Secondary structure and small RNA-seq evidence for dme-mir-954

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr4:646737-646853 + GACTCATGCA--------------------CGTCT-TACAAACACAAGATTTTCTGGGTGTTGCGTTGTG------------TG--------TACCTGTGTACAGGCGTATTCACATGCA--------ACATCCCTTACATCTTGCTTGATTATACTCCGCCCG---------------------------------------------------------------CC
droSim1 chrU:391095-391211 + GACGCATGCA--------------------CGTCT-TACAAACACAAGAATTTCTGCGCGTAGAGTTTTG------------TG--------TACATGTGTACGTGCGTATTCACATCCA--------ACATCCCTGACGTCTTGCTTGATTATACTCCGCCCG---------------------------------------------------------------CC
droSec1 super_30:369242-369358 + GACGCATGCA--------------------CGTCT-TACAAACACAAGAATTTCTGCGCGTAGAGTTTTG------------TG--------TACATGTGTACGTGCGTATTTACATCCA--------ACATCCCTGACGTCTTGCTTGATTATACTCCGCCCG---------------------------------------------------------------CC
droYak2 chr4:700584-700681 + GACTCATGCA--------------------CGTCTTTACAAACACAAGATATTCTACGCGTTGTGTTTTG------------TG--------TACAT--------------------GCA--------ACATCCCTGACGTCTTGCGCGATTATACTCTGCCCG---------------------------------------------------------------TC
droEre2 scaffold_4512:633126-633238 - GAGACATGCA--------------------CGTCTTTACAAACACAAGATATTCTGCGCGTTGTGTTTTG-------------ACATGTATGTACAT--------------------GCAACCGTTATGCGTTCCAAGGACCCTATTAGATCGGAACACGGTCA---------------------------------------------------------------GT
droAna3 scaffold_13337:22987804-22987813 + TCCGCCCGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T
dp4 chrXR_group8:8504771-8504835 + CT----------------------------------TACAAATTCTAGAATTTCTGTCTGTCTGTCTGTCTGTTTTTGTGTGTG--------TATGT----GTGTGTGTGC----------------------------------------------------------------------------------------------------------------------
droPer1 super_150:7787-7872 - AATGCATACA--------------------CGATA-TACATACATATGTGTGTGTGTGTGTGTGTGTGTG------------TG--------TGTGTGTGTGTGTGTG----------TA--------GACGTATGTGTAT-----GTGA-------------------------------------------------------------------------------
droWil1 scaffold_181130:1758155-1758267 + CACTTTTGTG--------------------CTGCG-TGTGAGT----GTGTGTGTGTGAGTTTAAGTGTG------------TG--------TATGTGCGAACATACGAATTTAGATAAA--------GATTCGTATACACATGACATTCGCATACTCACACCT---------------------------------------------------------------AC
droVir3 scaffold_13049:11239836-11239930 - TACATACGCA--------------------CA----TACATACATAGGTGTTCGTATG----------TA------------TG--------TACGTATGTAGGTGTG--CT---ATACACCCGTCAAAAGAGCTAATTTCCTTTCTTGGTTAT---------------------------------------------------------------------------
droMoj3 scaffold_6500:15364731-15364841 + GGGTCAGGCAAATTCGAATGTGAATTCAAAATACA-TACATACATATGTACAT---------GTATTGTG------------TG--------TGCAAGTGTACATGTGTGCTCACATGCA--------AACTCACTTACATAATGTATG--------------------------------------------------------------------------------
droGri2 scaffold_14822:646607-646724 + AACAAATGCA--------------------GCGCA-TGT----------------TT------------------------------------------TGATTCACAAGCCTGAACATA--------TCCTAGCATAT------------C------------GTTGGTAACGGGGCTCTGCAGAATACACACACAAACATATTGATGCTCGCGTTGATTATCATGCC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr4:646737-646853 + GACTCATGCACGTCTTACAAACACAAGATTTTCTGGGTGTTGCGTTGTGTGTACCTGTGTACAGGCGTATTCACATGCAACATCCCTTACATCTTGCTTGATTATACTCCGCCCGCC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GACGCATGCACGTCTTACAAACACAAGAATTTCTGCGCGTAGAGTTTTGTGTACATGTGTACGTGCGTATTCACATCCAACATCCCTGACGTCTTGCTTGATTATACTCCGCCCGCCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
C-------------TTACAAATTCTAGAATTTCTGTCTGTCTGTCTGTCTGTTTTTGTGTGTGTATGTGTGTGTGTGC---------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-25.0,  p-value=0.009901 dG=-25.0,  p-value=0.009901 dG=-24.9,  p-value=0.009901 dG=-24.9,  p-value=0.009901 dG=-24.4,  p-value=0.009901

droSim1

dG=-10.5,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-9.9,  p-value=0.009901 dG=-9.5,  p-value=0.009901 dG=-9.5,  p-value=0.009901

droSec1

dG=-9.5,  p-value=0.009901 dG=-8.7,  p-value=0.009901 dG=-8.6,  p-value=0.009901 dG=-8.6,  p-value=0.009901 dG=-8.5,  p-value=0.009901

droYak2

dG=-5.4,  p-value=0.009901 dG=-4.7,  p-value=0.009901 dG=-4.7,  p-value=0.009901 dG=-4.6,  p-value=0.009901 dG=-4.5,  p-value=0.009901

droEre2

dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.2,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-11.7,  p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

dG=0.0,  p-value=0.009901 dG=0.2,  p-value=0.009901 dG=0.6,  p-value=0.029703

droPer1

dG=-1.2,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-1.1,  p-value=0.009901 dG=-1.1,  p-value=0.009901 dG=-1.0,  p-value=0.009901

droWil1

dG=-22.4,  p-value=0.009901

droVir3

dG=-11.4,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-8.7,  p-value=0.009901

droMoj3

dG=-14.5,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.8,  p-value=0.009901

droGri2

dG=-0.7,  p-value=0.009901 dG=-0.5,  p-value=0.009901 dG=0.0,  p-value=0.029703 dG=0.2,  p-value=0.009901

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