Secondary structure and small RNA-seq evidence for dme-mir-318

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:6234009-6234106 +	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droSim1	chr3R:15159142-15159239 -	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droSec1	super_0:15709308-15709405 -	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droYak2	chr3R:10262524-10262621 +	G-------TCCTC--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCAC-T--ACAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA
droEre2	scaffold_4770:15383893-15383990 -	G-------TCCTC--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA
droAna3	scaffold_13340:867198-867296 -	G-------TCCTC--CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT--GCGAGCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA
dp4	chr2:7233334-7233438 -	CGTGTGCCTCTTT--TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACAT-T--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA
droPer1	super_0:1094016-1094113 -	C-------TCTTT--TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACAT-T--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA
droWil1	scaffold_181108:652-751 +	G-------TCAGA--CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCAT-TCCACGAGCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA
droVir3	scaffold_13047:1194317-1194415 +	T-------GATTT--GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA
droMoj3	scaffold_6540:5225327-5225427 +	G-------TGATTAAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA
droGri2	scaffold_14906:5077291-5077389 -	G-------ATTTC--GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:6234009-6234106 +	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droSim1	chr3R:15159142-15159239 -	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droSec1	super_0:15709308-15709405 -	G-------TCCTT--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA
droYak2	chr3R:10262524-10262621 +	G-------TCCTC--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCAC-T--ACAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA
droEre2	scaffold_4770:15383893-15383990 -	G-------TCCTC--CGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACAC-T--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCA
droAna3	scaffold_13340:867198-867296 -	G-------TCCTC--CGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTTT--GCGAGCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCA
dp4	chr2:7233334-7233438 -	CGTGTGCCTCTTT--TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACAT-T--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA
droPer1	super_0:1094016-1094113 -	C-------TCTTT--TGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACAT-T--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA
droWil1	scaffold_181108:652-751 +	G-------TCAGA--CGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCAT-TCCACGAGCATCACTGGGCTTTGTTTATCTCATAAAGGAGAAATGAATACA
droVir3	scaffold_13047:1194317-1194415 +	T-------GATTT--GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGTGAAATTTGTTCA
droMoj3	scaffold_6540:5225327-5225427 +	G-------TGATTAAGGATTTCAATTTATGGGATACACTAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTTGTTCA
droGri2	scaffold_14906:5077291-5077389 -	G-------ATTTC--GGATTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCAGATGT--CCAAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTAGTTCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

G-------TCCTTCGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACTTCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................TCACTGGGCTTTGTTTATCTCA...................	22	1	6.00	6	6
................................................................TCACTGGGCTTTGTTTATCT.....................	20	1	1.00	1	1
................................................................TCACTGGGCTTTGTTTATCTC....................	21	1	1.00	1	1

dp4

CGTGTGCCTCTTTTGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATTTCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................TCACTGGGCTTTGTTTATCTCA...................	22	1	22.00	22	10	12
................................................................TCACTGGGCTTTGTTTATCTC....................	21	1	5.00	5	1	4
................................................................TCACTGGGCTTTGTTTATCT.....................	20	1	2.00	2	0	2
.................................................................CACTGGGCTTTGTTTATCTCA...................	21	1	1.00	1	0	1
..................................................................ACTGGGCTTTGTTTATCTCA...................	20	1	1.00	1	1	0

Secondary Structure

dm3

dG=-24.2, p-value=0.009901

droSim1

dG=-24.2, p-value=0.009901

droSec1

dG=-24.2, p-value=0.009901

droYak2

dG=-24.2, p-value=0.009901	dG=-23.4, p-value=0.009901

droEre2

dG=-24.2, p-value=0.009901

droAna3

dG=-25.9, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-25.0, p-value=0.009901

dp4

dG=-23.4, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.4, p-value=0.009901

droPer1

dG=-23.4, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.4, p-value=0.009901

droWil1

dG=-25.7, p-value=0.009901	dG=-25.1, p-value=0.009901	dG=-24.8, p-value=0.009901

droVir3

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

droMoj3

dG=-24.6, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.7, p-value=0.009901

droGri2

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

Generated: 03/07/2013 at 05:20 PM