Secondary structure and small RNA-seq evidence for dme-mir-1009

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:19880562-19880652 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droSim1 chr2R:18425639-18425729 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droSec1 super_9:3164536-3164626 - CTCTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droYak2 chr2R:19858946-19859036 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGAGGAGTATCTCAAAA--ATTA-----TTACATTTCAGGGCGATAGTTACCCG
droEre2 scaffold_4845:21253645-21253735 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTGTTGAGTTA---------CCCACGTAGAGTATCTCAAAA--TTTG-----TTACATTTCAGAGCGATAGCTACCCA
droAna3 scaffold_13266:5750531-5750620 - CTATCGATTCAAGATGTAAGTTTTGAATACTTCTACTCTA---------TCTTGGA-ATGTCTCTCATAA--TTGT-----CCATCTTCTAGAACGATAGCTATCCA
dp4 chr3:7562600-7562686 - ATGTCCATACAAGATGTAAGTTCGAGAATC--------------CCAAACACATAAGTTCTTTTTTAACA------TCCAAATATTTTGTAGAGCGACAACATTCCA
droPer1 super_2:7758003-7758089 - ATGTCCATACAAGATGTAAGTTCGAGAATC--------------CCAAAAACATAAGTTCTTTTTTAACA------TCCAAATATTTTGTAGAGCGACAACATTCCA
droWil1 scaffold_180700:5103983-5104075 + TTATCTATCCAGGATGTAAGTATTTAAA--------GTTATTTTCAT----AATGACGGGAAATCAATGATTTGCATTC--ACTCATTGCAGAGTGATAACCTCCCA
droVir3 Unknown -----------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6496:14788216-14788309 + TTATCTCTACAGGAGGTAAGGACCAATTGGTA--AAGT------GAGAAATTGGAAGAAATTTATTGAAA--TTTA---TACTCGTGTTTAGGACAAGGAGTTCACA
droGri2 Unknown -----------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:19880562-19880652 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droSim1 chr2R:18425639-18425729 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droSec1 super_9:3164536-3164626 - CTCTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droYak2 chr2R:19858946-19859036 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGAGGAGTATCTCAAAAATTATTACATTTCAGGGCGATAGTTACCCG
droEre2 scaffold_4845:21253645-21253735 - CTGTCCATTCAAGACGTAAGTGTAAGACTTTGTTGAGTTACCCACGTAGAGTATCTCAAAATTTGTTACATTTCAGAGCGATAGCTACCCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATT---------------------GTTACATTTCAGAGCGATAGCTATCCASizeHit CountTotal NormTotalGSM343915
Embryo
.....................................................TCTCAAAAATT---------------------GTTACATTTCAG...............2319.0099
...............GTAAGTGTAAGACTTTCTTGAGT..........................................................................2312.0022
...............GTAAGTGTAAGACTTTCTTGAGTT.........................................................................2411.0011
...............GTAAGTGTAAGACTTTCTTGAGTTA........................................................................2511.0011
dp4
ATGTCCATACAAGATGTAAGTT-------------------------CGAGAATCCCAAACACATAAGTTCTTTTTTAACATCCAAATATTTTGTAGAGCGACAACATTCCASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-11.6,  p-value=0.009901 dG=-11.6,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droSim1

dG=-11.6,  p-value=0.009901 dG=-11.6,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droSec1

dG=-11.6,  p-value=0.009901 dG=-11.6,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droYak2

dG=-15.9,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.2,  p-value=0.009901

droEre2

dG=-11.5,  p-value=0.009901 dG=-10.8,  p-value=0.009901

droAna3

dG=-3.8,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-2.8,  p-value=0.009901 dG=-2.8,  p-value=0.009901

dp4

dG=-1.7,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-0.9,  p-value=0.009901 dG=-0.7,  p-value=0.009901

droPer1

dG=-1.7,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-0.9,  p-value=0.009901 dG=-0.7,  p-value=0.009901

droWil1

dG=-7.7,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-6.7,  p-value=0.009901 dG=-6.2,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

dG=-4.6,  p-value=0.009901 dG=-4.5,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.6,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 04:46 PM