Secondary structure and small RNA-seq evidence for dme-mir-4942

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:23332312-23332452 + TATGACATCTGCCTGTT-----------ATGAA-------TACATATATT-TTTATGTTTG--AG-TCAACATC--GA------------------------------------------GTTGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGGCATCGA----AATATGTCCATATCTAATATATAGTTCCATTCTGTTTTATT
droSim1 chr3L:22456065-22456207 + AATGACAGCTGCCTGTT-----------ATAAG-------TAATTGTATT-TTTATGTTTG--AGCTAAACATC--GA-----------------------------------------TTATGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGCCATCAA----AGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT
droSec1 super_41:217199-217341 + AATGACATCTGCCTGTT-----------GTAAG-------TAATTGTATT-TTTATGTTTG--AGCTAAACATC--GA-----------------------------------------TTATGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGCCATCAA----AGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT
droYak2 chr3L:23917805-23917956 + TATGATATCTGAATATTTAGTTTTTCTTTTGC---------ATATTTATT-TTTAATATTG--AGCTTCACATA--TA-----------------------------------------TATTGCCGATGTTTAC---AAAACATCGATGACATTGTT----------TTTGGCATCGT----CATATGCCCATCACTAATATATAGTCCCCTTCTGTTTCATT
droEre2 scaffold_4784:22817455-22817604 - GGC---ATCTGTATAGG-----------ATGAA-------TAAATTAATT-TTTAAGTTTG--ACCACAACTTT--CA-----------------------------------------TTTTGCCGATGTTTAG---AAAACATCGATGACACCGCA-----TCATCGTTGTCATCGACTTACATATGTACATCTCTAATATATAGTATCATTCTGTTTTATT
droAna3 scaffold_12916:14167403-14167537 + TGCT---------CGTT-----------AGAGA-------TGAT-AAACA-TCGATGTTGGCTTGCCAAACATC--GA-----------------------------------------TGTCAACGATGTTTTC---AAAACATCGATGACATCGAT----------GTTAACATCGA----TGTTTCTCCACCTCTGACCACTGGAGTGAATTATTTTTAGT
dp4 chrXL_group1e:10317112-10317245 + TCAAACATATTATTTTT--------ATTGTAAATATCCTA----------------GTTAT--GGTGTAAATCT--GA-----------------------------------------AAATATCGATGTTTGAGAAAAAACATCGATGACATCCAT----------GTTAACATCGA----TGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------
droPer1 super_69:203478-203603 - CATATT-----ATTATT-----------GTAAATATCCTA----------------TTTAT--AGTGTAAATCT--GA-----------------------------------------AAATATCGATGTTTGAGAAAAAACATCGATGACATCCAT----------GTTAACATCGA----TGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------
droWil1 scaffold_181155:90645-90784 - TATTGTTTCCGCCTCTT-----------CTGAT-------CAATCTATTT-CTAATTTATT--TGCT-AACTT---CTTCTCGACTACGTACATATCTACTACGTACAACTCTAGTCAGATATATCCATATCCTATAACG-----------------------------------------------------------AAATCCAACTGCATTCTTAATCGTG
droVir3 scaffold_13036:829247-829384 - TTTATCGTTTATATTTGAAATT------ATTAA-------TTAAATTATT-ATTATTTTTA--AGTAATACAAA-----------------------------------------------------------------ATAAATTAAGGAAATAAAAGTGCAAATTTGTTGTTTTCAA----AG-ATACATTTAATTAATTTTTATTTTTTTTTTATTTTATT
droMoj3 scaffold_6500:19787300-19787437 - TATTATG---AGCTGAA-----------ATAAA-------TATAAAAATA-TTTA--ATTA--AATTCAACAAAATGATGTC------------------------------------------TAGATATTAAA---AAAAAAAAAAAAAATAAAAT----------ATATATATATA----TATATATATATATAT-ATATATATATATATTTTTTTTTTTT
droGri2 scaffold_14853:4224791-4224937 - TATATC-TATGCGTCTGTAGATACT----TGCA-------TAAGTGTATCATCTATGTACG--GTTTACATATA--GT-----------------------------------------GT---ATGGTTTATAA---AAAATATTTCTCAATACGCC----------GTTAGTACAAA----AAAAAAGTAGTGTATAAAAAATGCTTGCACTTTGTTTTAGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:23332312-23332452 + TATGACATCTGCCTGTTATGAATACATATATTTTTATGTTTGAGTCAACATCGAGTTGCCGATGTTTGGAAAACATCGATGACATCGCTGTTGGCATCGAAATATGTCCATATCTAATATATAGTTCCATTCTGTTTTATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AATGACAGCTGCCTGTTATAAGTAATTGTATTTTTATGTTTGAGCTAAACATCGATTATGCCGATGTTTGG---AAAACATCGATGACATCGCTGTTGCCATCAAAGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATTSizeHit CountTotal NormTotalGSM343915
Embryo
.............................................................................................................................ATAGTTCCATTCTGTTATAT.2011.0011
dp4
TCAAACATATTATTTTTATT---GTAAATATCCTAGTTATGGTG-TAAATCTGAAAA-TATCGATGTTTGAGAAAAAACATCGATGACATCCATGTTAACATCGATGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-26.2,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.4,  p-value=0.009901

droSim1

dG=-18.1,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.3,  p-value=0.009901

droSec1

dG=-18.1,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.3,  p-value=0.009901

droYak2

dG=-11.6,  p-value=0.009901 dG=-11.5,  p-value=0.009901 dG=-11.5,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.3,  p-value=0.009901

droEre2

dG=-14.5,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.7,  p-value=0.009901

droAna3

dG=-30.3,  p-value=0.009901 dG=-29.8,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.2,  p-value=0.009901

dp4

dG=-18.6,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.8,  p-value=0.009901

droPer1

dG=-16.4,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.6,  p-value=0.009901

droWil1

dG=-6.7,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.3,  p-value=0.009901 dG=-6.1,  p-value=0.009901 dG=-6.1,  p-value=0.009901

droVir3

dG=-4.9,  p-value=0.009901 dG=-4.3,  p-value=0.009901

droMoj3

dG=-0.9,  p-value=0.009901 dG=-0.5,  p-value=0.009901 dG=-0.2,  p-value=0.009901 dG=0.0,  p-value=0.009901 dG=0.1,  p-value=0.009901

droGri2

dG=-5.0,  p-value=0.009901 dG=-4.9,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.8,  p-value=0.009901

Generated: 03/07/2013 at 05:39 PM