Secondary structure and small RNA-seq evidence for dme-mir-979

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19455855-19455979 + TTAATCAC---TGGAA-----------------------CATACATGTGAG-----------GATGTCACAAATACA--------------CTGA---ATTTGGGGGGAATTCT--------TATGTATATAC-AAATTCTTCCCGAACTCAGGCTAATTTTGTG---------------GCA---------------------------TCCGTATACACAAAA----------------------------------GT------ATA
droSim1 chrX_random:5079602-5079664 + TTAATATA---C--------------------------------------------------------------------------------------------------------------------------AAATTCTTCACGAATTCAGGCTAATTTTGTA---------------GGA---------------------------GCCGTATATACAAAA----------------------------------GT------ATA
droSec1 super_8:1738459-1738521 + TTAATATA---C--------------------------------------------------------------------------------------------------------------------------AAAATCTTCACGAATTCAGGCTACTTTTGTA---------------GGA---------------------------ACCGTATATACAAAA----------------------------------GT------ATA
droYak2 chrX:11883259-11883281 - TTAATGGC---TGGGA-----------------------AATAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT------AAA
droEre2 scaffold_4690:9691773-9691867 + TTAATCGT---TGGCA-----------------------AATACGTATGG------------GGTGCCACA------CAAATCGATTAGCTCTGA---ATTCGGGCGGAATTCTGAAGCACGCAT-----------------------------CCACTTTTGTA---------------GCA---------------------------TCC---------------------------------------------------------
droAna3 scaffold_13417:2459297-2459411 - TAAGTTAC---TTATA-----------------------ATTAAATTTAAA-----------TATTTCGAAATAAAA--------------CTATAAAATAATTGTCTTATTTCAG------------------AAAATATGTACATATTTATACCAATCTT--------------------------------------------------------------------------------TACATATTTCAATAAAAAT------ATA
dp4 chrXL_group1e:12509670-12509797 - TTAAGCAT---TTTAATTTTTGTATTTTTCAAGATCGAAAATATTTATGC-GCGTAAATTTAAGAGTAAGTCCTTA-GTAAGTAAGGAAG-------------------AAC------------------------------------TACGCTCTGGATTTGAT---------------ATA---------------------------CTCGTGAAGTTAAAA----------------------------------CA------ATA
droPer1 super_14:1989251-1989367 - CTAAGTCA---TCGTG-----------------------CGCATCTGTTGG-----------GGAGTAAAAACTAAA--------------A-------TTAGAGTGGAAACTC--------TATTTTGAGTTGAATTTTTCCATGAAAATCTGCTACATTTTGG---------------G-T-----------------------------------------------------------------TTTAAATTTGTAT------TTT
droWil1 scaffold_181096:7961895-7962008 + TAGATTATGATTAGAATAAGCACACACAACACACGCACA-----------------------------------------------------------------------CACACACACACACATCTATATAT-AAATCAACCAAGAAAACA---CAATATCGAA---------------GAAA--------------------------TTAGAAAGTATATAT----------------------------------AT------ATA
droVir3 scaffold_13042:902091-902097 - TCAATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6328:2896306-2896380 - ATGAGAAA---GGG----------------------------------------------------CTATA------GAAATTGATGACG---------------------------------------------ATATAATCCAAAACTAAGATTACAATAATA---------------ATA---------------------------ATaataaac-----------------------------------------a------aaa
droGri2 scaffold_15081:2040284-2040418 - TTGTAATT---TAAGA--------------------------------------------------------------------------------------------------------------------------TGAAGATGAAGACA----------ATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAGTTGAAAATGTCATTCTCTGGTTATTGGATTAAAATGAGGACACTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19455855-19455979 + TTAATCACTGGAACATACATGTGAGGATGTCACAAATACACTGAATTTGGGGGGAATTCTTATGTATATACAAATTCTTCCCGAACTCAGGCTAATTTTGTGGCATCCGTATACACAAAAGTATA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTAAT-----------------------------------------------------------------------ATACAAA--TTCTTCACGAATTCAGGCTAATTTTGTAGGAGCCGTATATACAAAAGTATASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTAAGCATTTTAATTTTTGTATTTTTCAAGATCGAAAATATTTATGCGCGTAAATTTAAGAGTAAGTCCTTAGTAAGTAAGGAAGAA--------CTACGCTCTGGATTTGATATACTCGTGAAGTTAAAACAATASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.6,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901

droSim1

dG=-1.5,  p-value=0.009901 dG=-0.6,  p-value=0.019802

droSec1

dG=-0.2,  p-value=0.009901 dG=0.0,  p-value=0.039604 dG=0.0,  p-value=0.039604 dG=0.1,  p-value=0.009901 dG=0.3,  p-value=0.019802

droYak2

No secondary structure predictions returned

droEre2

dG=-10.1,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-9.2,  p-value=0.009901 dG=-9.1,  p-value=0.009901

droAna3

dG=-1.1,  p-value=0.009901 dG=-0.8,  p-value=0.009901 dG=-0.7,  p-value=0.009901 dG=-0.7,  p-value=0.009901 dG=-0.5,  p-value=0.009901

dp4

dG=-6.5,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.0,  p-value=0.009901

droPer1

dG=-10.2,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-9.9,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-9.8,  p-value=0.009901

droWil1

dG=0.0,  p-value=1.0 dG=1.0,  p-value=1.0

droVir3

No secondary structure predictions returned

droMoj3

dG=-0.6,  p-value=0.009901 dG=-0.2,  p-value=0.009901 dG=0.0,  p-value=0.009901 dG=0.3,  p-value=0.019802 dG=0.4,  p-value=0.009901

droGri2

dG=0.0,  p-value=1.0

Generated: 03/07/2013 at 07:18 PM