Secondary structure and small RNA-seq evidence for dme-mir-4950

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:3277158-3277280 + TTTATACATTTG--TTTAT-----------------------AATGCACATAATAAATGCCAACC------ATTCATCATGA-AATTATAAATAGTAT--CATTTCAAGATGCATGG-TAAG-GCTT------TATTTT---------------------------------------------G--------TTTTGCA---ATCAAAGACATCTTTCTT
droSim1 chr3R:3321450-3321569 + TTTATATATATT-ATTTAT-----------------------TATGCTCAGCATAAATGCCAAGC------ATTCGTCGTGA-AATTATAAATTATATATTA--TATAAATTCATGG-TAAG-GCTT------CATTTT---------------------------------------------T--------TAACGCA---GTCTAAGACATC----TT
droSec1 super_6:3368064-3368189 + TTTATATATATT-ATTTAT-----------------------TATGCTCAGCATAAATGCCAAGC------ATTCGTCGTGA-AATTATAAATTATATATTATTTCTAGATTCATGG-TAAA-GTTT------CATTTT---------------------------------------------G--------TAACGCA---GTCTAAGACATCTTTCTC
droYak2 chr2L_random:3663454-3663574 - TTTAGCCAAGTT-A-ATT--------------------------TGGTAAAAACAAAAACCAGAA------ACCGGCTACAC-GATGAAACGCTAAATGCCATTTTAGCAGTC--AG-GTAATTATA------TATT--------------------------------------------------T--AT-TTTTAAA---TTTAAACCCATTTTTTAT
droEre2 scaffold_4784:2237866-2237984 - TTTCCAAATTTG-A-ATGC---AGA-TTTTT------------------AGACAATTGCTCCAGA------AACATT------------TAGAGGTATGCCACTTCAAAATACGA----TAATTGAAGGTTGAATTATG---------------------------------------------G-----AC--TTTAG----AACTTCAGCCTTCTTTTT
droAna3 scaffold_13340:2198726-2198841 + TTAATAATTTTA--TTTAT-----------------------CGAAC------TAATT-AGGCTT------TTCATACAGATTTAAGCTTAATATTAAATTA--TAG-------------------------------------------------------AGCACTGGCTGCGGTGGTATATA--T--AT--TTTTC----AATAAACACATTTTTATG
dp4 chrXR_group6:912830-912970 - TTTATACCACGC--ACTAGATTGGGTTCTCCAGATAACGAATGTTGTCCAGTAAAATCCCAATCCATTCAAATGGATTATGT-GACCA-------------GTGTTAAGATGCGTCG-AGGG-CAGT------CAGCTT---------------------------------------------G--------TGTTGCT---ATCTCGCTCCCCTCCGCC
droPer1 super_3:249021-249147 + TTTTAAATCTGTTCCCTAAAATATACTTTTTGAAC------------------GAG-------------------------A---------------------------------------G-AGTA------TATATGTATGTATGCCGAGCAACTTCTAGTACCCCCTACTCAAT-A----TGTTTTTTTTTGGCTTAGTAAAATAATACATCTATATC
droWil1 scaffold_180708:152570-152690 - TTTATATATATA-T-ATAT---GAT-GTAGA---TATA---TATTTTTTAT----ATTTAAATTTTT----------------------TTAAAGTGA--TTTTTGTCAA-GGCTAG-AAAA-GCTT------TATTTT-------------------------------------------TTGTTT-----TGTTTTA---GTTTATGCGATATTTCTT
droVir3 scaffold_135:841-956 - TATATATATGTG-A-ACAT---AAC-TTATA-------------------TAATA------------------------------------CATATGA--CATACTGCCAGAC--AAATAAA-CGTA------ACTATTTATGTTTGAA-------ATCAAGATCACCAAAATAAATGATGATTT--T--AT--TT--------------------TACAA
droMoj3 scaffold_6308:1934837-1934961 - TTTATATATTAT-A-AAAA---AAA-T-----------------TACTTAAATTAAAGCTTAGGA------AATATTTGTAT-CCATAAAAAATATGA--TATATTTTTATGCATGG-TAAA-TTTA------ATTTTT---------------------------------------------A--------ATTTCTA---ATAAAAAAAATTATATAT
droGri2 scaffold_14906:7885716-7885837 + ATTATTATTTTT--TTTTT-----------------------A--TTTCAAGTTAATTTACAATT------ATCGAACCGGT-TAAACTAAATTTTAGCTTA--TAGATATTTATTG--------------------------------------------------------CTTAATTAACTGTTTTT---TTTTGTT----GTTAAAACATTTTTTTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:3277158-3277280 + TTTATACAT-TTGTTTATAATGCACATAATAAATGCCAACCATTCATCATGAAATTATAAATAGTATCA--TTTCAAGATGCATGGTAAGGCTTTATTTTGTTTTGCAATCAAAGACATCTTTCTT
droSim1 chr3R:3321450-3321569 + TTTATATATATTATTTATTATGCTCAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTATATAT--TATATAAATTCATGGTAAGGCTTCATTTTTTAACGCAGTCTAAGACATCTT----
droSec1 super_6:3368064-3368189 + TTTATATATATTATTTATTATGCTCAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTATATATTATTTCTAGATTCATGGTAAAGTTTCATTTTGTAACGCAGTCTAAGACATCTTTCTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTTATATAT----------------------ATTATTTATTATGCTCAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTATATATTATATAAATTCATGGTAAGGCTTCATTTTTTAACGCAGTCTAAGACATCTT----SizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTTATACCACGCACTAGATTGGGTTCTCCAGATAACGAATGTTGTCCAGTAAAATCCCAATCCATTCAAATGGATTATG-----TGACCAGTGTTAAGATGCGTCGAGGGCAGTCAGCTTGTGTTGCTATCTCGCTCCCCTCCGCCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901

droSim1

dG=-11.9,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.8,  p-value=0.009901

droSec1

dG=-9.0,  p-value=0.009901 dG=-8.4,  p-value=0.009901 dG=-8.2,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-7.7,  p-value=0.009901

droYak2

dG=-9.3,  p-value=0.009901 dG=-8.3,  p-value=0.009901

droEre2

dG=-5.6,  p-value=0.009901 dG=-5.1,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-4.9,  p-value=0.009901 dG=-4.9,  p-value=0.009901

droAna3

dG=-7.2,  p-value=0.009901 dG=-6.8,  p-value=0.009901

dp4

dG=-10.5,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-7.1,  p-value=0.009901

droPer1

dG=0.0,  p-value=1.0

droWil1

dG=-6.4,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.1,  p-value=0.009901

droVir3

dG=0.0,  p-value=1.0

droMoj3

dG=-6.0,  p-value=0.009901 dG=-6.0,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-5.8,  p-value=0.009901

droGri2

dG=-5.3,  p-value=0.009901 dG=-5.2,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-4.7,  p-value=0.009901 dG=-4.6,  p-value=0.009901

Generated: 03/07/2013 at 05:49 PM