009901	dG=-36.8, p-value=0.009901	dG=-36.4, p-value=0.009901

droPer1

dG=-37.3, p-value=0.009901	dG=-36.9, p-value=0.009901	dG=-36.8, p-value=0.009901	dG=-36.4, p-value=0.009901

droWil1

dG=-34.4, p-value=0.009901	dG=-34.0, p-value=0.009901

droVir3

dG=-32.3, p-value=0.009901	dG=-32.3, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.9, p-value=0.009901	dG=-31.4, p-value=0.009901

droMoj3

dG=-36.5, p-value=0.009901	dG=-36.0, p-value=0.009901	dG=-35.8, p-value=0.009901	dG=-35.7, p-value=0.009901	dG=-35.6, p-value=0.009901

droGri2

dG=-32.2, p-value=0.009901	dG=-32.1, p-value=0.009901	dG=-31.8, p-value=0.009901	dG=-31.7, p-value=0.009901	dG=-31.2, p-value=0.009901

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