Secondary structure and small RNA-seq evidence for dme-mir-3641

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:2065104-2065202 +	GGCGAACTTTTTAATGTGAGTGTCCTGTTT------------ACAGCTGGTATATTTT---------TCGAAA---AGCC----------CTCTAAAC---------TGG------------T---CACTTCCAC-TCTACAGATCTATAACTACATA
droSim1	chrX:1441441-1441539 +	GGCGAACTGTTCAATGTGAGTTTCCTACTT------------ACAGCTGGTATATTTC---------TCGAAC---AGTC----------CTCTAAAC---------TGG------------T---CCCTTCCGC-TCCGCAGATCTACAACTACATA
droSec1	super_10:1848730-1848828 +	GGCGAACTGTTCAATGTGAGTTTCCTACTT------------ACAGCTGGTATATTTC---------GCGAAC---AGTC----------CTCTAAAC---------TGG------------T---CCCTTCCGC-TCCGCAGATCTACAACTACATA
droYak2	chrX:6259202-6259289 -	GGCGAACTCTTCAATGTGAGTTTCCTATGT------------TTCGCATGTACATAT---------------------------------ATCTAAAT---------TGG------------T---TCCTTCTCC-TCTGCAGATCTACAACTACATA
droEre2	scaffold_4644:2028284-2028382 +	GGCGAACTGTTCAATGTGAGTATCCTGTGA------------TCCGCTTGTACTTATC---------TCGAGC---AGTT----------CTCTAAAC---------TGG------------T---CCCTGATCC-TCTGCAGATCTACAACTACATA
droAna3	scaffold_13117:1070684-1070773 -	GGCGAGCTCTTCAACGTAAGTTTCCCCGCT------------TAAAC------------GCCTAAGA-----T----TTT----------CCCTAAAC---------CGT------------T---GCTGTTCTG-TCTCTAGATCTACAACTATATC
dp4	chrXL_group1e:3790116-3790235 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATT------------TCAGCCT---------CGAATTCGG-----C---AGTCACTTGATAC---------TCTCCCACCTCCCTCTCCCTCTGCCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droPer1	super_17:723995-724114 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATT------------TCAGCCT---------CGAATTCGG-----C---AGTCACTTAATAC---------TCTCCCACCTCCCTCTCCCTCTGCCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droWil1	scaffold_181096:7421152-7421244 -	GGCGAGCTTTTCAACGTGAGTTACTCAGTC------------CA----A---------AGAAACTGG-----TTTTAGTTA--TGAT-----------TAACTC-----A------------C----TTTTTTTT-GTTATAGATTTACAACTATATA
droVir3	scaffold_12928:7113520-7113613 +	GGCGAGTTGTTCAACGTAAGTCGATGACCTCGCG--------T------------------ATGTGGGCGTAC---TTTC----------A------CTGACGC---CTG------------C---CTCTTTGTC-TATTCAGATTTACAACTACATT
droMoj3	scaffold_6328:2787435-2787524 +	GGGGAGTTGTTCAACGTAAATTCT--ATTC------------TCACTTAACACA----AGAATCAAA-----T----CTC---------------ATC---------TAA------------T---T-TTTCGCT-CGTTTAGATTTACAACTACATT
droGri2	scaffold_14853:3491672-3491772 -	GGAGAGTTGTTTAATGTAAGCTAA--ACTTCGCCCATCCTCTCCAGCTG-----------------------------TT---TGGTTAACTTTCAAC---------TGT------------TTGTC-CTCCATC-TCCTCAGATTTACAACTACATT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:2065104-2065202 +	GGCGAACTTTTTAATGTGAGTGTCCTGTTTACAGCTGGTATATTTTTCGAAAAGCCCTCTAAACTGGTCACTTCCACTCTACAGATCTATAACTACATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGCGAACTGTTCAATGTGAGTTTCCTACTTACAGCTGGTATATTTCTCGAA-----CAGTC-CTCTAAACTGGTC------CCTTCCGCT-------------------CCGCAGATCTACAACTACATA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCAGCC----------TCGAATTCGGCAGTCACTTGATACTCTCCCACCTCCCTCTCCCTCTGCCTCTCCATCATCCTCTTCCAGATCTACAACTACATC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-13.6, p-value=0.009901	dG=-13.6, p-value=0.009901	dG=-12.9, p-value=0.009901	dG=-12.9, p-value=0.009901	dG=-12.7, p-value=0.009901

droSim1

dG=-9.2, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-8.6, p-value=0.009901	dG=-8.5, p-value=0.009901	dG=-5.1, p-value=0.009901

droSec1

dG=-9.2, p-value=0.009901	dG=-9.2, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-5.1, p-value=0.009901

droYak2

dG=-2.6, p-value=0.009901	dG=-2.5, p-value=0.009901	dG=-2.4, p-value=0.009901	dG=-1.6, p-value=0.009901

droEre2

dG=-12.5, p-value=0.009901	dG=-7.1, p-value=0.009901

droAna3

dG=-2.5, p-value=0.009901	dG=-2.1, p-value=0.009901	dG=-2.0, p-value=0.009901	dG=-1.8, p-value=0.029703	dG=-1.7, p-value=0.009901

dp4

dG=-7.97, p-value=0.009901	dG=-7.8, p-value=0.009901	dG=-7.37, p-value=0.009901	dG=-7.2, p-value=0.009901	dG=-5.27, p-value=0.009901

droPer1

dG=-7.97, p-value=0.009901	dG=-7.37, p-value=0.009901	dG=-5.27, p-value=0.009901

droWil1

dG=-11.6, p-value=0.009901	dG=-11.2, p-value=0.009901	dG=-10.6, p-value=0.009901

droVir3

dG=-12.5, p-value=0.009901	dG=-12.2, p-value=0.009901

droMoj3

dG=-0.6, p-value=1.0	dG=-0.5, p-value=1.0	dG=-0.4, p-value=1.0	dG=0.0, p-value=1.0	dG=0.1, p-value=1.0

droGri2

dG=-6.5, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-5.9, p-value=0.009901	dG=-5.9, p-value=0.009901	dG=-5.6, p-value=0.009901

Generated: 03/07/2013 at 05:22 PM