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

Legend:maturestarmismatch

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 + ATGGATGACGTCAAGGTGAGTG--------------GGTCGCACGGAGCGTCATT-------------------------TGGAAT-------------------TC------------CCATGGC-------TG------ACGAA-------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATGGATGACGTCAAGGTGAGTGAGGCGCACGGAGCGC-CATTTGGAATTCCCCTGGCTGAGAAAACGCTA-AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
ATGGACGACGTGAAGGTGAGTGGGGCGCTGCACGTGCCCGCTTGAGACTTGCTTGGCAATATCAACGCTAAAGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..........................GCTGCACGTGCCCGCTTGAGACT............................................................................2311.00110

Secondary Structure

dm3

-18.0 -17.9 -17.8 -17.0

droSim1

-23.6 -23.1 -22.8 -22.7 -22.6

droSec1

-22.2 -22.0 -21.6

droYak2

-17.6 -16.8 -16.6 -16.6

droEre2

-15.4 -15.4 -15.4 -15.4 -14.5 -14.5

droAna3

-27.4 -27.1 -27.1 -27.0 -27.0 -27.0

dp4

-25.1

droPer1

-22.4

droWil1

-27.0 -27.0 -26.9 -26.9 -26.6 -26.5

droVir3

-15.1 -15.1 -14.9 -14.9 -14.9 -14.8

droMoj3

-17.4 -17.0 -17.0 -17.0 -16.5 -16.5

droGri2

-18.3 -17.8 -17.4

Generated: 01/05/2013 at 05:18 PM