Secondary structure and small RNA-seq evidence for dme-mir-967

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12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:12459989-12460115 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAGATA-----------------------------CCT--------CTGGAGAAGCG--CGTGACCTGACCCCAGCAGGA-----------GAACCCAACCCGCTT----TTCCACCTA----------------G--------------GTGTCTC--T-----------CTCTCTCTTT--ATCTGTTCCTC------AGCTCG
droSim1	chr2L:12267908-12268042 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAGATA-----------------------------CCT--------CCGGAGAAGCG--CGTGACCTGACCCCAGCAGGA-----------GAACCCAACCCGCTT----TTCCGCCTA----------------G--------------GTGTCTC--TCTCTCTC---TCTCACTC--TATCTCAGTTCCTC------AGCTCG
droSec1	super_16:651020-651150 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAGATA-----------------------------CCT--------CCGGAGAAGCG--CGTGACCTGACCCCAGCAGGA-----------GAACCCAACCCGCTT----TTCCGCCTA----------------G--------------GTGTCTC--T----CTC---TCTCTCTC--TATCTCAGTTCCTC------AGCTCG
droYak2	chr2L:8897071-8897221 -	GAGAACTGCAGGAGACGGAGACTTGGAGAGCAGAGAC---------AGAGATGA-----------TACCT--------CTGGAGAAGCG--CGTGACCTGACCCCAGCA--------------GAACCCAACCCGCTT----TTCCGCCTA----------------G--------------ATGTCTC--TATCTCGC---TCTCCCTC--T--CTCTGTTCCTCTTGCACAGCTCG
droEre2	scaffold_4929:12958952-12959089 +	GAGAACTGCAGGA------GACTTGGAGAGCAGAGAT---------------GA-----------TACCT--------CTGGAGAAGCG--CGTGACCTGACCCCAGCAGGA-----------GAACCCAGCCCGCTT----TTCCGCCTA----------------G--------------GTGTCTC--TCACTCTC---TCTCTCTC--TCTCTCTTCTCCTC------AGCCCG
droAna3	scaffold_12916:12931176-12931307 +	GAGAAATGCATGA------GATTTTGAGAGGAGAGATA-----------------------------CCT--------C---AGAAGCG--CGTGACCTGACCCCGTCCGTCTGTCCATCTATGAACCCAACCCGCTT----TTC---TCCAAACACCAGAGAGGAG-----------------------------GTCGAGAGTG----------------ACGG------TGTGTG
dp4	chr4_group3:3150562-3150729 -	GAGAACTGCATGA------GACTTGGAGAGAAGAGATACCCACAA--GAGGCAGGCAGTGAAGTGGAGTGGAGGGAGC---GAGAAGCG--CGTGACCTGACCCCAAGACC------------GAACCCAACCCGGTT----CTGTTCTCCAGTGTACAGACAGGCA-----------------------------CTC---TGTATGAGTA--TGTACCCTCCTT------CGCTC-
droPer1	super_1:4633245-4633407 -	GAGAACTGCATGA------GATTTGGAGAGAAGAGATACCCACAA--GAGACGGT---CCG--TGGAGTGGAGGGAGC---GAGAAGCG--CGTGACCTGACCCCAAGACC------------GAACCCAACCCGGTT----CTGTTCTCCAGTGTACAGACAGGCA-----------------------------CTC---TGTATGAGTA--TGTACCCTCCTT------CGCTC-
droWil1	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13246:1657163-1657301 -	AGAGCGAGCAAGC------AGC------------------------------GTT---TTGTGTCTACCTCAGAAAGC---G--AGACG--CG-----TGAACCCAAATGCG-----------AACCTCGACCCGACTCGAATTCCGACTC----------------AACGCAAACGCTCAACTGTCTG--T------C---TGTCTGTC--T--GTCTGTCTGTC------TGCCTG
droMoj3	scaffold_6500:4266220-4266364 +	AAGTAGTAGAAGA------AAAAGAAGAAGCAGCGGC------AACAGAAACGTT---TGGTGTCTACCTCAGAAAGC---G--ACACG--CA----TGAACCCCAAAAACG-----------AACCTCGACCCGACC----GACTACC----------------------------------AATTTCTAT------T---TGTCTGACTCT--GTCTCT-GCTG------TGTGTG
droGri2	scaffold_15252:15585528-15585616 +	GCAGA--AGAGTA-AAA--GG---AAGAAGCAGAC----------------------------------------------AAAAGACACGCG--TGTTGAACCCGAAAACGAACCCAACTTCAAATTCAACGCAC---------------------------------------------------------------------------------------TTG------CCTCT-

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:12459989-12460115 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAG---------ATACCTCTGGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAACCCGCTTTTCCACCTAGGTGTCTCTCTCTC------TCTTTATCT--GTTCCT------CAGCTCG
droSim1	chr2L:12267908-12268042 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAG---------ATACCTCCGGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAACCCGCTTTTCCGCCTAGGTGTCTCTCTCTCTCTCTCACTCTATCTCAGTTCCT------CAGCTCG
droSec1	super_16:651020-651150 -	GAGAACTGCAGGA------GACTTGGAGAGCAGAG---------ATACCTCCGGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAACCCGCTTTTCCGCCTAGGTGTCTCTCTCTCTC----TCTCTATCTCAGTTCCT------CAGCTCG
droYak2	chr2L:8897071-8897221 -	GAGAACTGCAGGAGACGGAGACTTGGAGAGCAGAGACAGAGATGATACCTCTGGAGAAGCGCGTGACCTGACCCCAGCA---GAACCCAACCCGCTTTTCCGCCTAGATGTCTCTATCTCGCTCTCCCTCTCTCT--GTTCCTCTTGCACAGCTCG
droEre2	scaffold_4929:12958952-12959089 +	GAGAACTGCAGGA------GACTTGGAGAGCAGAG------ATGATACCTCTGGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAGCCCGCTTTTCCGCCTAGGTGTCTCTCACTCTCTCTCTCTCTCTCTCTTCTCCT------CAGCCCG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GAGAACTGCAGGAGACTTGGAGAGCAGAGATACCTCC--------------------------------GGAGAAGCGCGTGACCTGACCCCAGCAGGAGAACCCAACCCGCTTTTCCGCCTAGGTGTCTC-----TCTCTCTCTCTCACTCTATCTCAGTTCCTCAGCTCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................AGAGATACCTCC--------------------------------GGAGAAGCG..............................................................................................	21	1	10.00	10	10
.........................AGAGATACCTCC--------------------------------GGAGAAGCGC.............................................................................................	22	1	2.00	2	2
...............................................................................................................CTTTTCCGCCTAGGTGTCTC-----TCT.................................	23	1	2.00	2	2
...............................................................................................................CTTTTCCGCCTAGGTGTCTC-----TC..................................	22	1	1.00	1	1
............................................................................................................CCGCTTTTCCGCCTAGGTGTC...........................................	21	1	1.00	1	1
.........................AGAGATACCTCC--------------------------------GGAGAAGCGCG............................................................................................	23	1	1.00	1	1
.........................AGAGATACCTCC--------------------------------GGAGAAGC...............................................................................................	20	1	1.00	1	1
...........................AGATACCTCC--------------------------------GGAGAAGCGCG............................................................................................	21	1	1.00	1	1

dp4

GAGAACTGCATGAGACTTGGAGAGAAGAGATACCCACAAGAGGCAGGCAGTGAAGTGGAGTGGAGGGAGCGAGAAGCGCGTGACCTGACCCCAAGAC-CGAACCCAACCCGGTTCTGTTCTCCAGTGTACAGACAGGCACTCTGTATGAG--TATGTACCCTCCTTCGCTC-	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................GCAGTGAAGTGGAGTGGAGGGAGC......................................................................................................	24	1	1.00	1	1	0

Secondary Structure

dm3

dG=-38.3, p-value=0.009901	dG=-37.7, p-value=0.009901

droSim1

dG=-39.3, p-value=0.009901	dG=-38.7, p-value=0.009901

droSec1

dG=-39.3, p-value=0.009901	dG=-38.7, p-value=0.009901

droYak2

dG=-34.3, p-value=0.009901	dG=-34.2, p-value=0.009901	dG=-34.0, p-value=0.009901	dG=-33.7, p-value=0.009901	dG=-33.6, p-value=0.009901

droEre2

dG=-35.6, p-value=0.009901	dG=-35.3, p-value=0.009901	dG=-35.0, p-value=0.009901	dG=-34.7, p-value=0.009901	dG=-34.6, p-value=0.009901

droAna3

dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.8, p-value=0.009901	dG=-18.6, p-value=0.009901	dG=-14.6, p-value=0.009901

dp4

dG=-31.5, p-value=0.009901	dG=-31.2, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-31.0, p-value=0.009901	dG=-25.7, p-value=0.009901

droPer1

dG=-37.9, p-value=0.009901	dG=-37.5, p-value=0.009901	dG=-32.1, p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

dG=-18.1, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.4, p-value=0.009901	dG=-17.0, p-value=0.009901

droMoj3

dG=-13.4, p-value=0.009901	dG=-13.1, p-value=0.009901	dG=-13.1, p-value=0.009901	dG=-12.8, p-value=0.009901	dG=-12.7, p-value=0.009901	dG=-10.73, p-value=0.009901

droGri2

dG=-7.9, p-value=0.009901	dG=-7.3, p-value=0.009901

Generated: 03/07/2013 at 07:16 PM