Secondary structure and small RNA-seq evidence for dme-mir-289

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:13613907-13614035 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTT----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1 chr3L:12997848-12997976 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1 super_0:5775586-5775714 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2 chr3L:13706954-13707082 + TAC------------------------GGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2 scaffold_4784:13614855-13614983 + AAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACGGACTGGGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3 scaffold_13337:21827571-21827739 - TTC-CGGCACTCCGGCATTCCAGCTC-GGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTCTG----CTACTGCC---ACTGCCACTGCCACTGCCACTGCCGCTC------------------------GGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
dp4 chrXR_group8:6818889-6819024 - TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---GACTC----------------------------------------CAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1 super_36:488140-488275 + TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---GACTC----------------------------------------CAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1 scaffold_180698:607141-607313 - TTT------------------------TTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACC---CGGACTGCTAGAACGACTCGGTTCCGACTCTTTTTCTGTCGGGGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3 scaffold_13049:19817984-19818083 - ---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG---------------------------------------------------------------------------GCCT-GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3 scaffold_6680:7513468-7513568 - G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC----------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2 scaffold_15110:17555344-17555443 + ---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG---------------------------------------------------------------------------GCCT-GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:13613907-13614035 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTT----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TA------CGGTTTTTAGGTTGAGTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATCCGTCGGGTTTTTAGGTTGAGTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGGACTCCAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-26.0 -26.0 -25.9 -25.9 -25.7 -25.7

droSim1

-27.1 -27.0 -27.0 -26.9 -26.8 -26.7

droSec1

-27.1 -27.0 -27.0 -26.9 -26.8 -26.7

droYak2

-21.9 -21.8 -21.6 -21.1 -21.0 -20.9

droEre2

-31.0 -31.0 -30.9 -30.9 -30.7 -30.7

droAna3

-29.6 -29.6 -29.4 -29.4 -29.1 -29.1

dp4

-28.3 -28.0 -28.0 -27.7 -27.4 -27.4

droPer1

-28.3 -28.0 -28.0 -27.7 -27.4 -27.4

droWil1

-43.5 -43.4 -43.3 -43.2 -43.2 -43.1

droVir3

-13.7 -13.6 -13.4 -13.4 -13.3 -13.3

droMoj3

-13.7 -13.6 -13.4 -13.3 -13.2 -13.0

droGri2

-13.7 -13.6 -13.4 -13.4 -13.3 -13.3

Generated: 01/05/2013 at 05:14 PM