Secondary structure and small RNA-seq evidence for dme-mir-1014

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:27579231-27579328 -	TGGCCTTTTCTCAAGGTATAATGGAAATAGATTTTAAT------CGCAGGC--------------GCGTCAGTGGT---------------TGA--ATTAAAATTCATTTTCATTTGCAGTTACTGGATACAACA
droSim1	chr3R:27196220-27196317 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTGGC--------------GCGTCAGTGGT---------------TGA--ATTAAAATTCATTTTCATTTGCAGTTACCGGATACAACA
droSec1	super_31:233822-233919 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTGGC--------------GCGTCAGTGGT---------------TGA--ATTAAAATTCATTTTCATTTGCAGTTACCGGATACAACA
droYak2	chr3R:28513868-28513965 -	TGGCCTTTTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAGGC--------------GCGTCAGTGGT---------------TGA--ATTAAAATTCATTTTCATTTGCAGTCACCGGATACAACA
droEre2	scaffold_4820:396401-396498 +	TGGCCTTTTCGCAAGGTATAATGGAAATAGATTTTAAT------CGCAGGC--------------GCGTCAGTGGT---------------TGA--ATTAAAATTCATTTTCATTTGCAGTCACCGGATACAACA
droAna3	scaffold_12911:3510618-3510715 +	TGGCATTCTCCCAAGGTATAATGAAAATTGATTTTAAT------CACACGG--------------ATCGGAGTGGC---------------AAA--ATTAAAATTCATTTTCATTTGCAGTCACGGGATACAATG
dp4	chr2:14711225-14711322 +	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGGGTTT--------------CGTTTGGCGGT---------------GAA--ATTAAAATTCATTTTCATTTACAGTGACCGGCATCAACA
droPer1	super_0:5703122-5703219 -	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGTGTTT--------------CGTTTGGCGGT---------------GAA--ATTAAAATTCATTTTCATTTACAGTGACCGGCATCAACA
droWil1	scaffold_181130:8196915-8197021 +	TGGCATTTTCTCAAGGTGAAATGAAAATAAATTTTAATTCGGATAGAAAGCTAAT--CTAAT--------TGT-AT---------------TGC--ATTAAAATTCGTTTTCATTTGCAGTATCTGGTCTAAATA
droVir3	Unknown	TGGCATTCTCTCAAGGTAT---GTACATATTTTTAAAT-----------------------------------------------------TTA--ACCAGTATTTACTTTTGTTCACAGTGACCGGCATAAATA
droMoj3	scaffold_6540:30646887-30646982 +	TTGCCTTCTCTCAAGGTAAG---TGC------TTTGACTTAGCA--AAAGTTATTTACTAGAAGTGTTTCTCTGC----------------------------TTTCGTTTCATCCACAGTGACCGGTGTAAATA
droGri2	scaffold_14624:997050-997159 -	TGGCCTTTTCACAGGGTATGCAGAGCTTG-ATTAT--T------TGATTGC--------------TCATTT--TACACATTATAAATAAATTATATATATATATACATATGTTATTGCAGTGACTGGCGTAAATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:27579231-27579328 -	TGGCCTTTTCTCAAGGTATAATGGAAATAGATTTTAATC------GCAGGCGCGTC----AGTGGTTGAATTAAAATTCATTTTCATTTGCAGTTACTGGATACAACA
droSim1	chr3R:27196220-27196317 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAATC------GCTGGCGCGTC----AGTGGTTGAATTAAAATTCATTTTCATTTGCAGTTACCGGATACAACA
droSec1	super_31:233822-233919 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAATC------GCTGGCGCGTC----AGTGGTTGAATTAAAATTCATTTTCATTTGCAGTTACCGGATACAACA
droYak2	chr3R:28513868-28513965 -	TGGCCTTTTCCCAAGGTATAATGGAAATAGATTTTAATC------GCAGGCGCGTC----AGTGGTTGAATTAAAATTCATTTTCATTTGCAGTCACCGGATACAACA
droEre2	scaffold_4820:396401-396498 +	TGGCCTTTTCGCAAGGTATAATGGAAATAGATTTTAATC------GCAGGCGCGTC----AGTGGTTGAATTAAAATTCATTTTCATTTGCAGTCACCGGATACAACA
droAna3	scaffold_12911:3510618-3510715 +	TGGCATTCTCCCAAGGTATAATGAAAATTGATTTTAATC------ACACGGATCGG----AGTGGCAAAATTAAAATTCATTTTCATTTGCAGTCACGGGATACAATG
dp4	chr2:14711225-14711322 +	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAATC------GGGTTTCGTTT----GGCGGTGAAATTAAAATTCATTTTCATTTACAGTGACCGGCATCAACA
droPer1	super_0:5703122-5703219 -	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAATC------GTGTTTCGTTT----GGCGGTGAAATTAAAATTCATTTTCATTTACAGTGACCGGCATCAACA
droWil1	scaffold_181130:8196915-8197021 +	TGGCATTTTCTCAAGGTGAAATGAAAATAAATTTTAATTCGGATAGAAAGCTAATCTAATTGT-ATTGCATTAAAATTCGTTTTCATTTGCAGTATCTGGTCTAAATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAATCGCTGGCGCGTCAGTGGTTGAATTAAAATTCATTTTCATTTGCAGTTACCGGATACAACA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................................................AAAATTCATTTTCATTTGCAGT..............	22	1	17.00	17	17
...............GTATAATGGAAATAGATTTTAAT............................................................	23	1	16.00	16	16
...............GTATAATGGAAATAGATTTTAA.............................................................	22	1	2.00	2	2
...............GTATAATGGAAATAGATTTTA..............................................................	21	1	1.00	1	1

dp4

TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAATCGGGTTTCGTTTGGCGGTGAAATTAAAATTCATTTTCATTTACAGTGACCGGCATCAACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............GTACAATGGAAATAGATTTTAAT............................................................	23	1	2.00	2	2	0
...............GTACAATGGAAATAGATTTT...............................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

dG=-19.7, p-value=0.009901	dG=-18.7, p-value=0.009901

droSim1

dG=-18.2, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901

droSec1

dG=-18.2, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901

droYak2

dG=-19.7, p-value=0.009901	dG=-18.7, p-value=0.009901

droEre2

dG=-19.7, p-value=0.009901	dG=-18.7, p-value=0.009901

droAna3

dG=-16.0, p-value=0.009901	dG=-15.0, p-value=0.009901

dp4

dG=-14.0, p-value=0.009901	dG=-13.5, p-value=0.009901

droPer1

dG=-14.0, p-value=0.009901	dG=-13.6, p-value=0.009901	dG=-13.5, p-value=0.009901	dG=-13.4, p-value=0.009901	dG=-13.0, p-value=0.009901

droWil1

dG=-14.7, p-value=0.009901	dG=-14.4, p-value=0.009901	dG=-14.1, p-value=0.009901	dG=-14.1, p-value=0.009901	dG=-13.9, p-value=0.009901

droVir3

dG=-1.7, p-value=0.009901

droMoj3

dG=-7.8, p-value=0.009901	dG=-7.8, p-value=0.009901	dG=-7.6, p-value=0.009901	dG=-7.6, p-value=0.009901	dG=-7.2, p-value=0.009901	dG=-5.9, p-value=0.009901

droGri2

dG=-7.1, p-value=0.009901	dG=-7.0, p-value=0.009901	dG=-7.0, p-value=0.009901	dG=-7.0, p-value=0.009901	dG=-6.9, p-value=0.009901	dG=-5.3, p-value=0.009901

Generated: 03/07/2013 at 04:49 PM