Secondary structure and small RNA-seq evidence for dme-mir-1007

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:21167397-21167491 -	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA------C--TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGGATCTTCT
droSim1	chrX:12920203-12920297 +	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA------C--TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCATCTTCT
droSec1	super_8:3474404-3474498 -	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA------C--TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCATCTTCT
droYak2	chrX:20343121-20343215 -	ACGAATCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--T-AGGATC--TTGGA------C--TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCATCTTCT
droEre2	scaffold_4690:17696754-17696848 -	ACGAATCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--T-GGGATC--TTGGA------C--TCTTGATAAGCTCAATTAACTGTTT----GCAGCGGACGGCATCTTCT
droAna3	scaffold_13334:1054378-1054469 +	ACGAATCCGTACAGTGTAAGCAGTGTTTGAACTCGATC--T----------TGGAA--TAGC--TCCCGATAAGCTCAATTAACTGTTT----GCAGCCGATGGCATCTTCT
dp4	chrXL_group1a:9060607-9060705 +	ACGAATCGATACAGTGTAAGCAGCGATTGA--TCAATCAAT-TGAATCGAATCGA------ATCGAATGATAAACTCCATTAACTGTTT----GCAGCCGATGGCATCTTCT
droPer1	super_15:1454063-1454161 +	ACGAATCGATACAGTGTAAGCAGCGATTGA--TCAATCAAT-TGAATCGAATCGA------ATCGAATGATAAACTCCATTAACTGTTT----GCAGCCGATGGCATCTTCT
droWil1	scaffold_180702:162895-162984 -	ATGAATCCATGCAATGTGAGTT--TTTTGATTTT---C--T-----TG--TTTAA------T--TTCGAAAAACTTTAATCGACTGTATTCTATCAGCTGATGGCATCTTCT
droVir3	scaffold_12970:7925725-7925826 -	ACGAATCAATGAAATGTAAGCAGTGCTTGAGCTTATTC--TCTGGCTTCATTTGAC--CA--TTTTCTGATAAGCTCAATTAACTGTTT----GCAGCGGATGCCGCCCTCT
droMoj3	scaffold_6482:1600635-1600734 +	ATGAGTCCATGAAATGTAAGCAGTGTTTGAACTAAATC--TCTGGCTA--CTTGGC--CG--TATATTGATAAGCTCAACTAACTGTTT----GCAGCGGACACCTATTTGG
droGri2	scaffold_15203:11134564-11134665 +	GCGAATCAATACAATGTAAGCAGTGTTTGAACTGAATA--TCTGGTTA--TCCGACTTCA--TATACTGATAAGCTCAATTCACTGTTT----GCAGCGGATGGCGTCTTCT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:21167397-21167491 -	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA----CT------CTTGATAAGCTCAATTAACTGTTTGCAGCGGACGGGATCTTCT
droSim1	chrX:12920203-12920297 +	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA----CT------CTTGATAAGCTCAATTAACTGTTTGCAGCGGACGGCATCTTCT
droSec1	super_8:3474404-3474498 -	ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--T-TGGTTC--TTGGA----CT------CTTGATAAGCTCAATTAACTGTTTGCAGCGGACGGCATCTTCT
droYak2	chrX:20343121-20343215 -	ACGAATCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--T-AGGATC--TTGGA----CT------CTTGATAAGCTCAATTAACTGTTTGCAGCGGACGGCATCTTCT
droEre2	scaffold_4690:17696754-17696848 -	ACGAATCTGTTCAGTGTAAGCAGTGTTTGAACTCGATC--T-GGGATC--TTGGA----CT------CTTGATAAGCTCAATTAACTGTTTGCAGCGGACGGCATCTTCT
droAna3	scaffold_13334:1054378-1054469 +	ACGAATCCGTACAGTGTAAGCAGTGTTTGAACTCGATC--T----------TGGAATAGCT------CCCGATAAGCTCAATTAACTGTTTGCAGCCGATGGCATCTTCT
dp4	chrXL_group1a:9060607-9060705 +	ACGAATCGATACAGTGTAAGCAGCGATTGA--TCAATCAAT-TGAATCGAATCGA----AT----CGAATGATAAACTCCATTAACTGTTTGCAGCCGATGGCATCTTCT
droPer1	super_15:1454063-1454161 +	ACGAATCGATACAGTGTAAGCAGCGATTGA--TCAATCAAT-TGAATCGAATCGA----AT----CGAATGATAAACTCCATTAACTGTTTGCAGCCGATGGCATCTTCT
droVir3	scaffold_12970:7925725-7925826 -	ACGAATCAATGAAATGTAAGCAGTGCTTGAGCTTATTC--TCTGGCTTCATTTGA----CC--ATTTTCTGATAAGCTCAATTAACTGTTTGCAGCGGATGCCGCCCTCT
droMoj3	scaffold_6482:1600635-1600734 +	ATGAGTCCATGAAATGTAAGCAGTGTTTGAACTAAATC--TCTGGCTA--CTTGG----CC--GTATATTGATAAGCTCAACTAACTGTTTGCAGCGGACACCTATTTGG
droGri2	scaffold_15203:11134564-11134665 +	GCGAATCAATACAATGTAAGCAGTGTTTGAACTGAATA--TCTGGTTA--TCCGA----CTTCATATACTGATAAGCTCAATTCACTGTTTGCAGCGGATGGCGTCTTCT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACGAATCTGTACAGTGTAAGCAGTGTTTGAACTCGATC--TTGGTTCT--TGGACTC--TTGATAAGCTCAATTAACTGTTTGCAGCGGACGGCATCTTCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................................................TAAGCTCAATTAACTGTTTGCAG...............	23	1	10.00	10	10
...............GTAAGCAGTGTTTGAACT....................................................................	18	1	5.00	5	5
...............................................................TAAGCTCAATTAACTGTTTGCA................	22	1	2.00	2	2
...................................................GGACTC--TTGATAAGCTCA..............................	18	1	1.00	1	1
...............GTAAGCAGTGTTTGAACTCGATC--TTGG.........................................................	27	1	1.00	1	1
.....................AGTGTTTGAACTCGATC--TTGGT........................................................	22	1	1.00	1	1
...............GTAAGCAGTGTTTGAACTC...................................................................	19	1	1.00	1	1
...............GTAAGCAGTGTTTGAACTCG..................................................................	20	1	1.00	1	1
......................GTGTTTGAACTCGATC--TTGG.........................................................	20	1	1.00	1	1
.............................................TCT--TGGACTC--TTGATAAGCTCA..............................	22	1	1.00	1	1

dp4

ACGAATCGATACAGTGTAAGCAGCGATTGA--TCAATCAATTGAATCGAATCGAATCGAATGATAAACTCCATTAACTGTTTGCAGCCGATGGCATCTTCT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-16.8, p-value=0.009901	dG=-16.6, p-value=0.009901

droSim1

dG=-16.8, p-value=0.009901	dG=-16.6, p-value=0.009901

droSec1

dG=-16.8, p-value=0.009901	dG=-16.6, p-value=0.009901

droYak2

dG=-17.8, p-value=0.009901	dG=-17.3, p-value=0.009901	dG=-17.1, p-value=0.009901

droEre2

dG=-17.3, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-17.1, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.7, p-value=0.009901

droAna3

dG=-17.8, p-value=0.009901

dp4

dG=-16.0, p-value=0.009901	dG=-15.6, p-value=0.009901	dG=-15.4, p-value=0.009901	dG=-15.2, p-value=0.009901

droPer1

dG=-16.0, p-value=0.009901	dG=-15.6, p-value=0.009901	dG=-15.4, p-value=0.009901	dG=-15.2, p-value=0.009901

droWil1

dG=-8.7, p-value=0.009901	dG=-8.7, p-value=0.009901	dG=-7.8, p-value=0.009901	dG=-7.8, p-value=0.009901	dG=-7.7, p-value=0.009901

droVir3

dG=-24.5, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-23.5, p-value=0.009901

droMoj3

dG=-18.3, p-value=0.009901	dG=-17.4, p-value=0.009901

droGri2

dG=-17.8, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.9, p-value=0.009901

Generated: 03/07/2013 at 04:46 PM