Secondary structure and small RNA-seq evidence for dme-mir-4919

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:11833377-11833466 +	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCTATAATT---------------------------------TCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCTATAATT---------------------------------CCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	TGGACATACTAAATGGTGAGTCTT-----T--------------------AGGGGATTAGCAAGCCATAATT---------------------------------CCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	TGGACATACTGAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCCATGATT---------------------------------CCTCCCTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCCATATTT---------------------------------CCACACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGAG
droAna3	scaffold_13266:11891001-11891093 -	TGGACATACTGAATGGTGAGTTTACAAGTCG-------------------------GCACTAAT--------TTTTGAAGCGGGAATGTGAATATGA----------------------GCCGTAAATTGCAGAAGCGGTGCTGGGCG
dp4	chr3:18992460-18992549 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTGTC----------------------------------------------------------CACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG
droPer1	super_242:24174-24263 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTGTC----------------------------------------------------------CACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG
droWil1	scaffold_181150:1332685-1332769 -	TGGACATAATAGCGGGTGAGTGAA---------------------------AGAGAT-ACGAGATTACAATT---------------------------------TG-GATTACATTTT-TGGTTGGTCGCAGAAACGTCAATGGGTA
droVir3	scaffold_12875:17265801-17265883 +	TCGATGTGCTGAATGGTGAGCTTT--GCCTG-------------------AGTGGGTC--------------CACACC-----------AAATCCTAATC-----C--------------CATTTATTTGCAGAGGCTGTGCTGGGCG
droMoj3	scaffold_6496:10745157-10745258 -	TCGATGTGCTAAATGGTAAGTCCC--ACTTC--------------------AGGCACTTCTAATCT-----------------------GAATATTAATACTCTTTCTTTCTCTCTCTC-TCCTGTCTTGCAGAGGCTGTACTTGGCG
droGri2	scaffold_15245:16779329-16779419 +	TCGATGTTTTAAATGGTGCGTGCTTAACTTG-------------------------AAAGAGAT--------CTCACAAAT------------------------CCAATCTTAATTAAGTGATTCATTGCAGAGGCTGTTCTGGGTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:11833377-11833466 +	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCTATAATTTCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCTATAATTCCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	TGGACATACTAAATGGTGAGTCTTTAGGGGATTAGCAAGCCATAATTCCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	TGGACATACTGAATGGTGAGTCTCTAGGGGATTAGCAAGCCATGATTCCTCCCTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCCATATTTCCACACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGACATACTAAATGGTGAGTCTC-------------TAGGGGATTAGCAAGCTATAATTCCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...................................................................TAATCCCTGAACGACTTGCAG...............	21	1	8.00	8	8
...............GTGAGTCTC-------------TAGGGGATTAGC......................................................	21	1	7.00	7	7
...............GTGAGTCTC-------------TAGGGGATT.........................................................	18	1	1.00	1	1

dp4

TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTG-------------TCCACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-17.4, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.8, p-value=0.009901	dG=-16.5, p-value=0.009901

droSim1

dG=-17.3, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.7, p-value=0.009901

droSec1

dG=-17.4, p-value=0.009901	dG=-17.3, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-17.1, p-value=0.009901	dG=-17.1, p-value=0.009901

droYak2

dG=-17.4, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.7, p-value=0.009901

droEre2

dG=-17.4, p-value=0.009901	dG=-17.0, p-value=0.009901

droAna3

dG=-8.3, p-value=0.009901	dG=-7.7, p-value=0.009901	dG=-7.6, p-value=0.009901	dG=-7.6, p-value=0.009901

dp4

dG=-6.7, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.04, p-value=0.009901	dG=-5.9, p-value=0.009901

droPer1

dG=-6.7, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.04, p-value=0.009901	dG=-5.9, p-value=0.009901

droWil1

dG=-6.4, p-value=0.009901	dG=-5.6, p-value=0.009901

droVir3

dG=-10.3, p-value=0.009901	dG=-10.2, p-value=0.009901

droMoj3

dG=-4.8, p-value=0.009901	dG=-4.1, p-value=0.009901	dG=-4.0, p-value=0.009901	dG=-3.8, p-value=0.009901

droGri2

dG=-10.8, p-value=0.009901	dG=-10.8, p-value=0.009901	dG=-9.9, p-value=0.009901

Generated: 03/07/2013 at 05:34 PM