Secondary structure and small RNA-seq evidence for dme-mir-4953

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:18599846-18599969 + CGTAAGAATA-------------TTG-------CACTAAAGTTCACAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTATTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAACATG-----CATGT
droSim1 chr3R:18412164-18412275 + CGTAAAAATA-------------TTG-------CACGAAAGTTCGCAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACG--------------------GTGT
droSec1 super_0:18960705-18960813 + CGTAAAAATA-------------TTG-------CACGAAAGTTCGCAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACG--------------------GTGT
droYak2 chr3R:19450585-19450700 + TGCTCAAATT-------------TTG-------CACGAAAGTTCGATGGCGACCATGA-AT---GCGAATGAAG----A--------ATAT---------------------TTACCATTAGTGTTTTGCTCATTATTGAAGGTCATGGACATCCTTGA-----TTTTGCAAAATG--------TT
droEre2 scaffold_4820:9473651-9473779 - CGCTAAAATA-------------TGG-------CACGAAAGTTCACTGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCATAAAGATATGTTTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAATATGTTCTACGTGT
droAna3 scaffold_13340:12717426-12717507 - GGGGAAAAAA-------------TGA-------AAAGAA-----ACAAATGACCTTAGTAGGTCAGTGACTAAATTTTTGCCCATAA----GT-----------------------------GATTTAATCGTATATCAA----------------------------------------------
dp4 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12822:414561-414651 - TGCAAGCAAA-------------TTT-------TGCCTAAGTTCTGA------------------CTAATAACT----A--------ATGT---------------------ATGTACTTAATGTTATTGTGATAAATTAATGTTATTTGTAACCAA------------------------AATGT
droMoj3 scaffold_6540:33042485-33042630 - CGTAGTTTGACCACATAGAGACATCAAGTCTAAGAGGAAAACTCA--------TTTGG-AC---ACTGATTAAAAATCAGTCCCGAT----GAGAGCGAT------------AT---ATTAACATTAATTTTCTTATTGCATTTTACGTATATTTTTTTTTTGCTTTTAACA---------TACAT
droGri2 scaffold_15074:3394740-3394844 + GTATGATACA-------------------------TTAAAGTTCTCCATAATCAATTT-GT---GT-------------------------GTGTGTGTGTCATCGACAAATTTACCATCTTAACTACACTTATTTTCAAAAT-------------------A-TTTCACATA--------TATTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:18599846-18599969 + CGTAAGAATATTGCACTAAAGTTCACAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTATTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAACATG-----CATGT
droSim1 chr3R:18412164-18412275 + CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG--------------------TGT
droSec1 super_0:18960705-18960813 + CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG--------------------TGT
droYak2 chr3R:19450585-19450700 + TGCTCAAATTTTGCACGAAAGTTCGATGGCGACCATGAATGCGAATGAAGAATATTTACCATTAGTGT-TTTGCTCATTATTGAAGGTCATGGACATCCTTGA-----TTTTGCAAAATGT--------T
droEre2 scaffold_4820:9473651-9473779 - CGCTAAAATATGGCACGAAAGTTCACTGGCGACCATGAATGTTAATAAAGAATATTTACCAT-AAAGATATGTTTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAATATGTTCTACGTGT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG---------------TGTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
----------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-18.8,  p-value=0.009901 dG=-18.4,  p-value=0.009901 dG=-18.1,  p-value=0.009901

droSim1

dG=-18.7,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.0,  p-value=0.009901

droSec1

dG=-18.7,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.0,  p-value=0.009901

droYak2

dG=-13.5,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-13.1,  p-value=0.009901 dG=-13.0,  p-value=0.009901 dG=-12.9,  p-value=0.009901

droEre2

dG=-15.7,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-14.9,  p-value=0.009901

droAna3

dG=-10.2,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-8.0,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

dG=-4.8,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901

droMoj3

dG=-13.3,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-12.8,  p-value=0.009901 dG=-12.8,  p-value=0.009901 dG=-12.6,  p-value=0.009901 dG=-7.9,  p-value=0.009901

droGri2

dG=-6.2,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.6,  p-value=0.009901 dG=-5.5,  p-value=0.009901

Generated: 03/07/2013 at 05:54 PM