Secondary structure and small RNA-seq evidence for dme-mir-2280

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:1831670-1831814 - TGGAGAAGAGTGATATCGTTTAAGATGC---------TGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACG--GACTAAAAATGCGTT-TG
droSim1 chr2L:1818710-1818856 - CGGAGCAGAGTGATATCGTTTGAGATGC---------TGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCG--GACTAAAAATGCTTTTTG
droSec1 super_14:1778365-1778510 - CGGAGCAAAGTGATATCGTTTGAAATGC---------TGTGAATATCCCGTTTTCTTTGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAACTTACTT-----------CCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACG--GACTAAAAATGCTTTTTG
droYak2 chr2L:1804987-1805119 - CGGAGCAAACTGATGTCGTTTAGGATGC---------TGTGAATATCCCATTTTGTTAGCTTGGCAATAAAAT-ATTG------------------------------TTGATTGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGTGGAT-ATTC--TA------------CAACAAATGGGTT-TT
droEre2 scaffold_4929:1878584-1878709 - CGGTG-----TGATTCTGCTTAAGGTGC---------TGTGAATATCCCATTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCATCGA-ACTAGTAATTTAATT-----------CCAAGCCAACTAAAGGGGAT-ATTCACTG---------------CAAATGCATT-TG
droAna3 scaffold_12916:15757494-15757644 + CGTAGAAGCTT-AC-----TAGTTC--------------------------------TGTTTGGTAATAAAGT-TATTCTTTTTTATCTCAAAATGACTCACGTTTTTTTTTTCGA-ATCATTAAATAACATTTATATTTTCCCTAAGC-------CCTGAAT-ACTTATTATAAAAAAGACGATTATAAAAGTATA-TG
dp4 chr4_group3:8561836-8561913 - TGTTGTGGACTTAT-----CGGAGGAACTTGGCGAATTTTGATTATATTTTGATGCCATTTTT---------------------------------------------------------------------------------------ATCTGAAT-----------------------------AAAATGTTCT-TT
droPer1 super_1:10015828-10015916 - TGTTGTGGACTTAT-----CGGAGGAACTTGGCGAATTTTGATTATATTTAGATTCCATTTTT---------------------------------------------------------------------------------------ATCTGAATAAAAT-GTTC--TT---------------TAGTTACGTT-GA
droWil1 scaffold_180708:11841716-11841868 + TGCAGATGCCACAT-----CGGAATTGTGAAGGGAAAATGGGTTATTTAGTTGCGTTAGTTTAACGAGGAATGAAGGG------------------------------TCCGTTGTATTTAATTACTTTTTT----GGTAC--ATTAGTTAATAAAAGGAAAC-AATTAATCAATTAA----CATTATAAACTCGTT-TT
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:1831670-1831814 - TGGAGAAGAGTGATATCGTTTAAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACGGACTAAAAATGCGTT-TG
droSim1 chr2L:1818710-1818856 - CGGAGCAGAGTGATATCGTTTGAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCGGACTAAAAATGCTTTTTG
droSec1 super_14:1778365-1778510 - CGGAGCAAAGTGATATCGTTTGAAATGCTGTGAATATCCCGTTTTCTTTGCTTGGCAATAAAATATTATTCACAGAAACTAGTAACTTACTTCCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACGGACTAAAAATGCTTTTTG
droYak2 chr2L:1804987-1805119 - CGGAGCAAACTGATGTCGTTTAGGATGCTGTGAATATCCCATTTTGTTAGCTTGGCAATAAAATATTGTTGATTGAAACTAGTAATTTACTTCCAAGCTAACTGAAGTGGAT-ATTC--TACAAC----------AAATGGGTT-TT
droEre2 scaffold_4929:1878584-1878709 - CGGT-----GTGATTCTGCTTAAGGTGCTGTGAATATCCCATTTTCTTAGCTTGGCAATAAAATATTATTCATCGA-ACTAGTAATTTAATTCCAAGCCAACTAAAGGGGAT-ATTCACTGCA-------------AATGCATT-TG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAGCAGAGTGATATCGT-------------------------TTGAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCGGACTAAAAATGCTTTTTGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGTTGTGGACTTAT--CGGAGGAACTTGGCGAATTTTGATTATATTTTGATGCCATTT------------------------------------------------------------------------------------------TTATCTGAAT-AAAATGTTCT-TTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-14.7,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-14.1,  p-value=0.009901

droSim1

dG=-14.7,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-14.1,  p-value=0.009901

droSec1

dG=-9.8,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-9.3,  p-value=0.009901

droYak2

dG=-23.2,  p-value=0.009901 dG=-22.7,  p-value=0.009901

droEre2

dG=-11.6,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.9,  p-value=0.009901

droAna3

dG=-6.0,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.3,  p-value=0.009901 dG=-5.3,  p-value=0.009901

dp4

dG=0.0,  p-value=1.0 dG=0.6,  p-value=1.0 dG=0.9,  p-value=1.0

droPer1

dG=-2.6,  p-value=0.009901

droWil1

dG=-8.1,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-7.9,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-5.8,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 04:53 PM