Secondary structure and small RNA-seq evidence for dme-mir-14

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:5441252-5441344 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSim1	chr2R:4072822-4072914 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSec1	super_1:3055916-3056008 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droYak2	chr2L:18072267-18072359 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droEre2	scaffold_4929:8915902-8915994 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droAna3	scaffold_13266:183955-184047 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
dp4	chr3:15883112-15883203 +	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droPer1	super_4:878748-878839 -	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droWil1	scaffold_180700:3302349-3302441 +	ACGTACTGCAACCTATGTGGGAGCGAGACGAGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droVir3	scaffold_10324:225313-225405 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droMoj3	scaffold_6496:2042842-2042934 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGATTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droGri2	scaffold_15245:15401666-15401758 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:5441252-5441344 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSim1	chr2R:4072822-4072914 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSec1	super_1:3055916-3056008 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droYak2	chr2L:18072267-18072359 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droEre2	scaffold_4929:8915902-8915994 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droAna3	scaffold_13266:183955-184047 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
dp4	chr3:15883112-15883203 +	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droPer1	super_4:878748-878839 -	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droWil1	scaffold_180700:3302349-3302441 +	ACGTACTGCAACCTATGTGGGAGCGAGACGAGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droVir3	scaffold_10324:225313-225405 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droMoj3	scaffold_6496:2042842-2042934 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGATTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droGri2	scaffold_15245:15401666-15401758 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................TCAGTCTTTTTCTCTCTCCTA.................	21	2	1436.50	2873	2873
.........................................................AGTCTTTTTCTCTCTCCTAT................	20	2	103.00	206	206
..................GGGAGCGAGACGGGGACTCAC......................................................	21	2	18.50	37	37
........................................................CAGTCTTTTTCTCTCTCCTATA...............	22	2	10.50	21	21
.......................................................TCAGTCTTTTTCTCTCTCC...................	19	2	8.00	16	16
...........................................................TCTTTTTCTCTCTCCTAT................	18	2	6.00	12	12
.................TGGGAGCGAGACGGGGACTCAC......................................................	22	2	3.50	7	7
.........................................................AGTCTTTTTCTCTCTCCTATA...............	21	2	2.50	5	5
..................GGGAGCGAGACGGGGACT.........................................................	18	2	1.00	2	2
...................GGAGCGAGACGGGGACTCACT.....................................................	21	2	1.00	2	2
.............TATGTGGGAGCGAGACGGGGA...........................................................	21	2	0.50	1	1
..........................................................GTCTTTTTCTCTCTCCTA.................	18	2	0.50	1	1

dp4

ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................TCAGTCTTTTTCTCTCTCCTAT................	22	2	17802.50	35605	18647	16958
.......................................................TCAGTCTTTTTCTCTCTCCTA.................	21	2	2349.50	4699	0	4699
.......................................................TCAGTCTTTTTCTCTCTCCT..................	20	2	2287.50	4575	0	4575
.........................................................AGTCTTTTTCTCTCTCCTAT................	20	2	267.00	534	304	230
.......................................................TCAGTCTTTTTCTCTCTCCTATA...............	23	2	186.50	373	209	164
.......................................................TCAGTCTTTTTCTCTCTCC...................	19	2	44.50	89	0	89
.........................................................AGTCTTTTTCTCTCTCCT..................	18	2	26.50	53	0	53
..................GGGAGCGAGACGGGGACTCACT.....................................................	22	2	24.50	49	0	49
..................GGGAGCGAGACGGGGACTCAC......................................................	21	2	22.00	44	34	10
........................................................CAGTCTTTTTCTCTCTCCTA.................	20	2	8.50	17	17	0
........................................................CAGTCTTTTTCTCTCTCCT..................	19	2	7.00	14	2	12
..................GGGAGCGAGACGGGGACT.........................................................	18	2	7.00	14	0	14
........................................................CAGTCTTTTTCTCTCTCCTATA...............	22	2	5.00	10	7	3
.......................................................TCAGTCTTTTTCTCTCTC....................	18	2	4.00	8	8	0
..................GGGAGCGAGACGGGGACTCA.......................................................	20	2	3.50	7	6	1
...................GGAGCGAGACGGGGACTCACT.....................................................	21	2	3.00	6	0	6
.................TGGGAGCGAGACGGGGAC..........................................................	18	2	2.50	5	0	5
.........................................................AGTCTTTTTCTCTCTCCTATA...............	21	2	2.50	5	5	0
.................TGGGAGCGAGACGGGGACTCAC......................................................	22	2	1.50	3	1	2
.......................................................TCAGTCTTTTTCTCTCTCCTATAC..............	24	2	1.00	2	2	0

Secondary Structure

dm3

dG=-28.3, p-value=0.009901

droSim1

dG=-28.3, p-value=0.009901

droSec1

dG=-28.3, p-value=0.009901

droYak2

dG=-28.3, p-value=0.009901

droEre2

dG=-28.3, p-value=0.009901

droAna3

dG=-28.3, p-value=0.009901

dp4

dG=-26.6, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.6, p-value=0.009901

droPer1

dG=-26.6, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.6, p-value=0.009901

droWil1

dG=-29.2, p-value=0.009901

droVir3

dG=-28.3, p-value=0.009901

droMoj3

dG=-28.0, p-value=0.009901	dG=-27.1, p-value=0.009901	dG=-27.1, p-value=0.009901

droGri2

dG=-28.3, p-value=0.009901

Generated: 03/07/2013 at 04:51 PM