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 + GGCCATTAGGACAGGGTAGGTTGAA-----ATCGGATACAA---CTAAAAG-----TT-ATTTTTAATTGT-------------------AT--------CCG-GTCTT-C-ATTTTAGGTCTTCGATTGTTCC

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

-19.9 -19.8

droSim1

-6.0 -5.9

droSec1

-6.0 -5.9 -5.2 -5.1

droYak2

-5.1 -4.9 -4.2

droEre2

-4.6 -4.4 -4.1 -4.0 -3.9 -3.9

droAna3

-4.4 -3.9 -3.8

dp4

-8.7

droPer1

-8.3 -8.3 -7.8 -7.6 -7.5

droWil1

-12.1 -12.0 -11.7 -11.3 -11.3 -11.3

droVir3

-11.1 -11.0 -10.8 -10.5 -10.2 -10.2

droMoj3

-9.9 -9.8 -9.6 -9.6 -9.6 -9.5

droGri2

-5.3 -5.3 -5.2 -5.2 -5.2 -5.2

Generated: 01/05/2013 at 05:19 PM