Secondary structure and small RNA-seq evidence for dme-mir-1006

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16724780-16724873 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droSim1	chr2L:16422879-16422972 -	CGGGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droSec1	super_7:371570-371663 -	CGGGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droYak2	chr2R:4378132-4378225 +	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droEre2	scaffold_4845:19796345-19796438 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droAna3	scaffold_12943:3938325-3938418 +	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTCCAATACCAGCTG
dp4	chr4_group3:3057660-3057753 +	CGCGTCAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG
droPer1	super_1:4544383-4544476 +	CGCGTCAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG
droWil1	scaffold_180708:1783971-1784066 +	CGTGTTAATTTCCAGGTGAGTTTGAAATTGAAATGCCTAAATTGTTTTGTGTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATATCAATTA
droVir3	scaffold_12963:6536524-6536617 -	CGTGTCAACTTTCAGGTGAGTTTGAAATTGAAATATGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droMoj3	scaffold_6500:25691037-25691130 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droGri2	scaffold_15252:9753534-9753627 -	CGCGTCAATTTCCAAGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16724780-16724873 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droSim1	chr2L:16422879-16422972 -	CGGGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droSec1	super_7:371570-371663 -	CGGGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droYak2	chr2R:4378132-4378225 +	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droEre2	scaffold_4845:19796345-19796438 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droAna3	scaffold_12943:3938325-3938418 +	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTCCAATACCAGCTG
dp4	chr4_group3:3057660-3057753 +	CGCGTCAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG
droPer1	super_1:4544383-4544476 +	CGCGTCAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--TGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG
droWil1	scaffold_180708:1783971-1784066 +	CGTGTTAATTTCCAGGTGAGTTTGAAATTGAAATGCCTAAATTGTTTTGTGTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATATCAATTA
droVir3	scaffold_12963:6536524-6536617 -	CGTGTCAACTTTCAGGTGAGTTTGAAATTGAAATATGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droMoj3	scaffold_6500:25691037-25691130 -	CGTGTCAACTTCCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG
droGri2	scaffold_15252:9753534-9753627 -	CGCGTCAATTTCCAAGTGAGTTTGAAATTGAAATGTGTAAATTGTTTG--GTCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGGGTCAACTTCCAGGTGAGTTTGAAATTGAAATGCGTAAATTGTTTGGTACAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGTTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
........................................................TAAATTCGATTTCTTATTCATAG...............	23	1	20.00	20	20
...............GTGAGTTTGAAATTGAAATGCGTAAA.....................................................	26	1	7.00	7	7
........................................................TAAATTCGATTTCTTATTCAT.................	21	1	6.00	6	6
........................................................TAAATTCGATTTCTTATTCATA................	22	1	2.00	2	2
.......................................................TTAAATTCGATTTCTTATTCAT.................	22	1	1.00	1	1
...............GTGAGTTTGAAATTGAAATGCGTA.......................................................	24	1	1.00	1	1
...............GTGAGTTTGAAATTGAAATGCGTAA......................................................	25	1	1.00	1	1
.......................................................TTAAATTCGATTTCTTATTCATAG...............	24	1	1.00	1	1
........................................................TAAATTCGATTTCTTATTCA..................	20	1	1.00	1	1

dp4

CGCGTCAACTTTCAGGTGAGTTTGAAATTGAAATGTGTAAATTGTTTGTGCCAATTTAAATTCGATTTCTTATTCATAGGTGCAATACCAGCTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
........................................................TAAATTCGATTTCTTATTCAT.................	21	1	127.00	127	15	112
........................................................TAAATTCGATTTCTTATTCATAG...............	23	1	111.00	111	50	61
........................................................TAAATTCGATTTCTTATTCA..................	20	1	54.00	54	3	51
........................................................TAAATTCGATTTCTTATTCATA................	22	1	43.00	43	15	28
...............GTGAGTTTGAAATTGAAATGTGT........................................................	23	1	12.00	12	0	12
...............GTGAGTTTGAAATTGAAATGTGTAAA.....................................................	26	1	7.00	7	4	3
...............GTGAGTTTGAAATTGAAATGTGTA.......................................................	24	1	5.00	5	3	2
...............GTGAGTTTGAAATTGAAATGTG.........................................................	22	1	4.00	4	2	2
.......................................................TTAAATTCGATTTCTTATTCAT.................	22	1	3.00	3	1	2
........................................................TAAATTCGATTTCTTATTC...................	19	1	3.00	3	0	3
.......................................................TTAAATTCGATTTCTTATTCA..................	21	1	2.00	2	0	2
.............................GAAATGTGTAAATTGTTTGTGCCA.........................................	24	1	1.00	1	1	0
..........................................................AATTCGATTTCTTATTCATAG...............	21	1	1.00	1	0	1
...............GTGAGTTTGAAATTGAAAT............................................................	19	1	1.00	1	0	1
.........................................TTGTTTGTGCCAATTTAAATTCG..............................	23	1	1.00	1	0	1
.........................................................AAATTCGATTTCTTATTCATA................	21	1	1.00	1	0	1

Secondary Structure

dm3

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droSim1

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droSec1

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droYak2

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droEre2

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droAna3

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

dp4

dG=-16.1, p-value=0.009901	dG=-15.5, p-value=0.009901	dG=-15.1, p-value=0.009901

droPer1

dG=-16.1, p-value=0.009901	dG=-15.5, p-value=0.009901	dG=-15.1, p-value=0.009901

droWil1

dG=-17.4, p-value=0.009901	dG=-16.8, p-value=0.009901

droVir3

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droMoj3

dG=-18.5, p-value=0.009901	dG=-17.9, p-value=0.009901

droGri2

dG=-16.1, p-value=0.009901	dG=-15.5, p-value=0.009901

Generated: 03/07/2013 at 04:45 PM