Secondary structure and small RNA-seq evidence for dme-mir-11

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:17448204-17448308 -	AGATCTAT--GTGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droSim1	chr3R:4022563-4022667 +	AGATCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droSec1	super_6:4043853-4043957 +	AGATCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droYak2	chr3R:6285759-6285863 -	AGTTCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCTGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GAAATCCTCAAAGCA------------------------
droEre2	scaffold_4770:4217167-4217271 +	AGATCTCC--ATGAGGCGC-ACTTGCCAAGAACTTTCTCTGTGACCTGCGTGTACT------------GAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GGAATCCTCGAAGCA------------------------
droAna3	scaffold_13340:5675670-5675780 +	ATCTCTA-ATATGAGGCGC-ACTTGCCAAGAACTCTCTCTGTGACTTGTGTCCTTTTT--TT------CGAAACTCACATCACAGTCTGAGTTCTTGCTGAGAGCGGGAATCCTCCAATCG------------------------
dp4	chr2:23857524-23857651 -	AACACTCGATTTGAGGCCC-TCTTGTCAAGAACTTATTCTGTGACCTGCGTGACATTT--------------AGCCACATCACAGTCTGAGTTCTTGCTGAGCGT-GAACT-CGCCAACCAACATGAGTGAATAGCCCCCAAAAA
droPer1	super_3:6634087-6634214 -	AACACTCGATTTGAGGCTC-TCTTGTCAAGAACTTATTCTGTGACCTGCGTGACATTT--------------AGCCACATCACAGTCTGAGTTCTTGCTGAGCGT-GAACT-CGCCAACCAACATGAGTGAATAGCCCCCAAAAA
droWil1	scaffold_181089:8479022-8479138 +	ACAGCAAA--GAGAAGCCCTTCTTGTCAAGATCTCTCTCTGTGACCTGCGTGAGATTT--ATCATATATGAAAACCGCATCACAGTCTGAGTTCTTGCTGAGCGGTGAGCTAAGCAAGACA------------------------
droVir3	scaffold_13047:6338937-6339046 +	GGTTTTA---TTGAAGCGC-ACTTATCAAGAACTTTTTCTGTGACTTGCGTGAACTCTTATA------TGCAAACCGCATCACAGTCTGAGTTCTTGCTTAGCGC-GCACTTCGCACAGCA------------------------
droMoj3	scaffold_6540:1740109-1740221 -	CGCATTCGATTTGAAGCGC-ACTTAACAAGAACTTTTTCTGTGACCTGCGTGAATTCCTATA------TGCAAACCGCATCACAGTCTGAGTTCTTGCTTAGCGC-GCACTTCGCACAGCA------------------------
droGri2	scaffold_14906:11659470-11659581 +	CGAATTCGAAATGAAGCCC-ACTCGTCAAGAACTCTCTCTGTGACTTGCGTGAACTTTCATG------TGAAAATCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GCT-TTCGCACCACA------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:17448204-17448308 -	AGATCTAT--GTGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droSim1	chr3R:4022563-4022667 +	AGATCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droSec1	super_6:4043853-4043957 +	AGATCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC-GAAATCCTCGAAGCA------------------------
droYak2	chr3R:6285759-6285863 -	AGTTCTCC--ATGAGGCGC-ACTTGTCAAGAACTTTCTCTGTGACCTGCGTGTACT------------TAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GAAATCCTCAAAGCA------------------------
droEre2	scaffold_4770:4217167-4217271 +	AGATCTCC--ATGAGGCGC-ACTTGCCAAGAACTTTCTCTGTGACCTGCGTGTACT------------GAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GGAATCCTCGAAGCA------------------------
droAna3	scaffold_13340:5675670-5675780 +	ATCTCTA-ATATGAGGCGC-ACTTGCCAAGAACTCTCTCTGTGACTTGTGTCCTTTTT--TT------CGAAACTCACATCACAGTCTGAGTTCTTGCTGAGAGCGGGAATCCTCCAATCG------------------------
dp4	chr2:23857524-23857651 -	AACACTCGATTTGAGGCCC-TCTTGTCAAGAACTTATTCTGTGACCTGCGTGACATTT--------------AGCCACATCACAGTCTGAGTTCTTGCTGAGCGT-GAACT-CGCCAACCAACATGAGTGAATAGCCCCCAAAAA
droPer1	super_3:6634087-6634214 -	AACACTCGATTTGAGGCTC-TCTTGTCAAGAACTTATTCTGTGACCTGCGTGACATTT--------------AGCCACATCACAGTCTGAGTTCTTGCTGAGCGT-GAACT-CGCCAACCAACATGAGTGAATAGCCCCCAAAAA
droWil1	scaffold_181089:8479022-8479138 +	ACAGCAAA--GAGAAGCCCTTCTTGTCAAGATCTCTCTCTGTGACCTGCGTGAGATTT--ATCATATATGAAAACCGCATCACAGTCTGAGTTCTTGCTGAGCGGTGAGCTAAGCAAGACA------------------------
droVir3	scaffold_13047:6338937-6339046 +	GGTTTTA---TTGAAGCGC-ACTTATCAAGAACTTTTTCTGTGACTTGCGTGAACTCTTATA------TGCAAACCGCATCACAGTCTGAGTTCTTGCTTAGCGC-GCACTTCGCACAGCA------------------------
droMoj3	scaffold_6540:1740109-1740221 -	CGCATTCGATTTGAAGCGC-ACTTAACAAGAACTTTTTCTGTGACCTGCGTGAATTCCTATA------TGCAAACCGCATCACAGTCTGAGTTCTTGCTTAGCGC-GCACTTCGCACAGCA------------------------
droGri2	scaffold_14906:11659470-11659581 +	CGAATTCGAAATGAAGCCC-ACTCGTCAAGAACTCTCTCTGTGACTTGCGTGAACTTTCATG------TGAAAATCGCATCACAGTCTGAGTTCTTGCTGAGCGC-GCT-TTCGCACCACA------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGATCTC--CATGAGGCGCACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACTTAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGCGAAATCC-----------------------TCGAAGCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................CATCACAGTCTGAGTTCTTGC.............................................	21	1	6532.00	6532	6532
................................................................CATCACAGTCTGAGTTCTTGCT............................................	22	1	4488.00	4488	4488
................................................................CATCACAGTCTGAGTTCTTG..............................................	20	1	484.00	484	484
.........................CAAGAACTTTCTCTGTGACCCG...................................................................................	22	1	205.00	205	205
.................................................................ATCACAGTCTGAGTTCTTGC.............................................	20	1	93.00	93	93
.................................................................ATCACAGTCTGAGTTCTTGCT............................................	21	1	55.00	55	55
................................................................CATCACAGTCTGAGTTCTT...............................................	19	1	17.00	17	17
....................................................................ACAGTCTGAGTTCTTGCT............................................	18	1	6.00	6	6
.................................................................ATCACAGTCTGAGTTCTTG..............................................	19	1	4.00	4	4
.........................CAAGAACTTTCTCTGTGACCCGCG.................................................................................	24	1	4.00	4	4
.........................CAAGAACTTTCTCTGTGACCC....................................................................................	21	1	3.00	3	3
.....TC--CATGAGGCGCACTTGT.........................................................................................................	18	1	3.00	3	3
...............................................................GCATCACAGTCTGAGTTCTTGC.............................................	22	1	3.00	3	3
...................................................................CACAGTCTGAGTTCTTGC.............................................	18	1	2.00	2	2
...................................................................CACAGTCTGAGTTCTTGCT............................................	19	1	2.00	2	2
..................................................................TCACAGTCTGAGTTCTTGCT............................................	20	1	2.00	2	2

dp4

AACACTCGATTTGAGGCCCTCTTGTCAAGAACTTATTCTGTGACCTGCGTGACATTT--AGCCACATCACAGTCTGAGTTCTTGCTGAGCGTGAACTCGCCAACCAACATGAGTGAATAGCCCCCAAAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................CATCACAGTCTGAGTTCTTGCT............................................	22	1	43314.00	43314	16988	26326
................................................................CATCACAGTCTGAGTTCTTGC.............................................	21	1	16443.00	16443	3038	13405
................................................................CATCACAGTCTGAGTTCTTG..............................................	20	1	2682.00	2682	270	2412
.................................................................ATCACAGTCTGAGTTCTTGCT............................................	21	1	657.00	657	207	450
.................................................................ATCACAGTCTGAGTTCTTGC.............................................	20	1	268.00	268	63	205
................................................................CATCACAGTCTGAGTTCTT...............................................	19	1	121.00	121	7	114
...............................................................ACATCACAGTCTGAGTTCTTGC.............................................	22	1	93.00	93	62	31
...............................................................ACATCACAGTCTGAGTTCTTGCT............................................	23	1	87.00	87	73	14
.........................CAAGAACTTATTCTGTGACCTG...................................................................................	22	1	79.00	79	68	11
....................................................................ACAGTCTGAGTTCTTGCT............................................	18	1	36.00	36	14	22
...............................................................ACATCACAGTCTGAGTTCTTG..............................................	21	1	27.00	27	5	22
.................................................................ATCACAGTCTGAGTTCTTG..............................................	19	1	23.00	23	2	21
................................................................CATCACAGTCTGAGTTCTTGCTG...........................................	23	1	18.00	18	8	10
...............................................................ACATCACAGTCTGAGTTCTT...............................................	20	1	9.00	9	0	9
.....TCGATTTGAGGCCCTCTTGT.........................................................................................................	20	1	7.00	7	7	0
..................................................................TCACAGTCTGAGTTCTTGC.............................................	19	1	6.00	6	3	3
..............................................................CACATCACAGTCTGAGTTCTTGC.............................................	23	1	5.00	5	3	2
......CGATTTGAGGCCCTCTTGT.........................................................................................................	19	1	5.00	5	5	0
..................................................................TCACAGTCTGAGTTCTTGCT............................................	20	1	5.00	5	3	2

Secondary Structure

dm3

dG=-26.3, p-value=0.009901	dG=-25.9, p-value=0.009901

droSim1

dG=-26.3, p-value=0.009901	dG=-25.9, p-value=0.009901

droSec1

dG=-26.3, p-value=0.009901	dG=-25.9, p-value=0.009901

droYak2

dG=-27.2, p-value=0.009901	dG=-26.8, p-value=0.009901

droEre2

dG=-27.2, p-value=0.009901	dG=-26.8, p-value=0.009901

droAna3

dG=-26.0, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

dp4

dG=-24.9, p-value=0.009901	dG=-24.5, p-value=0.009901

droPer1

dG=-24.9, p-value=0.009901	dG=-24.5, p-value=0.009901

droWil1

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-21.9, p-value=0.009901

droVir3

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

droMoj3

dG=-22.8, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.1, p-value=0.009901

droGri2

dG=-30.9, p-value=0.009901	dG=-30.4, p-value=0.009901

Generated: 03/07/2013 at 04:49 PM