Secondary structure and small RNA-seq evidence for dme-mir-4909

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:3598907-3598996 + GGCCATTAGGACAGGGTAGGTTGAA-----ATCGGATACAA---CTAAAAG-----TT-ATTTTTAATTGT-------------------AT--------CCG-GTCTT-C-ATTTTAGGTCTTCGATTGTTCC
droSim1 chr2R:2322894-2322983 + GGCCATTAGAACAGGGTAGGTAGAA-----ATCGGATTAAA---CTAAAAC-----TT-ATTTTTGATTGT-------------------CT--------CTT-GTTTT-C-ATTTGAGGTCTTCGATTGTGCC
droSec1 super_1:1254446-1254535 + GGCCATTAGAACAGGGTAGGTAGAA-----ATCGGATTAAA---CTAAAAC-----TT-ATTTTTGATTGT-------------------CT--------CTT-GTCTT-C-ATTTGAGGTCTTCGATTGTGCC
droYak2 chr2L:16271881-16271969 + GGCCATTAGGACAGGGTAGGTAGAT------TCGGGTTTAA---CTAAAAG-----TA-AGATTTAATAGT-------------------TT--------TCT-TTCCA-C-ACTTTAGGTCTTCAATTGTGCC
droEre2 scaffold_4929:19008519-19008607 - GGCCATTAGAACAGGGTAGGTAGGT------TCGGATATAA---CTAAAAG-----TA-AGATTTAATAGT-------------------TT--------TCT-TGCAT-C-ACTTTAGGTCTTCGATTGTGCC
droAna3 scaffold_13266:10106458-10106549 + GGCTATTCGAACGGGGTGAGTGAAAATTATTATGGA---AA---TTGATGG-----CA-------GAATCT-------------------CTCTAAAAAACT---CTTT-T-ATTGCAGTTCCTCAATTGTACC
dp4 chr3:6515146-6515237 - GGCCATAAGAACAGGGTGAGTGTAT-----AATGGAAGTAG---CACATTG--T--TT-AAATACGAAAGT-------------------AA--------CCTTGTTCC-T-GATGCAGTTCATCGATTGTGCC
droPer1 super_2:6735406-6735497 - GGCCATAAGAACAGGGTGAGTGTAT-----AAAGAAAGTAG---CATATTG--T--TT-AAATACGACAGT-------------------AA--------CCTTGTTCC-T-GATGCAGTTCATCGATTGTGCC
droWil1 scaffold_180700:1009012-1009118 + GGCTATACGTACGGGGTAAGTGAGG--------GGGTATGAAAAATAAGTTTATAG------AATGGCAGTTAATATTTGTTTT-----TCTTTT---TTCT---TTT--TATGTATAGTTCCTCTATAGTCCC
droVir3 scaffold_12875:823172-823263 + GGCCATACGCACGGGGTGAGTACGGCTG---ACTGCGATAA---CTGCACG-----CACATTCACGGCATT-------------------CA--------CTC--TCC--CATGAGCAGTTCGTCGATTGTGCC
droMoj3 scaffold_6496:3846141-3846250 + GGCCGTGCGAACAGGGTGAGTAGAC-----AGGAGA-AAAA---CTAACTGTATAACGCTTCCATTACATT-------CAACTATCCTCTCT--------CTTTGTCTCTTGTGAACAGTTCTGCTATTGTTCC
droGri2 scaffold_15245:10130930-10131015 - GGCCATACGCACGGGGTAAGTGTATCTGATACTGGGCATCG--------AA-----TA-AAATCTGACACT-------------------AA--------T-----CCA-T-GGCTCAGTTCGTCCATTGTGCC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:3598907-3598996 + GGCCATTAGGACAGGGTAGGTTGAAATCGGATACAACTAAAAGTTATTTTTAATTGTATCCGGTCTTCATTTTAGGTCTTCGATTGTTCC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGCCATTAGAACAGGGTAGGTAGAAATCGGATTAAACTAAA-ACTTATTTTTGATTGTCTCT-TGTTTTCATTTGAGGTCTTCGATTGTGCCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGCCATAAGAACAGGGTGAGTGTATAATGGAAGTAGCACATTGTTTAAATACGAAAGTAACCTTGTTCCTGATGCAGTTCATCGATTGTGCCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-19.9,  p-value=0.009901 dG=-19.8,  p-value=0.009901

droSim1

dG=-6.0,  p-value=0.009901 dG=-5.9,  p-value=0.009901

droSec1

dG=-6.0,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-5.2,  p-value=0.009901 dG=-5.1,  p-value=0.009901

droYak2

dG=-5.1,  p-value=0.009901 dG=-4.9,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-3.1,  p-value=0.009901

droEre2

dG=-4.6,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.9,  p-value=0.009901

droAna3

dG=-4.4,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901

dp4

dG=-8.7,  p-value=0.009901

droPer1

dG=-8.3,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901

droWil1

dG=-12.1,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-11.7,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.3,  p-value=0.009901

droVir3

dG=-11.1,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-10.0,  p-value=0.009901

droMoj3

dG=-9.9,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.6,  p-value=0.009901

droGri2

dG=-5.3,  p-value=0.009901 dG=-5.3,  p-value=0.009901 dG=-5.2,  p-value=0.009901 dG=-5.2,  p-value=0.009901 dG=-5.2,  p-value=0.009901

Generated: 03/07/2013 at 05:30 PM