Secondary structure and small RNA-seq evidence for dme-mir-1012

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:22687056-22687144 -	A--AATCCAAAAGAACGGTGGGTAGAACTTT-GATTAATATTGCTTGAAAA-ATATTAGTC-----------AAAGA----------------------------------------TTT-------------TCCCCATAGATTTATCAATTTCGG
droSim1	chr3R:22517515-22517602 -	T--AATCCAAAAGAACGGTGGGTAGAACTTT-GATTAATATTGCTTGA-GA-ATATTAGTC-----------AAAGA----------------------------------------TTT-------------TCCCCATAGATTTATCAATTTCGG
droSec1	super_13:1460550-1460637 -	T--AATCCAAAGGAACGGTGGGTAGAACTTT-GATTAATATTGCTTGA-GA-ATATTAGTC-----------AAAGA----------------------------------------TTT-------------TCCCCATAGATTTATCAATTTCGG
droYak2	chr3R:23804845-23804934 +	C--AATCCAAAAGAACGGTGGGTAGAACTTT-GATTAATATTGCTTGCAAG-ATATTAGTC-----------AAAGG----------------------------------------T------------TTTTCCCCATAGATTTATCAATTTCGG
droEre2	scaffold_4820:5353889-5353978 +	A--AATCCAAAAGAACGGTGGGTAAATCTTT-GATTAGTATTGGTTTCAAT-ATATTAGTC-----------AAATG----------------------------------------T------------TTTTCCCACTAGATTTATCAATCTTGG
droAna3	scaffold_13340:16646757-16646843 +	C--GATATAAAAAAGCGGTAGGT-----TTC-AACCAA-ATTTCCTTTGAGAGT-TCAGTT-----------AA------CTTTATATA------------------------------T-------------TCTTTTTAGCTTCACTAACTTCGG
dp4	chr2:4781321-4781418 +	A--AATAATTCAGAGCGGTGGGTAGTCTCTC-ATATATAGTTATAAAA-GA-AC-----------GAACACCAGTGGTTAAGCAATGCA------------------------------T-------------TTCTTGTAGATTCATCAATTTCGG
droPer1	super_19:478308-478405 +	A--AATAATTCAGAGCGGTGGGTAGTCTCTC-ATATATAGTTATAAAA-GA-AC-----------GAACACCAGTGGTAAAGCAATGCA------------------------------T-------------TTCTTGTAGATTCATCAATTTCGG
droWil1	scaffold_181130:2629008-2629094 +	C--AATTTGTCAGAACGGTATGG---------------TAGTGCAAGAAAG-CCGAAATTC-----------AAAA-----------------------------------------ACACCCTAATTGTAACAATTTGCAGATTTGTCAACTTTGG
droVir3	scaffold_13047:12018101-12018191 -	C--GATCTAAAGAAACGGTACGGATT--GTT-TATTTAAA-TGCTTTA-------------------------------------TATA----------------TTTATCTATAA-GCTATCT------TTTTGTTTGCAGTTTCATTAACTTTGG
droMoj3	scaffold_6540:29763927-29764041 +	C--GATTTAAAAAAACGGTGTGTAAATATGG-ATTATTATTTATAAAT-TA-TC-----------GAAAACTTAACTTCTAA---TGTT----------------TTTATATTTAT-ATTTTCA------ACATACTCTCAGTTTCATCAACTTCGG
droGri2	scaffold_14624:2192647-2192787 -	ATTGATATCAAGAAGCGGTACGTTCTACATTTGGT-TGAACTATTCTT-GA-ACTTGAGCCGAAAAAACTTTAGCTGTA-TTTTAAACATTCTTTTTCAATCTCTTTTGTGTGTGTGT------------TTTTATTTGCAGTTTCATTAACTTTGG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:22687056-22687144 -	AAATCCAAAAGAACGGTGGGTAGAACTTTGATTAATATTGCTTGAAAAATATTAGTCAAAGATTTT-CCCCATAGATTTATCAATTTCGG
droSim1	chr3R:22517515-22517602 -	TAATCCAAAAGAACGGTGGGTAGAACTTTGATTAATATTGCTTG-AGAATATTAGTCAAAGATTTT-CCCCATAGATTTATCAATTTCGG
droSec1	super_13:1460550-1460637 -	TAATCCAAAGGAACGGTGGGTAGAACTTTGATTAATATTGCTTG-AGAATATTAGTCAAAGATTTT-CCCCATAGATTTATCAATTTCGG
droYak2	chr3R:23804845-23804934 +	CAATCCAAAAGAACGGTGGGTAGAACTTTGATTAATATTGCTTGCAAGATATTAGTCAAAGGTTTTTCCCCATAGATTTATCAATTTCGG
droEre2	scaffold_4820:5353889-5353978 +	AAATCCAAAAGAACGGTGGGTAAATCTTTGATTAGTATTGGTTTCAATATATTAGTCAAATGTTTTTCCCACTAGATTTATCAATCTTGG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TAATCCAAAAGAACGGTGGGTAGAACTTTGATTAATATTGCTTGAGAAT-------ATTAGTCAAAGA---TTTTCCCCATAGATTTATCAATTTCGG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............GTGGGTAGAACTTTGATTAATA.............................................................	22	1	138.00	138	138
.........................................................TTAGTCAAAGA---TTTTCCCCATAG...............	23	1	105.00	105	105
...............GTGGGTAGAACTTTGATTAAT..............................................................	21	1	66.00	66	66
.........................................................TTAGTCAAAGA---TTTTCCCCAT.................	21	1	26.00	26	26
.........................................................TTAGTCAAAGA---TTTTCCCCATA................	22	1	18.00	18	18
.........................................................TTAGTCAAAGA---TTTTCCCCATAGA..............	24	1	2.00	2	2
...............GTGGGTAGAACTTTGATTAA...............................................................	20	1	2.00	2	2
...............GTGGGTAGAACTTTGATTAATAT............................................................	23	1	2.00	2	2
...............GTGGGTAGAACTTTGATT.................................................................	18	1	1.00	1	1

dp4

AAATAATTCAGAGCGGTGGGTAGTCTCTCATATATAGTTATAAAAGAACGAACACCAGTGGTTAAGCAATGCATTTCTTGTAGATTCATCAATTTCGG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-23.4, p-value=0.009901

droSim1

dG=-22.9, p-value=0.009901

droSec1

dG=-22.9, p-value=0.009901

droYak2

dG=-22.2, p-value=0.009901	dG=-22.2, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.9, p-value=0.009901

droEre2

dG=-19.1, p-value=0.009901	dG=-19.0, p-value=0.009901	dG=-18.8, p-value=0.009901	dG=-18.6, p-value=0.009901	dG=-18.4, p-value=0.009901

droAna3

dG=-3.0, p-value=0.009901	dG=-2.9, p-value=0.009901	dG=-2.5, p-value=0.009901	dG=-2.5, p-value=0.009901	dG=-2.3, p-value=0.009901

dp4

dG=-8.4, p-value=0.009901	dG=-7.9, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-6.7, p-value=0.009901

droPer1

dG=-8.4, p-value=0.009901	dG=-7.9, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-6.7, p-value=0.009901

droWil1

dG=-4.6, p-value=0.009901	dG=-4.4, p-value=0.009901	dG=-4.3, p-value=0.009901	dG=-4.2, p-value=0.009901	dG=-4.1, p-value=0.009901	dG=-3.1, p-value=0.019802

droVir3

dG=-6.6, p-value=0.009901	dG=-5.8, p-value=0.009901	dG=-5.8, p-value=0.009901

droMoj3

dG=-9.0, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-8.3, p-value=0.009901	dG=-8.3, p-value=0.009901	dG=-8.2, p-value=0.009901

droGri2

dG=-13.0, p-value=0.009901	dG=-12.4, p-value=0.009901	dG=-12.3, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-9.0, p-value=0.009901

Generated: 03/07/2013 at 04:47 PM