Secondary structure and small RNA-seq evidence for dme-let-7

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:18472019-18472126 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSim1	chr2L:18160930-18161037 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSec1	super_7:2097967-2098074 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droYak2	chr2R:4988819-4988926 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droEre2	scaffold_4845:5799401-5799508 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droAna3	scaffold_12916:2379166-2379273 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGCAACTA-AGAATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCATTT
dp4	chr4_group3:3635640-3635746 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droPer1	super_1:5116219-5116325 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droWil1	scaffold_180708:11623134-11623240 +	AAAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTATTCAATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCACA---
droVir3	scaffold_12963:18451337-18451441 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATTTA-TAGAGCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCA---
droMoj3	scaffold_6500:6184568-6184672 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTTA-TAGACCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACTATAAGCCGCA---
droGri2	scaffold_3792:132-239 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATCTA-TCTAGCATACTATACAGCTTGCTAGCTTTCTTTGCTTGACTATAAGCAGCATAG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:18472019-18472126 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSim1	chr2L:18160930-18161037 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSec1	super_7:2097967-2098074 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droYak2	chr2R:4988819-4988926 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droEre2	scaffold_4845:5799401-5799508 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droAna3	scaffold_12916:2379166-2379273 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGCAACTA-AGAATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCATTT
dp4	chr4_group3:3635640-3635746 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droPer1	super_1:5116219-5116325 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droWil1	scaffold_180708:11623134-11623240 +	AAAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTATTCAATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCACA---
droVir3	scaffold_12963:18451337-18451441 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATTTA-TAGAGCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCA---
droMoj3	scaffold_6500:6184568-6184672 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTTA-TAGACCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACTATAAGCCGCA---
droGri2	scaffold_3792:132-239 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATCTA-TCTAGCATACTATACAGCTTGCTAGCTTTCTTTGCTTGACTATAAGCAGCATAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................TGAGGTAGTAGGTTGTATAGT..............................................................	21	1	29.00	29	29
.........................TGAGGTAGTAGGTTGTATAGTA.............................................................	22	1	26.00	26	26
.........................TGAGGTAGTAGGTTGTATAG...............................................................	20	1	5.00	5	5
...............................................................CTATACAATGTGCTAGCTTTCT.......................	22	1	2.00	2	2
.........................TGAGGTAGTAGGTTGTATA................................................................	19	1	1.00	1	1
.........................TGAGGTAGTAGGTTGTAT.................................................................	18	1	1.00	1	1

dp4

AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT-CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................TGAGGTAGTAGGTTGTATAGT..............................................................	21	1	34347.00	34347	35	34312
.........................TGAGGTAGTAGGTTGTATAG...............................................................	20	1	20657.00	20657	4	20653
.........................TGAGGTAGTAGGTTGTATAGTA.............................................................	22	1	5937.00	5937	19	5918
.........................TGAGGTAGTAGGTTGTATA................................................................	19	1	851.00	851	0	851
.........................TGAGGTAGTAGGTTGTAT.................................................................	18	1	695.00	695	0	695
..........................GAGGTAGTAGGTTGTATAGT..............................................................	20	1	88.00	88	0	88
..........................GAGGTAGTAGGTTGTATAGTA.............................................................	21	1	43.00	43	0	43
..........................GAGGTAGTAGGTTGTATAG...............................................................	19	1	23.00	23	0	23
...............................................................CTATACAATGTGCTAGCTTTCT.......................	22	1	19.00	19	0	19
.........................TGAGGTAGTAGGTTGTATAGTAG............................................................	23	1	8.00	8	0	8
...............................................................CTATACAATGTGCTAGCTTTC........................	21	1	7.00	7	0	7
...........................AGGTAGTAGGTTGTATAG...............................................................	18	1	4.00	4	0	4
...........................AGGTAGTAGGTTGTATAGT..............................................................	19	1	4.00	4	0	4

Secondary Structure

dm3

dG=-24.7, p-value=0.009901

droSim1

dG=-24.7, p-value=0.009901

droSec1

dG=-24.7, p-value=0.009901

droYak2

dG=-24.7, p-value=0.009901

droEre2

dG=-24.7, p-value=0.009901

droAna3

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

dp4

dG=-24.7, p-value=0.009901

droPer1

dG=-24.7, p-value=0.009901

droWil1

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

droVir3

dG=-26.8, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.2, p-value=0.009901

droMoj3

dG=-26.2, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.6, p-value=0.009901

droGri2

dG=-28.1, p-value=0.009901	dG=-27.5, p-value=0.009901	dG=-27.1, p-value=0.009901

Generated: 03/07/2013 at 04:43 PM