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

-44.2 -44.2 -43.7 -43.7 -43.6 -43.6

droSim1

-46.4 -46.4 -45.9 -45.9 -45.8 -45.8

droSec1

-47.8 -47.8 -47.3 -47.3 -47.2 -47.2

droYak2

-41.0 -41.0 -40.0 -40.0

droEre2

-38.1 -38.1 -37.6 -37.6 -37.1 -37.1

droAna3

-40.6 -40.6 -40.6 -40.6 -40.4 -40.4

dp4

-30.9 -30.5 -30.0

droPer1

-36.1 -35.7 -35.7 -35.3 -35.2 -35.2

droWil1

-0.7 -0.2 -0.1 0.0 0.0 0.0

droVir3

-7.4 -7.3 -7.3 -7.2 -7.2 -7.1

droMoj3

-3.3 -2.4

droGri2

No secondary structure predictions returned

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