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

-23.4

droSim1

-22.9

droSec1

-22.9

droYak2

-22.2	-22.2	-21.9	-21.9	-21.9	-21.5

droEre2

-19.1	-19.0	-18.8	-18.6	-18.4	-18.3

droAna3

-3.0	-2.9	-2.5	-2.5	-2.3	-2.2

dp4

-8.4	-7.9	-7.5

droPer1

-8.4	-7.9	-7.5

droWil1

-4.6	-4.4	-4.3	-4.2	-4.1	-4.0

droVir3

-6.6	-5.8	-5.8

droMoj3

-9.0	-8.9	-8.3	-8.3	-8.2	-8.2

droGri2

-13.0	-12.4	-12.3	-12.1

Generated: 01/05/2013 at 05:06 PM