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 + GGTTATCCCTGCCACA-------------TGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-GTCGAGC--AGCGTCTTGGGGTTGTTCG------TGGATTAAGTTCG-----------------ATTCCTAT
droSim1 chr2R_random:1106077-1106202 + GGATATCCCTGCCACA-------------TGGCCACGTGCCTGCAAGACGCCTTCGGCCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-GTCGAGC--AGCGTCTTGGGGTTGTTCC------TGGATTAAGTTCG-----------------ATTCCTAT
droSec1 super_1:1540674-1540799 + GGATATCCCTGCCACA-------------TGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-GTCGAGC--AGCGTCTTGGGGTTGTTCC------TGGATTAAGTTCG-----------------ATTCCTAT
droYak2 chr2L:16559915-16560042 + GGATATCCCTGCCACA-------------TGGCCACGTGCCTGCAAGACGCCTTCGACCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-AACGAACGGAGCGTCTTGGGGTTGTTTC------GGGATTACGTTCG-----------------ATTCCGAT
droEre2 scaffold_4929:18723379-18723500 - GGATA-CCCAGCCACA-------------TGGCCACGTGCCTGCAAGACGCCTTCGGCCGGCG-----------C-AAAGTTTCAATTTGATATTCCTTGGCCG-GTCGA-----GCGTCTTGGGGTTGTTTC------GGGATTGAGTTCG-----------------ATTCCGAT
dp4 chr3:5536552-5536721 + GGTTG-CGCTGCTGCTTATGGTGCTGGTGTTGCCACGTGCC-ACAAGACGCCTTCATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCCTTGCCGA-----GCGTCTTGGGGTTGTTTCAGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCATCCGTGC
droPer1 super_2:5730715-5730884 + GGTTG-CGCTGCTGCTTATGGTGCTGGTGTTGCCACGTGCC-ACAAGACGCCTTCATCTGGCGGTTGGTCTGGACAAAAGTTTCAATTTGATATTCCTTTGCCTTGCCGA-----GCGTCTTGGGGTTGTTTCAGGGCATGGATTAAGTTTTCAGGCAACTGGAGCAGCATCCGTGC

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

-48.0 -47.6 -47.6 -47.5 -47.2 -47.2

droSim1

-39.5 -39.3 -39.1 -39.0 -39.0 -38.9

droSec1

-42.5 -42.1 -42.0 -42.0 -41.7 -41.7

droYak2

-31.4 -31.0 -30.9 -30.9 -30.9 -30.6

droEre2

-38.8 -38.4 -38.3 -38.3 -38.3 -38.0

droAna3

-37.1 -37.0 -36.8 -36.7 -36.6 -36.6

dp4

-35.8 -35.4 -35.3 -35.0 -34.9 -34.9

droPer1

-35.8 -35.4 -35.3 -35.0 -34.9 -34.9

droWil1

-30.2 -29.8 -29.8 -29.6 -29.6 -29.6

droVir3

-51.3 -51.1 -51.0 -50.8 -50.8 -50.7

droMoj3

-9.1 -8.9 -8.5 -8.5 -8.4 -8.3

droGri2

-68.7 -68.7 -68.5 -68.5 -68.4 -68.4

Generated: 01/05/2013 at 05:28 PM