Secondary structure and small RNA-seq evidence for dme-mir-3642

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:11622590-11622695 +	ATGGATGACGTCAAGGTGAGTG--------------GGTCGCACGGAGCGTCATT-------------------------TGGAAT-------------------TC------------CCATGGC-------TG------ACGAA-------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	chr3L:10995092-10995212 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGAGCGCCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	super_0:3809862-3809984 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGAGCGTCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	chr3L:11651195-11651318 +	ATGGATGACGTCAAGGTGAGTG--------------CGGCGCACGAACCGCCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------ACGAAACGCTAA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	scaffold_4784:11607138-11607238 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGACCGCCATT-------------------------TCGAAT-------------------TC------------CCCTGTC-------TG------------------------------ACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droAna3	scaffold_13337:5894397-5894534 +	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGT------------------TGCAG------CAAAGTGC-TGGAAC-------------------TT------------AATAAGC-------TA------ATGAAACGCTAA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	chrXR_group6:10064193-10064317 -	ATGGACGACGTGAAGGTGAGTG--------------GGGCGC------------------TGCAC------GTGCCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	super_61:344655-344779 -	ATGGACGACGTGAAGGTGAGTG--------------GGGCGC------------------TGCAC------GTGTCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	scaffold_180698:2114822-2114981 +	ATGGACGACGTAAAGGTGAGTG--------------TAACA--------------------GCACTAGTGTGTGTACGCCTGTGC-GTGTGTGTGTGTGTGTGTGCGTATATTT-----TCATGTA-------ATTATCCAACG-ACCGCTAATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	scaffold_13049:23825799-23825928 +	ATGAATGATGTCAAGGTGAGTG--------------CGCGGCGCGGCGGCTGCTT-----------------------CTTAATAA-------------------TT--------GATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	scaffold_6680:18448682-18448807 +	ATGAACGACGTGAAGGTGAGTG--------------AGCGGAATG-----C---------TGAAC----------------------------------------TGAATTTATTGATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	scaffold_15110:13832957-13833097 -	ATGAGCGATGTAAAGGTGAGTT--------------CGGA-------GCGTTATTCTAGTTGATT------GTGTTTAATTTTTAT-------------------AT------------ATTTGGCAATTGTTAA------TCAATTCGTTAA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:11622590-11622695 +	ATGGATGACGTCAAGGTGAGTGGGTCGCACGGAGCGTCATTTGGAATTCCCATGGCTGACGAAACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATGGATGACGTCAAGGTGAGTGAGGCGCACGGAGCGC-CATTTGGAATTCCCCTGGCTGAGAAAACGCTA-AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

ATGGACGACGTGAAGGTGAGTGGGGCGCTGCACGTGCCCGCTTGAGACTTGCTTGGCAATATCAACGCTAAAGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................GCTGCACGTGCCCGCTTGAGACT............................................................................	23	1	1.00	1	1	0

Secondary Structure

dm3

dG=-18.0, p-value=0.009901	dG=-17.9, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.0, p-value=0.009901

droSim1

dG=-22.4, p-value=0.009901	dG=-21.6, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-17.0, p-value=0.009901

droSec1

dG=-19.7, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.7, p-value=0.009901	dG=-16.2, p-value=0.009901

droYak2

dG=-17.6, p-value=0.009901	dG=-16.8, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901

droEre2

dG=-15.4, p-value=0.009901	dG=-15.4, p-value=0.009901	dG=-15.4, p-value=0.009901	dG=-15.4, p-value=0.009901	dG=-14.5, p-value=0.009901

droAna3

dG=-25.7, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-24.3, p-value=0.009901

dp4

dG=-23.5, p-value=0.009901	dG=-17.6, p-value=0.009901

droPer1

dG=-20.8, p-value=0.009901	dG=-14.9, p-value=0.009901

droWil1

dG=-25.3, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-22.8, p-value=0.009901

droVir3

dG=-13.3, p-value=0.009901	dG=-13.2, p-value=0.009901	dG=-13.2, p-value=0.009901	dG=-13.0, p-value=0.009901	dG=-12.7, p-value=0.009901	dG=-11.5, p-value=0.009901

droMoj3

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

droGri2

dG=-18.3, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.4, p-value=0.009901

Generated: 03/07/2013 at 05:28 PM