Secondary structure and small RNA-seq evidence for dme-mir-10

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:2635213-2635319 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droSim1	chr3R:2666345-2666451 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droSec1	super_6:2726434-2726540 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droYak2	chr3R:7777990-7778096 +	C------CTC-----ATCACTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGG----------
droEre2	scaffold_4770:2882555-2882661 -	C------CTC-----ATCAGTTTGCTCTACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGG----------
droAna3	scaffold_13340:5417353-5417464 +	C------CTA-----TCCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATTTCCATCGTAAA-----AT
dp4	chr2:19739488-19739592 +	T------CTC-----A--AGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTACATTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATGTACAACGA----------
droPer1	super_3:2487675-2487785 +	TTTGGTTCTC-----A--AGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTACATTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATGTACAACGA----------
droWil1	scaffold_181089:12007310-12007419 -	--------------------TTTGTTCTACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTTTTTAAGGACAAATTCGGTTCTAGAGAGGTTTAAGTGGTTCAATGTTCTACAAACAAACCAAA
droVir3	scaffold_13047:6092057-6092155 +	--------------------TTTGTTCCACGTCCACCCTGTAGATCCGAATTTGTTGTACACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTCTGTGGCTCATTGTCCAGCGA----------
droMoj3	scaffold_6540:16502892-16503003 +	T------GTCTAAGTTCCACTCTGTTCCACGTCTACCCTGTAGATCCGAATTTGTTGTACCATAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTATGTGGCTCATTGTCCAGCGA----------
droGri2	scaffold_14906:11443552-11443654 +	T---------------TCACTTTGTTCCACGTCTACCCTGTAGATCCGAATTTGTTGTACACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGCTCAATGCCCACCGA----------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:2635213-2635319 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droSim1	chr3R:2666345-2666451 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droSec1	super_6:2726434-2726540 -	C------CTC-----ATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA----------
droYak2	chr3R:7777990-7778096 +	C------CTC-----ATCACTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGG----------
droEre2	scaffold_4770:2882555-2882661 -	C------CTC-----ATCAGTTTGCTCTACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGG----------
droAna3	scaffold_13340:5417353-5417464 +	C------CTA-----TCCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATTTCCATCGTAAA-----AT
dp4	chr2:19739488-19739592 +	T------CTC-----A--AGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTACATTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATGTACAACGA----------
droPer1	super_3:2487675-2487785 +	TTTGGTTCTC-----A--AGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTACATTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATGTACAACGA----------
droWil1	scaffold_181089:12007310-12007419 -	--------------------TTTGTTCTACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGTTTTTAAGGACAAATTCGGTTCTAGAGAGGTTTAAGTGGTTCAATGTTCTACAAACAAACCAAA
droVir3	scaffold_13047:6092057-6092155 +	--------------------TTTGTTCCACGTCCACCCTGTAGATCCGAATTTGTTGTACACTAGTT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTCTGTGGCTCATTGTCCAGCGA----------
droMoj3	scaffold_6540:16502892-16503003 +	T------GTCTAAGTTCCACTCTGTTCCACGTCTACCCTGTAGATCCGAATTTGTTGTACCATAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTATGTGGCTCATTGTCCAGCGA----------
droGri2	scaffold_14906:11443552-11443654 +	T---------------TCACTTTGTTCCACGTCTACCCTGTAGATCCGAATTTGTTGTACACTAGCT-TTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGCTCAATGCCCACCGA----------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCTCATCAGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCTTTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATATCCATCGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................ACCCTGTAGATCCGAATTTGTT..............................................................	22	1	26268.00	26268	26268
...............................................................CAAATTCGGTTCTAGAGAGGTTT.....................	23	1	3740.00	3740	3740
.......................ACCCTGTAGATCCGAATTTGT...............................................................	21	1	491.00	491	491
...............................................................CAAATTCGGTTCTAGAGAGGTT......................	22	1	278.00	278	278
.......................ACCCTGTAGATCCGAATTTGTTT.............................................................	23	1	167.00	167	167
...............................................................CAAATTCGGTTCTAGAGAGGT.......................	21	1	104.00	104	104
...............................................................CAAATTCGGTTCTAGAGAGG........................	20	1	26.00	26	26
................................................................AAATTCGGTTCTAGAGAGGTTT.....................	22	1	18.00	18	18
.......................ACCCTGTAGATCCGAATTTG................................................................	20	1	11.00	11	11
.........................CCTGTAGATCCGAATTTGTT..............................................................	20	1	10.00	10	10
........................CCCTGTAGATCCGAATTTGTTT.............................................................	22	1	8.00	8	8
...............................................................CAAATTCGGTTCTAGAGAG.........................	19	1	6.00	6	6
......................TACCCTGTAGATCCGAATTTGT...............................................................	22	1	5.00	5	5
..........................CTGTAGATCCGAATTTGTT..............................................................	19	1	4.00	4	4
......................TACCCTGTAGATCCGAATTTGTT..............................................................	23	1	4.00	4	4
.......................ACCCTGTAGATCCGAATTT.................................................................	19	1	4.00	4	4
................................................................AAATTCGGTTCTAGAGAGGTT......................	21	1	4.00	4	4
...............................................................CAAATTCGGTTCTAGAGA..........................	18	1	3.00	3	3
........................CCCTGTAGATCCGAATTTGTT..............................................................	21	1	3.00	3	3

dp4

TCTCA--AGTTTGCTCCACGTCTACCCTGTAGATCCGAATTTGTTTTACATTAGCTTTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGGTTCAATGTACAACGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................ACCCTGTAGATCCGAATTTGTT..............................................................	22	1	21402.00	21402	18078	3324
...............................................................CAAATTCGGTTCTAGAGAGGTTT.....................	23	1	6412.00	6412	3262	3150
...............................................................CAAATTCGGTTCTAGAGAGGTT......................	22	1	1152.00	1152	348	804
.......................ACCCTGTAGATCCGAATTTGT...............................................................	21	1	986.00	986	463	523
...............................................................CAAATTCGGTTCTAGAGAGGT.......................	21	1	317.00	317	84	233
.......................ACCCTGTAGATCCGAATTTGTTT.............................................................	23	1	192.00	192	154	38
...............................................................CAAATTCGGTTCTAGAGAGG........................	20	1	104.00	104	26	78
.......................ACCCTGTAGATCCGAATTTG................................................................	20	1	91.00	91	15	76
......................TACCCTGTAGATCCGAATTTGT...............................................................	22	1	33.00	33	24	9
................................................................AAATTCGGTTCTAGAGAGGTTT.....................	22	1	29.00	29	17	12
...............................................................CAAATTCGGTTCTAGAGAG.........................	19	1	27.00	27	14	13
......................TACCCTGTAGATCCGAATTTGTT..............................................................	23	1	13.00	13	10	3
...............................................................CAAATTCGGTTCTAGAGA..........................	18	1	12.00	12	7	5
........................CCCTGTAGATCCGAATTTGTT..............................................................	21	1	9.00	9	8	1
................................................................AAATTCGGTTCTAGAGAGGTT......................	21	1	9.00	9	3	6
........................CCCTGTAGATCCGAATTTGTTT.............................................................	22	1	8.00	8	8	0
.............................................TTACATTAGCTTTAAGGA............................................	18	1	8.00	8	6	2
.........................CCTGTAGATCCGAATTTGTT..............................................................	20	1	6.00	6	5	1
.......................ACCCTGTAGATCCGAATTT.................................................................	19	1	6.00	6	6	0
...............................................................CAAATTCGGTTCTAGAGAGGTTTG....................	24	1	4.00	4	2	2
.......................ACCCTGTAGATCCGAATT..................................................................	18	1	4.00	4	4	0
......................TACCCTGTAGATCCGAATTTG................................................................	21	1	4.00	4	3	1

Secondary Structure

dm3

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droSim1

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droSec1

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droYak2

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droEre2

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droAna3

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

dp4

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droPer1

dG=-25.5, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droWil1

dG=-25.4, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.4, p-value=0.009901

droVir3

dG=-24.6, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-23.7, p-value=0.009901	dG=-23.6, p-value=0.009901

droMoj3

dG=-26.8, p-value=0.009901

droGri2

dG=-24.7, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.7, p-value=0.009901

Generated: 03/07/2013 at 04:44 PM