Secondary structure and small RNA-seq evidence for dme-mir-2493

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:10956461-10956596 - TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCATGTGCATGG----AGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATGG
droSim1 chr3R:10501806-10501941 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATAG
droSec1 super_0:10986595-10986730 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATAG
droYak2 chr3R:15471091-15471226 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACAGG--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATGTGTGCGAGGCGTTGGCGTTCTGACC----AGAA------GAAGAGGAAGATAA
droEre2 scaffold_4770:10485021-10485154 - TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACAC--ACAGA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCATGT------------GTATGTGTGCGAGGCGTTGGCGTTCTGACC----AGAA------GAAGAGGAAGATAA
droAna3 scaffold_13340:6023187-6023339 - TATAA------------TGTGTGTGTGTGTG--TGTTTGT-GCTATTATTAAAACCCCC----------------------------------------CTC----------GCAAGCACCC-CCCACT--GCCAC-TGCATAG----AGCAAAAAAAAAAAAAAAA-------------CTATAGTGGTGT------------GTG-GCAGGCGAGGCGTTGGCGTTTTGACC----AAAA------GCTGAAGAAGAGGA
dp4 chr2:20937547-20937682 - TATAA------------CGTGTGTGTGAGTG------TGT-GCTATTATTAAACTCCCT---------CCCTAA---------------------------------------CAC----G--CACACA--ACTATGT-TATG----------------TA-----A-------------GTGTGTGTGTGT------------GTGTGTGTGTGAGGCGTTGGCGTTTTGACC----AGAAGCTGAAGAAGAGGAAGAATA
droPer1 super_3:3688114-3688249 - TATAA------------CGTGTGTGTGAGTG------TGT-GCTATTATTAAACTCCCT---------CCCTAA---------------------------------------CAC----G--CATACA--ACTATGT-TGTG----------------TA-----A-------------GTGTGTGTGTGT------------GTGTGTGTGTGAGGCGTTGGCGTTTTGACC----AGAAGCTGAAGAAGAGGAAGAATA
droWil1 scaffold_181130:7306738-7306938 + CAAATGGTATGCGTCTATGTGTATGTGTGTGCCTGTGTGTGGCTATTATTAAAAATCCACACCTCCTACCCCAACCCCCCGTTACATATACACACAACCAATACATCCATACGCCCACACATACACATA--CATGAAAAGAAAA----GGA------AAAAAAAGAA-------------CT------------------------------ATGAGGCGTTGGCGTTCGTTCCGGGCACTA------CAAGAAGAAGAAGA
droVir3 scaffold_13047:7645546-7645687 - CATAT------------TGTACGTG------------TGT-GCTATTATTAAAATGCCA----------------------------------------CAC----------GCACGCACAC--ATAGAGACGGGGGGACACGGACACGGCA-----AAAAGAAAAACTATTCTC--------AGAGTGTGT------------GTGCGCCTACGAGGCGTTGGCGTTTTGGCT----AGAA------GAAGC--------A
droMoj3 scaffold_6540:3604660-3604829 - TATAT------------TGTATGTG------------TGT-GCTATTATTAAAATACCA----------------------------------------CAT----------GCACGCACACACAGAGA--GGCAGAGACACGGACACAGCA-----AAAAGAAAAACTATTTACAGTTGCTGCGACTGTGTGTATATACATATATGCGCCTACGAGGCGTTGGCGTTTCAGCA----AGCG------AGAGAGTGAGAGAG
droGri2 scaffold_15245:14649244-14649349 + AACAA----------------------------------------------------GC----------------------------------------AAC----------ACACACACACACACACA--CACACACGCA-------GACA-----AAGA-----A-------------ACACACACTCAC------------ATACATC-TTGATGTGTTCATATTTATGCCA---AGTC------AAACTCAAAAGCTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:10956461-10956596 - TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCATGTGCATGGAGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATGG
droSim1 chr3R:10501806-10501941 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATAG
droSec1 super_0:10986595-10986730 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATAG
droYak2 chr3R:15471091-15471226 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACAGGGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAAGAAGAGGAAGATAA
droEre2 scaffold_4770:10485021-10485154 - TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACA--CACAGAGCCGTGTGCATGGGGCAAAAAACTATGGCCATGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAAGAAGAGGAAGATAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TATAATGTGTGT------GTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGC------AGAAGAGGAAGATAGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATAACGTGTGTGTGAGTGTGTGCTATTATTAAACTCCCT----CCCTAACACGCACACAACTATGT-TATG-------TAAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTGACCAGAAGCTGAAGAAGAGGAAGAATASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..................................................................................GTGTGTGTGTGTGTGTGTGTGTG...........................................2361.00606
...................................................................................TGTGTGTGTGTGTGTGTGT..............................................19150.13202

Secondary Structure

dm3

dG=-36.0,  p-value=0.009901 dG=-36.0,  p-value=0.009901

droSim1

dG=-35.5,  p-value=0.009901 dG=-35.5,  p-value=0.009901

droSec1

dG=-35.5,  p-value=0.009901 dG=-35.5,  p-value=0.009901

droYak2

dG=-41.9,  p-value=0.009901 dG=-41.1,  p-value=0.009901 dG=-41.1,  p-value=0.009901 dG=-41.0,  p-value=0.009901 dG=-41.0,  p-value=0.009901

droEre2

dG=-33.0,  p-value=0.009901 dG=-32.9,  p-value=0.009901

droAna3

dG=-22.7,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.4,  p-value=0.009901

dp4

dG=-20.7,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.9,  p-value=0.009901

droPer1

dG=-18.3,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-17.9,  p-value=0.009901 dG=-17.9,  p-value=0.009901

droWil1

dG=-8.87,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.2,  p-value=0.009901 dG=-8.04,  p-value=0.009901

droVir3

dG=-25.6,  p-value=0.009901 dG=-25.5,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901 dG=-22.8,  p-value=0.009901

droMoj3

dG=-24.67,  p-value=0.009901 dG=-24.67,  p-value=0.009901 dG=-24.07,  p-value=0.009901 dG=-24.07,  p-value=0.009901 dG=-23.87,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droGri2

dG=-4.4,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.7,  p-value=0.019802

Generated: 03/07/2013 at 04:56 PM