Secondary structure and small RNA-seq evidence for dme-mir-2492

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:11441440-11441545 + ACAAAATTCACACTCGAAT-TTTTTTGGGATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAA-ATT-CAGAAGACAACAACGCA
droSim1 chrX_random:3203326-3203430 + ACAAAATTCACACTCGAAT-TTTT-TGGGATCTCTTTATAAAGCGTTTATTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAA-AGT-CAGAAG---ACAACGCA
droSec1 super_36:155641-155745 + ATAAAATTCACTCTCGAAT-TTTT-TGGGATCTCTTTATAAAGCATTTATTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAA-AGC-CAGAAG---ACAACGCA
droYak2 chrX:10720999-10721105 - ACAAAATTCACACTCGAAT-TTTTTGGCAATCTGTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAATACA-ACAAAATAGGAAAAAAA
droEre2 scaffold_4690:3720646-3720750 - ACAAAATTCACACTCGAATTTT---GGGTATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTAAAAAAA-ATATGAAAAGACAACAACCAA
droAna3 scaffold_13047:188962-189053 + ACAAAATTCACACTCGCTT-TT---GGCCAAC--TCCATAAAGCGTTAATTA---TCTG---------GCATTCTGAGAGCCAAAAGCTA-AAT-CAAATTCGATCGGAGCG
dp4 chrXL_group1e:1762210-1762257 + ACAAAATTCACACTCGAAT-TT---GGGGATCGCGTAGCGAGG--------------------------------------------------------GG----GGGGCAA
droPer1 super_18:601670-601716 + ACAAAATTCACACTCGAAT-TT---GGGGATCGCGTAGCAAGGG-------------------------------------------------------------GGGGCAA
droWil1 scaffold_180777:122952-122984 + ATAAACTCAATACACGAAT-TTGGTACTGATTTC------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6500:22511787-22511827 + TCC---------------------------------------------------------------------GTCAATCATCTCCTTAAA-ACT-CTAAAGCAAACCAAGCA
droGri2 scaffold_15203:463820-463836 - GTGAAATTCACACTCGA-----------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:11441440-11441545 + ACAAAATTCACACTCGAATTTTTTTGG-GATCTCTTTATAAAGCGTTTAT---TATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAAAT-TCAGAAGACAACA-ACGCA
droSim1 chrX_random:3203326-3203430 + ACAAAATTCACACTCGAATTTTTT-GG-GATCTCTTTATAAAGCGTTTATTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAAAG-TCAGAAGACA----ACGCA
droSec1 super_36:155641-155745 + ATAAAATTCACTCTCGAATTTTTT-GG-GATCTCTTTATAAAGCATTTATTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAAAG-CCAGAAGACA----ACGCA
droYak2 chrX:10720999-10721105 - ACAAAATTCACACTCGAATTTTTT-GGCAATCTGTTTATAAAGCGTTTAT---TATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAATA-CAACAAAATAGGAAAAAAA
droEre2 scaffold_4690:3720646-3720750 - ACAAAATTCACACTCGAATTT--T-GGGTATCTCTTTATAAAGCGTTTAT---TATTTATTTATTATGTTTTGTCGAGAGCTTAAAAAAAATATGAAAAGACAACA-ACCAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ACAAAATTCACACTCGAATTT-TTTGGGATCTCTTTATAAAGCGTTTATTATTATTTATTTATTATGTTTTGTCGAGAGCTTTCAAAAAAGTCAGAAGACA---ACGCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
ACAAAATTCACACTCGAATT---TGGGGATCGCGTA-----GC-------------------------------GAGG---------------GGGGGGCA---A----SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-20.4 -20.4 -20.4 -20.4 -20.4 -20.4

droSim1

-20.1 -20.0 -19.3 -19.2 -19.1 -19.1

droSec1

-19.5 -19.4 -18.7 -18.6 -18.5

droYak2

-10.6 -10.4 -10.0 -9.9 -9.8 -9.8

droEre2

-14.0 -13.8 -13.6 -13.4 -13.2 -13.0

droAna3

-15.7 -15.3 -15.0

dp4

-3.4

droPer1

0.0 0.3 0.9

droWil1

0.0 0.5

droVir3

No secondary structure predictions returned

droMoj3

0.0

droGri2

0.0

Generated: 01/05/2013 at 05:10 PM