Secondary structure and small RNA-seq evidence for dme-mir-1001

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:23468173-23468292 - AGCCCGC-----------------------------------------------------------------------------------------GATG-ATGTAAGCTGGC-CTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCC---CGATCCTTGGGTTTC------------------TGCTCTCGGGCAAGGTCAGTAGTGCCCGCGAAGGGCCC
droSim1 chr3R_random:1114763-1114882 - AGCCCGC-----------------------------------------------------------------------------------------GATG-ATGTAAGCTGGC-CTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCC---CGATCCTTGGGTTTC------------------TGCTCTCGGGCAAGGTCAGCAGTGCCCGCGAAGGGCCC
droSec1 super_22:111563-111682 - AGCCCGC-----------------------------------------------------------------------------------------GATG-ATGTAAGCTGGC-CTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCC---CGATCCTTGGGATTC------------------TGCTCTCGGGCAAGGTCAGCAGTGCCCGCGAAGGGCCC
droYak2 chr3R:23018685-23018798 + G------------------------------------------------------------------------------------------------ATG-ATGTAAACTGGC-CTGTCCCTGGGTAAACTCCCAATGATCCGGTGTACATTGAATTC---GGATCCTTGGGTTTG------------------AGCCCAAGGACAAGGACAGTAGTGCCCGCGAAGGGCCC
droEre2 scaffold_4820:4569064-4569195 + AGCCCGCGTAAGGTGTATA-----------------------------------------------------------------------------GATG-ATGTAAACTGGC-CTGTCCCTGGGCAAACTCCCAATGATGCGGTGTACATAGAATCC---CGATCCTTGGGCTTC------------------TGCCCACGGGCAAGGACAGTAGTGCCCGCGAAGGGCCC
droAna3 scaffold_13340:19221720-19221830 + GTGTATA-----------------------------------------------------------------------------------------GATG-ATGTGAGCTGTC-CTGTCCCTGGGAGG----------ATCACCTGTAGTATTAAATTAAATGGAACAAAGGTCTC------------------CCCCTAGGGGCAAGGACAGCATTGGCCACGA--GGCTC
dp4 chr2:3822386-3822523 - AGATGAT-----------------------------------------------------------------------------------------GATACATATAAGCTGATTCTCTCCCAGTGGCGGACACACGGCAGATGGTGGCTTTACCGATC---CGATAATTGAATTTTAACCAAAAGAAAACCACCTGCATTCGGGTGCCGCCCCT-GGGTCTGAG-AGGGCTG
droPer1 super_7:528167-528304 + AGATGAT-----------------------------------------------------------------------------------------GATACATATAAGCTGATTCTCTCCCAGGGGCGGATACACGGCAGATGGTGGCTTTACCGATC---CGATAATTGAATTTTAACCAAAAGAAAACCACCTGCTTTCGGGTGCCGCCCCT-GGGTCTGAG-AGGGCTG
droWil1 scaffold_181089:3707083-3707253 - CAAATGG--AAAGTGTATGGAGGCAAGAGTGTCCAGATTGCCTTGGCCAAATATTGGGATTATGCTCAATACCGATCCCACATAATTGTTAATTCGTTTA-GTATTATCTA-----------------TTATCTATTATTATTAT---------------------------------------GATTATTATCGAATTATTATTATTATTCTT-ATGATTATT-GAGATCC
droVir3 Unknown AGCTGAA-----------------------------------------------------------------------------------------ATTT-GTTTATACC----CTTT-CCAATGTTAAGCCCCTTGGAAAATGTA-----TGAATCT---CGTAACAT-------------------------------------------TCGTAACAAGATGTTCGCCA
droMoj3 Unknown AGCTGAA-----------------------------------------------------------------------------------------ATTG-GTTTATGCTC-----------------TTTCCCAAGCGTATAATGAATAC-------------------------------------------------CAAAGAAAATACCTAACACTCGTAAGAAG---
droGri2 Unknown AGCTAGC-----------------------------------------------------------------------------------------CA--------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:23468173-23468292 - AGCCCGC------------GATGATGTAAGCTGGCCTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCCCGATCCTTGGGTTTCTGCTCTCGGGCAAGGTCAGTAGTGCCCGCGAAGGGCCC
droSim1 chr3R_random:1114763-1114882 - AGCCCGC------------GATGATGTAAGCTGGCCTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCCCGATCCTTGGGTTTCTGCTCTCGGGCAAGGTCAGCAGTGCCCGCGAAGGGCCC
droSec1 super_22:111563-111682 - AGCCCGC------------GATGATGTAAGCTGGCCTGTCCCTGGGTAAACTCCCAAGGATCAGGTGGAGATTGAATCCCGATCCTTGGGATTCTGCTCTCGGGCAAGGTCAGCAGTGCCCGCGAAGGGCCC
droYak2 chr3R:23018685-23018798 + -------------------GATGATGTAAACTGGCCTGTCCCTGGGTAAACTCCCAATGATCCGGTGTACATTGAATTCGGATCCTTGGGTTTGAGCCCAAGGACAAGGACAGTAGTGCCCGCGAAGGGCCC
droEre2 scaffold_4820:4569064-4569195 + AGCCCGCGTAAGGTGTATAGATGATGTAAACTGGCCTGTCCCTGGGCAAACTCCCAATGATGCGGTGTACATAGAATCCCGATCCTTGGGCTTCTGCCCACGGGCAAGGACAGTAGTGCCCGCGAAGGGCCC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AGCCCGCGATG-ATGTAAGCTGGCC-TGTCCCTG-GGTAAACTCCCAAGGATCAGGTGGAGA-TTG--AATCCCGATCCTTGGGTTTC------------------TGCTCTCGGGCAAGGTCAGCAGTGCCCGCGAAGGGCCCSizeHit CountTotal NormTotalGSM343915
Embryo
................................TG-GGTAAACTCCCAAGGATCAGG........................................................................................23110.001010
...........................................................................ATCCTTGGGTTTC------------------TGCTCTCG..............................2111.0011
.........................................................................CGATCCTTGGGTTTC------------------TGCTCTCG..............................2311.0011
dp4
AGATGATGATACATATAAGCTGATTCTCTCCCAGTGGCGGACAC--ACGG--CAGATGGTGGCTTTACCGATCCGATAATTGAATTTTAACCAAAAGAAAACCACCTGCATTCGGGTGCCGCCCCT-GGGTCTGAG-AGGGCTGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-31.1,  p-value=0.009901 dG=-30.6,  p-value=0.009901 dG=-30.5,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901

droSim1

dG=-31.1,  p-value=0.009901 dG=-30.6,  p-value=0.009901 dG=-30.5,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901

droSec1

dG=-32.5,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-31.9,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.5,  p-value=0.009901

droYak2

dG=-32.2,  p-value=0.009901

droEre2

dG=-29.3,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droAna3

dG=-24.7,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.5,  p-value=0.009901

dp4

dG=-16.4,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.0,  p-value=0.009901 dG=-16.0,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-14.9,  p-value=0.009901

droPer1

dG=-15.8,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.3,  p-value=0.009901

droWil1

dG=-0.7,  p-value=0.009901 dG=-0.2,  p-value=0.009901 dG=-0.1,  p-value=0.009901 dG=0.0,  p-value=0.009901 dG=0.0,  p-value=0.009901

droVir3

dG=-5.5,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-4.9,  p-value=0.009901 dG=-3.5,  p-value=0.009901

droMoj3

dG=-0.1,  p-value=0.019802 dG=0.0,  p-value=0.019802 dG=0.6,  p-value=0.009901 dG=0.8,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 04:45 PM