Secondary structure and small RNA-seq evidence for dme-mir-4970

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:10741869-10742002 + CATGTTTAGATCGGA--CCCAAAGGTGGGCGAC--AAG---GGCTGGGAGCAGC-----AGTTGCTGGCGGTATTCTGAAGCTGCTCTTCCG----------------TGG---GTTGCTCTTGCTCC-------------------TGACCCTCCTCTTCCT------------------------CCGCTTCATCCT----------C-C---TCCGCAT
droSim1 chr2L:10541288-10541421 + CATGTTTAGATCGGA--CCCAAAGGTGGGCGAC--AAG---GGATGGGAGCAGC-----AGTTGCTGGCGGTATTCTGAAGTTTCTTTTTCG----------------TGG---GCAGCTCTCGCTCC-------------------TGACCCTCCTCTTCCT------------------------CCGCTTCGTCTT----------C-C---CCCGCAT
droSec1 super_3:6159513-6159646 + CATGTTTAGATCGGA--CCCAAAGGTGGGCGAC--AAG---GGATGGGAGCAGC-----AGTTGCTGGCGGTATTCTGAAGTTGCTTTTTCG----------------TGG---GCAGCTCTCGCTCC-------------------TGACCCTCCTCTTCCT------------------------CCGCTTCGTCTT----------C-C---CCCGCAT
droYak2 chr2L:7146365-7146495 + CATGTTCAAATCGGA--GCCAAAGGTGGGCGAG--AGG---GGCTGTGAGCAGC-----CGTTGCTGGCGGTGTTCTGTCTCTGCTCCTCCG----------------CCG---GCTGCTGTTGCTCC-------------------TGACCCTCCTCGTCCT------------------------CCGCGTCTTCC-----------------TCGCCGT
droEre2 scaffold_4929:14689286-14689416 - CATGTTCAAATCGGA--CCCAAAGGTAGGTGAG--AGG---GGCTGGGAGCAGC-----CGTTGCTGGCGGTATTCTGCCTCTGCTCCTCCA----------------CCG---GCTGCTGTTGTTCC-------------------TGAACCACCTCGTCCT------------------------CTGGTTCGTCAT----------C-G---C---CTT
droAna3 scaffold_13117:2651271-2651404 - CAGCATTAGGGCGATCCTCCGCCAGTGGTTGATCGAAG---GCATGGGATCCAC-----CCC----AGCGTCTATCTGAAAACGATGTTTAT----------------CCA---CCTGCTCCTGCTCC-------------------TGCTCCTCATCCTCCT------------------------TCCCTTCGTCTT----------C-G---TCATCAT
dp4 chr3:14693225-14693346 - CATGTTCAGATCCGA--TCCAAATGTGGGGGAC--AAG---GGCTGGGAACAGC-----CATTGCTCTGAGTGATGTGCTGCTCC-------TCCCG---CTCTCCCGTTGGCA-------------------------------------------------GTTCCTCATCCTCCTCGTCCGGGTCT-----------------------------AGTT
droPer1 super_4:2921871-2921992 + CATGTTCAGATCCGA--TCCAAATGTGGGGGAC--AAG---GGCTGGGAACAGC-----CATTGCTCTGAGTGATGTGCTGCTCC-------TCCCG---CTCTCCCGTTGGCA-------------------------------------------------GTTCCTCATCCTCCTCGTCCGGGTCT-----------------------------AGTT
droWil1 scaffold_180708:9012130-9012236 - CATGTTTAAATCTGA--ACCAAATGTGGCCGAC--AAT---GGTTGAGAGCAGC-----CATTTGTTA-----------------------------------------------------------------------------------------------GTTGTTCATCCTCTTCA-CAGGCTCC---AGCAGCTTGCTCACCCCC-C---TCAGCGT
droVir3 scaffold_12963:15905405-15905563 - CATGTTTAAATCGGA--GCCATAGGTAGCCGAC--AATGCCGGCTGCGAGCAGC-----CATTGCTTAGGGTTATCTGCGGCTTC-------TGTGGTGCCTGTTCCGTT----------------GCGTTAATCGGCTGGGAGTAGAGCTCACCGGCGGCC------------------------------TCCAGATCGCTGTCGCCT-CCTGTCGCGAT
droMoj3 scaffold_6500:3051871-3052002 + CGTGCGTAGCT---G--CTCGTGGCTGGGTGGC--GTG---GCATTGTAGAGTCTCAGCTGCTG-----------CTGCTGCTGCTGCTCAG----------------ACT---CCTGCTCTTGCTCA-------------------TGCCCCTCCAGCTCCT------------------------CCTCTTCAGCCTCGCTGT----CGC---TCAGCGG
droGri2 scaffold_15252:8305990-8306138 - CATGTTCAAATCGGA--GCCATAGGTGGCCGAC--ATG---GGTTGTGACCACT-----CATTGGCCGATGCTTGCGGTTCCTTC----TCG----------------GGT---TCCGGTTCCGCTTCGGTCGCTGGCTGGGAATAGGGTTCCTCAGCTGCAT------------------------TCGCTTCCTGAT----------C-G---CTGTCCT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:10741869-10742002 + CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGCTGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGCTGCTCTTCCGTGGGTTGCTCTTGCTCCTGACCCTCCTCTTCCTCCGCTTCATCCTCCTCCGCAT
droSim1 chr2L:10541288-10541421 + CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTTCTTTTTCGTGGGCAGCTCTCGCTCCTGACCCTCCTCTTCCTCCGCTTCGTCTTCCCCCGCAT
droSec1 super_3:6159513-6159646 + CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTGCTTTTTCGTGGGCAGCTCTCGCTCCTGACCCTCCTCTTCCTCCGCTTCGTCTTCCCCCGCAT
droYak2 chr2L:7146365-7146495 + CATGTTCAAATCGGAGCCAAAGGTGGGCGAGAGGGGCTGTGAGCAGCCGTTGCTGGCGGTGTTCTGTCTCTGCTCCTCCGCCGGCTGCTGTTGCTCCTGACCCTCCTCGTCCTCCGCGTCTTCCT---CGCCGT
droEre2 scaffold_4929:14689286-14689416 - CATGTTCAAATCGGACCCAAAGGTAGGTGAGAGGGGCTGGGAGCAGCCGTTGCTGGCGGTATTCTGCCTCTGCTCCTCCACCGGCTGCTGTTGTTCCTGAACCACCTCGTCCTCTGGTTCGTCATCGC---CTT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CATGTTTAGATCGGACCCAAAGGTGGGCGACAAGGGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTT------CTTTTTCGTGGGCAGCTCTCGCTCCTGACCCTCCTCTTCCTCCGCTTCGTCTTCCCCCGCA------TSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CATGTTCAGATCCGATCCAAATGTGGGGGACAAGGGCTGGGAACAGCCATTGCTCTGAGTGATGTGCTGCTCCTCCCGCTCTCCCGTTGGCAGTTCC------------------------TCATCCTCCTCGTCCGGGTCTAGTTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-32.5,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-31.6,  p-value=0.009901

droSim1

dG=-33.4,  p-value=0.009901 dG=-33.3,  p-value=0.009901 dG=-33.2,  p-value=0.009901 dG=-33.1,  p-value=0.009901

droSec1

dG=-33.2,  p-value=0.009901 dG=-33.1,  p-value=0.009901

droYak2

dG=-34.7,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901

droEre2

dG=-31.4,  p-value=0.009901 dG=-31.4,  p-value=0.009901 dG=-31.3,  p-value=0.009901 dG=-31.3,  p-value=0.009901 dG=-31.2,  p-value=0.009901

droAna3

dG=-11.4,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-9.9,  p-value=0.009901

dp4

dG=-23.2,  p-value=0.009901 dG=-23.1,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.3,  p-value=0.009901

droPer1

dG=-23.2,  p-value=0.009901 dG=-23.1,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.3,  p-value=0.009901

droWil1

dG=-8.4,  p-value=0.009901 dG=-7.9,  p-value=0.009901

droVir3

dG=-27.2,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droMoj3

dG=-25.2,  p-value=0.009901 dG=-25.2,  p-value=0.009901 dG=-24.4,  p-value=0.009901 dG=-24.3,  p-value=0.009901 dG=-24.3,  p-value=0.009901

droGri2

dG=-30.6,  p-value=0.009901 dG=-30.4,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.6,  p-value=0.009901

Generated: 03/07/2013 at 06:16 PM