Secondary structure and small RNA-seq evidence for dme-mir-13b-1

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:11243115-11243212 -	CACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-ACAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droSim1	chr3R:10237959-10238056 +	CGCG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droSec1	super_0:10705190-10705287 +	CGCG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droYak2	chr3R:15188722-15188819 +	CACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droEre2	scaffold_4770:10769258-10769355 -	AACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droAna3	scaffold_13340:12827469-12827566 -	--CA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAAGGCTTGTGACCTTATGT---ATTTCGCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAC
dp4	chr2:9825076-9825174 +	AGCA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGACCTTATGT---ACTCTTGAATCATATCACAGCCATTTTGACGAGTTTGGGTACAGAAATTTCAA
droPer1	super_0:10659921-10660019 -	AGCA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGACCTTATGT---ACTCTTGAATCATATCACAGCCATTTTGACGAGTTTGGGTACAGAAATTTCAA
droWil1	scaffold_181089:2143062-2143162 -	TGCA-----------------------------------------------------ACTTTCTTATACCATGTCGTTAAAATGTTTGTGACTTTATGTTGTGTCT-CTATTCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droVir3	scaffold_13047:13335778-13335875 +	TGCA-----------------------------------------------------ATTTTCTTATACCATGTCGTTAAAATGCCTGTGACCTTATGT---ATTT-TATATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droMoj3	scaffold_6540:10568509-10568606 +	TGCA-----------------------------------------------------ATTTTCTTATACCATGTCGTTAAAATGTCTGTGACCGTATGT---ATTC-ACTATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droGri2	scaffold_14906:4357489-4357639 -	CGTGCAGTCGCCGCCTCCTCCTGTTCCTCCTCCTTCTCCTTTGTGTGTTTCTTTCTTTCTTTCTTATACCATGTCGTTAAAATGCTTGTGACCTTATGT---ATTT-TATATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATGTCAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:11243115-11243212 -	CACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-ACAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droSim1	chr3R:10237959-10238056 +	CGCG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droSec1	super_0:10705190-10705287 +	CGCG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droYak2	chr3R:15188722-15188819 +	CACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droEre2	scaffold_4770:10769258-10769355 -	AACG-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGT---ATTC-GCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droAna3	scaffold_13340:12827469-12827566 -	--CA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAAGGCTTGTGACCTTATGT---ATTTCGCAATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAC
dp4	chr2:9825076-9825174 +	AGCA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGACCTTATGT---ACTCTTGAATCATATCACAGCCATTTTGACGAGTTTGGGTACAGAAATTTCAA
droPer1	super_0:10659921-10660019 -	AGCA-----------------------------------------------------TCTTTCTTATACCATGTCGTTAAAATGTTTGTGACCTTATGT---ACTCTTGAATCATATCACAGCCATTTTGACGAGTTTGGGTACAGAAATTTCAA
droWil1	scaffold_181089:2143062-2143162 -	TGCA-----------------------------------------------------ACTTTCTTATACCATGTCGTTAAAATGTTTGTGACTTTATGTTGTGTCT-CTATTCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droVir3	scaffold_13047:13335778-13335875 +	TGCA-----------------------------------------------------ATTTTCTTATACCATGTCGTTAAAATGCCTGTGACCTTATGT---ATTT-TATATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droMoj3	scaffold_6540:10568509-10568606 +	TGCA-----------------------------------------------------ATTTTCTTATACCATGTCGTTAAAATGTCTGTGACCGTATGT---ATTC-ACTATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA
droGri2	scaffold_14906:4357489-4357639 -	CGTGCAGTCGCCGCCTCCTCCTGTTCCTCCTCCTTCTCCTTTGTGTGTTTCTTTCTTTCTTTCTTATACCATGTCGTTAAAATGCTTGTGACCTTATGT---ATTT-TATATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATGTCAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGCGTCTTTCTTATACCATGTCGTTAAAATGTTTGTGAACTTATGTATTCGC-AATCATATCACAGCCATTTTGACGAGTTTGGGTAAAGAAATCTCAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................................................TATCACAGCCATTTTGACGAG....................	21	3	1005.00	3015	3015
..............................................................ACAGCCATTTTGACGAGT...................	18	3	130.67	392	392
....................TCGTTAAAATGTTTGTGAACTTATG......................................................	25	1	37.00	37	37
..........................................................TATCACAGCCATTTTGACGA.....................	20	3	32.00	96	96
..........................................................TATCACAGCCATTTTGACGAGTTTG................	25	3	8.67	26	26
...........................................................ATCACAGCCATTTTGACGAGT...................	21	3	5.00	15	15
.........................................................ATATCACAGCCATTTTGACGAG....................	22	3	2.67	8	8
....................TCGTTAAAATGTTTGTGAACTT.........................................................	22	1	1.00	1	1

dp4

AGCATCTTTCTTATACCATGTCGTTAAAATGTTTGTGACCTTATGTACTCTTGAATCATATCACAGCCATTTTGACGAGTTTGGGTACAGAAATTTCAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................................................TATCACAGCCATTTTGACGAGTT..................	23	3	3574.00	10722	0	10722
..........................................................TATCACAGCCATTTTGACGAGTTT.................	24	3	77.00	231	231	0
....................TCGTTAAAATGTTTGTGACCTTATG......................................................	25	1	72.00	72	71	1
..............................................................ACAGCCATTTTGACGAGTT..................	19	3	38.67	116	0	116
..........................................................TATCACAGCCATTTTGACGA.....................	20	3	27.67	83	0	83
...........................................................ATCACAGCCATTTTGACGAGTT..................	22	3	11.00	33	0	33
..........................................................TATCACAGCCATTTTGACG......................	19	3	7.00	21	0	21
..........................................................TATCACAGCCATTTTGACGAGTTTG................	25	3	3.00	9	9	0
....................TCGTTAAAATGTTTGTGACCTT.........................................................	22	1	3.00	3	3	0
............................................................TCACAGCCATTTTGACGAGTT..................	21	3	2.33	7	0	7
.............................................................CACAGCCATTTTGACGAGTT..................	20	3	1.67	5	5	0
............................................................TCACAGCCATTTTGACGAGT...................	20	3	1.33	4	0	4
.....................CGTTAAAATGTTTGTGACCTTATG......................................................	24	1	1.00	1	1	0
....................TCGTTAAAATGTTTGTGACCTTAT.......................................................	24	1	1.00	1	1	0
......................GTTAAAATGTTTGTGACCTTATG......................................................	23	1	1.00	1	1	0
.........................................................ATATCACAGCCATTTTGACGAGT...................	23	3	1.00	3	0	3
.....................CGTTAAAATGTTTGTGACCTTAT.......................................................	23	1	1.00	1	1	0

Secondary Structure

dm3

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-21.9, p-value=0.009901

droSim1

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-22.0, p-value=0.009901

droSec1

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-22.0, p-value=0.009901

droYak2

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-22.0, p-value=0.009901

droEre2

dG=-22.9, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-22.0, p-value=0.009901

droAna3

dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.0, p-value=0.009901

dp4

dG=-22.8, p-value=0.009901

droPer1

dG=-22.8, p-value=0.009901

droWil1

dG=-22.7, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-21.9, p-value=0.009901

droVir3

dG=-25.1, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.1, p-value=0.009901

droMoj3

dG=-25.1, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.3, p-value=0.009901

droGri2

dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-21.9, p-value=0.009901

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