Secondary structure and small RNA-seq evidence for dme-mir-4981

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:3902738-3902863 + GGTTATC-------------------------------------CCTGC-CACATGGCCACGTGCCCG-CAAGACGCCTTCGGCCGGCG-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCG--------TGGATTAAGTTCGATTC--------------------------CTAT
droSim1 chr2R_random:1106077-1106202 + GGATATC-------------------------------------CCTGC-CACATGGCCACGTGCCTG-CAAGACGCCTTCGGCCGGCG-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTCGATTC--------------------------CTAT
droSec1 super_1:1540674-1540799 + GGATATC-------------------------------------CCTGC-CACATGGCCACGTGCCCG-CAAGACGCCTTCGGCCGGCG-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTCGAG--CAGCGTCTTGGGG-TTGTTCC--------TGGATTAAGTTCGATTC--------------------------CTAT
droYak2 chr2L:16559915-16560042 + GGATATC-------------------------------------CCTGC-CACATGGCCACGTGCCTG-CAAGACGCCTTCGACCGGCG-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTGGC-CG-----AACGAACGGAGCGTCTTGGGG-TTGTTTC--------GGGATTACGTTCGATTC--------------------------CGAT
droEre2 scaffold_4929:18723379-18723500 - GGATA-C-------------------------------------CCAGC-CACATGGCCACGTGCCTG-CAAGACGCCTTCGGCCGGCG-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTGGC-CG-----GTC-----GAGCGTCTTGGGG-TTGTTTC--------GGGATTGAGTTCGATTC--------------------------CGAT
droAna3 scaffold_13266:16222514-16222662 + GGAGATC-------------------------------------CTTG--CGTGTGGCCACGTGCCGGGTGAGACGCCTTCGGCCGGTA-------------------------------------------------------------------------------------------------------CAAAGTTTCAATTTGATATTCCTTTGGAGTTGCCTTCGGAGTTGAGCGTCTTGGGG-TTGTTCC--GGGCCATGGATTAAGTTG-----AGAAA-ATG------CAG----A-CTATGT
dp4 chr3:5536552-5536721 + GGTTG-C---------G------------CTGCTGCTTATGGTG----CTGGTGTTGCCACGTGCC-A-CAAGACGCCTTCATCTGGCGGTT------------------------------------------------------------------------------------------GGT-CTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CT-----T--GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTT---TCAGGCAACTGGAGCAGCA------TCCGTGC
droPer1 super_2:5730715-5730884 + GGTTG-C---------G------------CTGCTGCTTATGGTG----CTGGTGTTGCCACGTGCC-A-CAAGACGCCTTCATCTGGCGGTT------------------------------------------------------------------------------------------GGT-CTGGACAAAAGTTTCAATTTGATATTCCTTTGC-CT-----T--GCC--GAGCGTCTTGGGG-TTGTTTC--AGGGCATGGATTAAGTTT---TCAGGCAACTGGAGCAGCA------TCCGTGC
droWil1 scaffold_181141:2380508-2380690 - ACCCATTTCTGGTCTCG------------GTCTCAATTTTTTTA----CTGGTGTGGCCACGTGCCA--TACGAG-----------------------------------------------------------------------------------TA-GTAAGGTCTTGCA-ACAGGGCGGT-GCGAACAAAAGTTTCAATTTGATATTCCCTTGC-CTTGACTTGGCCG--TAGCGTCTTAGGG-ATGTTTCC-GAAGCAAGGATTAAGTTT---TCAAA----G------GCAG------CTGTGC
droVir3 scaffold_12875:14800808-14801017 + GCTTCTTTG------------------------TGTCCATGGCCCTTGC-CGTGTGGCCACGTGCCA--TCAGACGCCTTCGCGCAGT---TTGACTC--------------------------------------------TGGAATGGCTGAGGGCTG-GTGGGG---CGGA-ACGGGGCAGCGGGGATTGACAGTTTCAATTTGCAAGCATGTTGC-CT-----TTTGTA--GAACGTCTTGGGGGTTGTTCGCCAGCTGACGGATTAAGTTT---TGAGGGC-A----------GCCAGATGCTGCT
droMoj3 scaffold_6496:7113415-7113501 - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTACG--GAACGTCTTGGGG-TGTCTGA--------GGGATTAAGTTTAAGTCTGGGC-AT---------GCCAG--C--TGC
droGri2 scaffold_15245:14811478-14811742 + GTTTCTTTGTG-TCCAGACCCTTGCCGCCTTGCCGC--------CTTGC-CGTGTGGCCACGTGCCAGCAGAGACGCCTTCGCGCTCA---CTGACTCGTCCCGGCCCGGCAATTGTCAGAGACGCAGATGACTGTTGCGAATAGGTTGGCAGGGGGGGGAGT-CGG---CGGACAGGGGGAAGGGGTGGTTGACAGTTTCAATTTGCAAGCTTGTTGC-CT-----TTTGCA--GAACGTCTTGGGG-TTGTTTC--AGCTGGCGGATTAAGGTT---TCAGACAG-T-------CAGCC-------AGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:3902738-3902863 + GGTTATCCCTGCCACATGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGAGC--AGCGTCTTGGGGTTGTTCGTGGATTAAGTTCGATTCCTAT
droSim1 chr2R_random:1106077-1106202 + GGATATCCCTGCCACATGGCCACGTGCCTGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGAGC--AGCGTCTTGGGGTTGTTCCTGGATTAAGTTCGATTCCTAT
droSec1 super_1:1540674-1540799 + GGATATCCCTGCCACATGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGAGC--AGCGTCTTGGGGTTGTTCCTGGATTAAGTTCGATTCCTAT
droYak2 chr2L:16559915-16560042 + GGATATCCCTGCCACATGGCCACGTGCCTGCAAGACGCCTTCGACCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGAACGAACGGAGCGTCTTGGGGTTGTTTCGGGATTACGTTCGATTCCGAT
droEre2 scaffold_4929:18723379-18723500 - GGATA-CCCAGCCACATGGCCACGTGCCTGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGA-----GCGTCTTGGGGTTGTTTCGGGATTGAGTTCGATTCCGAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGATATCCCTGCCAC--A-----------TGGCCACGTGCCTGCAAGACGCCTTCGGCCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-GTCGAGCAGCGTCTTGGGGTTGTTC------CTGGATTAAGTTCG-----------------ATTCCTATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGTTG-CGCTGCTGCTTATGGTGCTGGTGTTGCCACGTGCC-ACAAGACGCCTTCATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCCTTGCCGA---GCGTCTTGGGGTTGTTTCAGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCATCCGTGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-37.6,  p-value=0.009901 dG=-37.2,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.8,  p-value=0.009901 dG=-36.7,  p-value=0.009901

droSim1

dG=-35.6,  p-value=0.009901 dG=-35.2,  p-value=0.009901 dG=-35.1,  p-value=0.009901 dG=-34.8,  p-value=0.009901 dG=-34.7,  p-value=0.009901

droSec1

dG=-37.6,  p-value=0.009901 dG=-37.2,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.8,  p-value=0.009901 dG=-36.7,  p-value=0.009901

droYak2

dG=-27.3,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.4,  p-value=0.009901

droEre2

dG=-34.7,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.2,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.8,  p-value=0.009901

droAna3

dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.0,  p-value=0.009901

dp4

dG=-21.8,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droPer1

dG=-21.8,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droWil1

dG=-16.4,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.1,  p-value=0.009901 dG=-15.5,  p-value=0.009901

droVir3

dG=-37.0,  p-value=0.009901 dG=-36.6,  p-value=0.009901 dG=-36.4,  p-value=0.009901 dG=-36.2,  p-value=0.009901 dG=-36.0,  p-value=0.009901

droMoj3

dG=-6.9,  p-value=0.009901 dG=-6.9,  p-value=0.009901 dG=-6.1,  p-value=0.009901

droGri2

dG=-52.9,  p-value=0.009901 dG=-52.4,  p-value=0.009901 dG=-52.3,  p-value=0.009901 dG=-52.2,  p-value=0.009901 dG=-52.2,  p-value=0.009901

Generated: 03/07/2013 at 07:00 PM