Secondary structure and small RNA-seq evidence for dme-mir-1017

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:20314319-20314517 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCCGAAAA-TGA--------------------------------------T----CCCTTTC-TCCCCTTTTCCCAACACA--T------------TTGT----------------------------------ATCCC-----ACTTCCTGCGCGTCTTCGTGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAACA
droSim1	chr3R:20155121-20155319 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTCTC-TCCCCTTTTCCCGACACT--T------------TTGT----------------------------------AACCC-----ACTTCCTGCACGACTTCATGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAATA
droSec1	super_0:20650438-20650636 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTCTC-TCCCCTTTTCCTCACACA--C------------TTGT----------------------------------ATCCC-----ACTTCCTGCGCGACTTCATGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAACA
droYak2	chr3R:26186848-26187051 -	CCGAGCCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAAAATA--------------------------------------T----CCCTTTC-CCTCTTTTTTCCAACACATTC------------TTGT----------------------------------ATCCC-----ACTTTTTTTGCGCCTTCTTGGATGT-----------------------GTGA------CTGCTGC-AATGG------CCATGGACTGTT-TAGATATCTTCTTCAATA
droEre2	scaffold_4820:7744417-7744612 -	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTTTC---CCCCTTTCCCAACACA--C------------TTGT----------------------------------ATCCC-----ACTTCTCGCGCGAC-TCTTGGACTT-----------------------GTGG------CTGCTTC-ACTGG------C--TGGACTATT-TAGATATCTTCTTCAACA
droAna3	scaffold_13088:356279-356461 +	CCGAGCCGTATCCGGGTGAGTTTAGTGGAGTT-TAATGCTTCTC-------ATCGCCGGCCC-----------TTTCGCGAAAGCTCTACCCAAACTCATCCCCTGAAAACC-------------------------------------------TTTTTTC-C------------CCCCATT--T------------TCTT----------------------------------CCCTT-----ACTGTTTTTGCAC---TTTGGATTT--------------------TATGTGGC-----CTGC------TGG------A--TGGCTTCTT-CAGATATATTTTTCAACA
dp4	chr2:18479367-18479560 -	CCGAACCGTATCCGGGTGAGTTTTGTGGAGTT-TAAAGTTAACA-------ATCGCCGACAATC----A--AATTACGCGAAAGCTCTACCCAAACTCATCCCTCACAA-------------------------------------------TTGTTTTCCT-CC---------CCCACCAAA--AATCTCCCTCACCCTGT----------------------------------AAATC-----ACT-------------------------------------------ATGCGGCT---GCTGC------TGGTATTCGGCTTGGACTGTTCCAGATATCTTCTTCAATA
droPer1	super_3:1203012-1203205 -	CCGAACCGTATCCGGGTGAGTTTTGTGGAGTT-TAAAGTTTACA-------ATCGCCGACAATC----A--AATTACGCGAAAGCTCTACCCAAACTCATCCCTCACAA-------------------------------------------TTGTTTTCCT-CC---------CCCACCAAA--AATCTCCCTCTCCCTGT----------------------------------AAATC-----ACT-------------------------------------------ATGCGGCT---GCTGC------TGGTATTCGGCTTGGACTGTTCCAGATATCTTCTTCAATA
droWil1	scaffold_181108:4383442-4383643 -	CTGAACCATATCCAGGTGAGTTTTGTAGAGTTTTAAAGCTATAA-------ATCGCCGGTAAATAGACGTTAAAGACGCGAAAGCTCTACCCAAACTCAC-CCCGG-AAA------------------------------------------TTTTTTTATT-C-T-CTTTTTTCCCAACAAA--A------------ATAA----------------------------------TGACA-----ATTT-------A---TCTTGGAAAT--------------------TTGGTAA------ACACTTTAAATAA------T--TGTATATAT-TAGATATATTTTTCAATA
droVir3	scaffold_13047:3684405-3684633 +	CCGAGCCGTATCCGGGTGAGTTTCGTAGAGTT-TAAAGCTCTTA--CTTTGCTCGCTGGCAC----GC-----CCACGCGAAAGCTCTACCCAAACTCAC--TATGCAAACCCCCAACCCATACCCAAATCCA--------------------------------------------------------------------------------TGCTCCTTGTCTCTCTCTCTCTCTCTTTCTCTC-----TCTCTCT-------------CTCTCTCTCCACTTTTGTTTCATGCTGCAC---TCGC------TGGCTCTTG---TTGAATGTT-CAGACATATTCTTTAATA
droMoj3	scaffold_6540:20694202-20694463 +	CCGAGCCCTATCCCGGTGAGTTTCGTAGAGTT-TAAAGCTCACA--CTTTGCTCGCCAACAA----GC-----GCACGCGAAAGCTCTACCCAAACTCAC--TATGAAAATCTATACTCCAAACCCGAATCCAATCTTCGTGGATTCCATCATCGTGTCTCT-CT---------CTCTCTCTC--TCTCTCTC-----------------------------------------------------TCTCTCTGTTTGTCTTTCTGGATCTCTTTCTTTCTTTTGGTATTTCATGCTGCTC---TCGC------TGGCCTTG-A--TCAAATGTT-CAGACATCTTCTTCAACA
droGri2	scaffold_14906:340737-340980 +	CGGAACCGTATCCGGGTGAGTTTCGTAGGGTT-TAAAGCAACAAAACTTTGCTCGCCGACAC----GC-----GTACGCGAAAGCTCTACCCAAACTCAC--TATGGAAACC-----------------------------------------CGTATCCCA-AC---------CCCCCAAAT--AATCC-----AACCAATATCCCAATCCTGGCCTGTTCGTTCTCGTGTTCTTTGCTTTTCTC-----TTCTGCTCTTTCTTG-------------------------CCTGCTGCGATTGCTGCTT------GTTTTG-C--TAAAATGTT-TAGACATATTCTTCAATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:20314319-20314517 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCCGAAAA-TGA--------------------------------------T----CCCTTTC-TCCCCTTTTCCCAACACA--T------------TTGT----------------------------------ATCCC-----ACTTCCTGCGCGTCTTCGTGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAACA
droSim1	chr3R:20155121-20155319 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTCTC-TCCCCTTTTCCCGACACT--T------------TTGT----------------------------------AACCC-----ACTTCCTGCACGACTTCATGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAATA
droSec1	super_0:20650438-20650636 +	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTCTC-TCCCCTTTTCCTCACACA--C------------TTGT----------------------------------ATCCC-----ACTTCCTGCGCGACTTCATGGATTT-----------------------GTAA------CTGCTTC-AATGG------C--TGGACGGTT-TAGATATCTTCTTCAACA
droYak2	chr3R:26186848-26187051 -	CCGAGCCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAAAATA--------------------------------------T----CCCTTTC-CCTCTTTTTTCCAACACATTC------------TTGT----------------------------------ATCCC-----ACTTTTTTTGCGCCTTCTTGGATGT-----------------------GTGA------CTGCTGC-AATGG------CCATGGACTGTT-TAGATATCTTCTTCAATA
droEre2	scaffold_4820:7744417-7744612 -	CCGAACCGTATCCGGGTGAGTTTAGTGGAGTT-TAAAGCTTCCC-------ATCGCCAGCAA-----------TTACGCGAAAGCTCTACCCAAACTCATCCCCTGAAAA-ATA--------------------------------------T----CCCTTTC---CCCCTTTCCCAACACA--C------------TTGT----------------------------------ATCCC-----ACTTCTCGCGCGAC-TCTTGGACTT-----------------------GTGG------CTGCTTC-ACTGG------C--TGGACTATT-TAGATATCTTCTTCAACA
droAna3	scaffold_13088:356279-356461 +	CCGAGCCGTATCCGGGTGAGTTTAGTGGAGTT-TAATGCTTCTC-------ATCGCCGGCCC-----------TTTCGCGAAAGCTCTACCCAAACTCATCCCCTGAAAACC-------------------------------------------TTTTTTC-C------------CCCCATT--T------------TCTT----------------------------------CCCTT-----ACTGTTTTTGCAC---TTTGGATTT--------------------TATGTGGC-----CTGC------TGG------A--TGGCTTCTT-CAGATATATTTTTCAACA
dp4	chr2:18479367-18479560 -	CCGAACCGTATCCGGGTGAGTTTTGTGGAGTT-TAAAGTTAACA-------ATCGCCGACAATC----A--AATTACGCGAAAGCTCTACCCAAACTCATCCCTCACAA-------------------------------------------TTGTTTTCCT-CC---------CCCACCAAA--AATCTCCCTCACCCTGT----------------------------------AAATC-----ACT-------------------------------------------ATGCGGCT---GCTGC------TGGTATTCGGCTTGGACTGTTCCAGATATCTTCTTCAATA
droPer1	super_3:1203012-1203205 -	CCGAACCGTATCCGGGTGAGTTTTGTGGAGTT-TAAAGTTTACA-------ATCGCCGACAATC----A--AATTACGCGAAAGCTCTACCCAAACTCATCCCTCACAA-------------------------------------------TTGTTTTCCT-CC---------CCCACCAAA--AATCTCCCTCTCCCTGT----------------------------------AAATC-----ACT-------------------------------------------ATGCGGCT---GCTGC------TGGTATTCGGCTTGGACTGTTCCAGATATCTTCTTCAATA
droWil1	scaffold_181108:4383442-4383643 -	CTGAACCATATCCAGGTGAGTTTTGTAGAGTTTTAAAGCTATAA-------ATCGCCGGTAAATAGACGTTAAAGACGCGAAAGCTCTACCCAAACTCAC-CCCGG-AAA------------------------------------------TTTTTTTATT-C-T-CTTTTTTCCCAACAAA--A------------ATAA----------------------------------TGACA-----ATTT-------A---TCTTGGAAAT--------------------TTGGTAA------ACACTTTAAATAA------T--TGTATATAT-TAGATATATTTTTCAATA
droVir3	scaffold_13047:3684405-3684633 +	CCGAGCCGTATCCGGGTGAGTTTCGTAGAGTT-TAAAGCTCTTA--CTTTGCTCGCTGGCAC----GC-----CCACGCGAAAGCTCTACCCAAACTCAC--TATGCAAACCCCCAACCCATACCCAAATCCA--------------------------------------------------------------------------------TGCTCCTTGTCTCTCTCTCTCTCTCTTTCTCTC-----TCTCTCT-------------CTCTCTCTCCACTTTTGTTTCATGCTGCAC---TCGC------TGGCTCTTG---TTGAATGTT-CAGACATATTCTTTAATA
droMoj3	scaffold_6540:20694202-20694463 +	CCGAGCCCTATCCCGGTGAGTTTCGTAGAGTT-TAAAGCTCACA--CTTTGCTCGCCAACAA----GC-----GCACGCGAAAGCTCTACCCAAACTCAC--TATGAAAATCTATACTCCAAACCCGAATCCAATCTTCGTGGATTCCATCATCGTGTCTCT-CT---------CTCTCTCTC--TCTCTCTC-----------------------------------------------------TCTCTCTGTTTGTCTTTCTGGATCTCTTTCTTTCTTTTGGTATTTCATGCTGCTC---TCGC------TGGCCTTG-A--TCAAATGTT-CAGACATCTTCTTCAACA
droGri2	scaffold_14906:340737-340980 +	CGGAACCGTATCCGGGTGAGTTTCGTAGGGTT-TAAAGCAACAAAACTTTGCTCGCCGACAC----GC-----GTACGCGAAAGCTCTACCCAAACTCAC--TATGGAAACC-----------------------------------------CGTATCCCA-AC---------CCCCCAAAT--AATCC-----AACCAATATCCCAATCCTGGCCTGTTCGTTCTCGTGTTCTTTGCTTTTCTC-----TTCTGCTCTTTCTTG-------------------------CCTGCTGCGATTGCTGCTT------GTTTTG-C--TAAAATGTT-TAGACATATTCTTCAATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCGAACCGTATCCGGGTGAGTTTAGTGGAGTTTAAAGCTTCCCATCGCCAGCAA-----TTACGCGAAAGCTCTACCCAAACTCATCCCCTG---------------------AAAAATATCCCTCTCTCCCCTTTTCCCGACACTTTTGTAACCCACTTCCTGCACGACTTCATGGATTTGTAACTGCTTCAATGGC-TGGACGGTT-TAGATATCTTCTTCAATA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.................................................................GAAAGCTCTACCCAAACTCATCC...........................................................................................................................................	23	1	16.00	16	16
.................................................................GAAAGCTCTACCCAAACTCATC............................................................................................................................................	22	1	8.00	8	8
.................................................................GAAAGCTCTACCCAAACTCATCCC..........................................................................................................................................	24	1	8.00	8	8
.................................................................GAAAGCTCTACCCAAACTCAT.............................................................................................................................................	21	1	1.00	1	1
...............GTGAGTTTAGTGGAGTTT..................................................................................................................................................................................................	18	1	1.00	1	1

dp4

CCGAACCGTATCCGGGTGAGTTTTGTGGAGTTTAAAGTTAACAATCGCCGACAATCAAATTACGCGAAAGCTCTACCCAAACTCATCCCTCACAATTGTTTTCCTCCCCCACCAAAAATCTC--------------------------------CCTCACCCTGTAAATCACTATGCGGCTGCTGCTGGTATTC-GGCTTGGACTGTTCCAGATATCTTCTTCAATA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.................................................................GAAAGCTCTACCCAAACTCATC............................................................................................................................................	22	1	26.00	26	6	20
.................................................................GAAAGCTCTACCCAAACTCATCC...........................................................................................................................................	23	1	24.00	24	8	16
.................................................................GAAAGCTCTACCCAAACTCATCCC..........................................................................................................................................	24	1	8.00	8	8	0
..................................................................AAAGCTCTACCCAAACTCATCCC..........................................................................................................................................	23	1	4.00	4	4	0
..................................................................AAAGCTCTACCCAAACTCATCC...........................................................................................................................................	22	1	3.00	3	1	2
.................................................................GAAAGCTCTACCCAAACTCAT.............................................................................................................................................	21	1	2.00	2	0	2
...............GTGAGTTTTGTGGAGTTT..................................................................................................................................................................................................	18	1	1.00	1	0	1

Secondary Structure

dm3

dG=-19.6, p-value=0.009901

droSim1

dG=-19.6, p-value=0.009901

droSec1

dG=-19.6, p-value=0.009901

droYak2

dG=-19.6, p-value=0.009901

droEre2

dG=-19.6, p-value=0.009901

droAna3

dG=-19.6, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.1, p-value=0.009901

dp4

dG=-19.2, p-value=0.009901

droPer1

dG=-19.2, p-value=0.009901

droWil1

dG=-21.2, p-value=0.009901	dG=-21.0, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.3, p-value=0.009901

droVir3

dG=-25.3, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.4, p-value=0.009901

droMoj3

dG=-23.0, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.1, p-value=0.009901

droGri2

dG=-23.4, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.0, p-value=0.009901

Generated: 03/07/2013 at 04:48 PM