Secondary structure and small RNA-seq evidence for dme-mir-4987

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:10840329-10840491 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSim1 chr2L:10648081-10648243 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSec1 super_3:6258415-6258577 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droYak2 chr2L:7248063-7248225 - AACAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATGAT-------
droEre2 scaffold_4929:14589948-14590110 + ACCAGTCGT---CTGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGAT-------
droAna3 scaffold_12916:14695622-14695781 - ACCAATCGT---CCGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
dp4 chr4_group4:3045338-3045500 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droPer1 super_10:2060188-2060350 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droWil1 scaffold_180703:3531157-3531322 + AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATGTT-------
droVir3 scaffold_12963:15772752-15772915 + ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3 scaffold_6500:18770378-18770547 + ATTCGTCGT---CGGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2 scaffold_15126:2074135-2074298 - ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:10840329-10840491 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSim1 chr2L:10648081-10648243 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSec1 super_3:6258415-6258577 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droYak2 chr2L:7248063-7248225 - AACAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATGAT-------
droEre2 scaffold_4929:14589948-14590110 + ACCAGTCGT---CTGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGAT-------
droAna3 scaffold_12916:14695622-14695781 - ACCAATCGT---CCGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
dp4 chr4_group4:3045338-3045500 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droPer1 super_10:2060188-2060350 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droWil1 scaffold_180703:3531157-3531322 + AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATGTT-------
droVir3 scaffold_12963:15772752-15772915 + ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3 scaffold_6500:18770378-18770547 + ATTCGTCGT---CGGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2 scaffold_15126:2074135-2074298 - ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATCAGTCGTCTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGTSizeHit CountTotal NormTotalGSM343915
Embryo
.............................GATGACACAGCGCGCTTGC...................................................................................................................1911.0011
dp4
AACAATCGTCTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.............................................TGCAACAGCGGGCGGCACGTTTCTC.............................................................................................2511.00110

Secondary Structure

dm3

dG=-33.8,  p-value=0.009901

droSim1

dG=-35.2,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droSec1

dG=-35.2,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droYak2

dG=-35.2,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droEre2

dG=-35.2,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droAna3

dG=-38.4,  p-value=0.009901 dG=-37.8,  p-value=0.009901

dp4

dG=-40.2,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-39.4,  p-value=0.009901 dG=-39.4,  p-value=0.009901

droPer1

dG=-40.2,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-39.4,  p-value=0.009901 dG=-39.4,  p-value=0.009901

droWil1

dG=-33.5,  p-value=0.009901 dG=-33.2,  p-value=0.009901

droVir3

dG=-39.1,  p-value=0.009901

droMoj3

dG=-37.0,  p-value=0.009901

droGri2

dG=-40.2,  p-value=0.009901

Generated: 03/07/2013 at 06:56 PM