Secondary structure and small RNA-seq evidence for dme-mir-1005

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:4343681-4343771 + CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCACAC------GAATA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droSim1 chr2L:4265544-4265633 + CTACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGTTTTTG--------------------------------GC-CAC------AAATA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droSec1 super_5:2441095-2441185 + CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCACAC------AAATG-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droYak2 chr2L:4375638-4375728 + CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCAGCC------AAAAA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droEre2 scaffold_4929:4420541-4420630 + CCACCATTCTGACCTGTGAGTTCAT-CGA----TTTCGAGGTTT-G--------------------------------CCAGCC------AAAAA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droAna3 scaffold_12916:13781299-13781395 - TAACGGTTTTGACTTGTAAGAACCA-AAACTACTTTCT--GTAT-C--------------------------------AAAGCC------AGAAA---CTAATCG---TAA--TTGAAAT-TATCTTAACCAGTCCCCATTGAGCTGT
dp4 chr4_group2:339129-339252 + CCACCATTTTGACATGTAAGTGTCC-ATA---TCCTCGAGGCTCCTGCAATGCACTGCAATGCACTGCAATGACCGCAATGCTG------ACGTA-------------TTATTTATGTTC-TCCGATCCCCAGTTCCCACTGAAATGT
droPer1 super_8:3550415-3550538 - CCACCATTTTGACATGTAAGTGTCC-ATA---TCCTCGAGGCTCCTGCAATGCACTGCAATGCACTGCAATGACCGCAATGCTG------ACGTA-------------TTATTTATGTTC-TCCGATCCCCAGTTCCCACTGAAATGT
droWil1 scaffold_180772:1844874-1844969 - TTACAATTCTATCATGTAAGTTAAAACGA----TTAAGTAATTTC---------------------------------ACACTT------ACATATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC
droVir3 Unknown CAGTGGTATTGACCTGTAAGTATG-----------------------------------------------------------------------------------------TTGAATT-TTCTTACTGCAGTTCCGCTGGAGATCG
droMoj3 scaffold_6500:22625692-22625724 + CCTCCATATTGCTCTGCGTGCAAGA-TGC----GCCCG--------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15252:16827853-16827948 - CCACCATTCTGACATGTAACC--AC-TGA----TCCTGATCCTT-G--------------------------------ATTG-CACTGCCCATTT---TGAATGCGTTTTC-------TT-TCTGCTTTGCAGTTCCCACGGAAATGG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:4343681-4343771 + CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCACACGAATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droSim1 chr2L:4265544-4265633 + CTACCATTCTGACCTGTGAGTTGATCGATTTCGAGTTTTTGGC-CACAAATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droSec1 super_5:2441095-2441185 + CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCACACAAATGTAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droYak2 chr2L:4375638-4375728 + CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCAGCCAAAAATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droEre2 scaffold_4929:4420541-4420630 + CCACCATTCTGACCTGTGAGTTCATCGATTTCGAGGTT-TGCCAGCCAAAAATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTACCATTCTGACCTGTGAGTTGATCGAT-TTCGAGTTTTTGGC-CACA---------------------------------AATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGTSizeHit CountTotal NormTotalGSM343915
Embryo
.........................................................................................TCTGGAATCTTTAATTCGCAG...............2115.0055
...............GTGAGTTGATCGAT-TTCGAGTT.......................................................................................2211.0011
dp4
CCACCATTTTGACATGTAAGTGTCCATATCCTCGAGGCTCCTGC-AATGCACTGCAATGCACTGCAATGACCGCAATGCTGACGTATTATTTATGTTCTCCGATCCCCAGTTCCCACTGAAATGTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.0,  p-value=0.009901 dG=-16.0,  p-value=0.009901 dG=-15.9,  p-value=0.009901

droSim1

dG=-16.1,  p-value=0.009901 dG=-16.0,  p-value=0.009901 dG=-15.5,  p-value=0.009901

droSec1

dG=-17.0,  p-value=0.009901 dG=-17.0,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.3,  p-value=0.009901

droYak2

dG=-18.5,  p-value=0.009901 dG=-18.1,  p-value=0.009901 dG=-18.1,  p-value=0.009901 dG=-17.6,  p-value=0.009901

droEre2

dG=-12.3,  p-value=0.009901 dG=-11.6,  p-value=0.009901

droAna3

dG=-4.0,  p-value=0.009901 dG=-3.6,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-3.2,  p-value=0.009901

dp4

dG=-14.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-12.2,  p-value=0.009901

droPer1

dG=-14.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-12.2,  p-value=0.009901

droWil1

dG=-5.5,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.8,  p-value=0.009901

droVir3

dG=-1.9,  p-value=0.009901 dG=-1.1,  p-value=0.009901 dG=-1.0,  p-value=0.009901

droMoj3

dG=-4.2,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.3,  p-value=0.009901

droGri2

dG=-6.2,  p-value=0.009901 dG=-6.0,  p-value=0.009901 dG=-5.6,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901

Generated: 03/07/2013 at 04:46 PM