Secondary structure and small RNA-seq evidence for dme-mir-2489

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:13609973-13610070 + AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACGT-------AAGTTCTAATG-----TATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droSim1 chr2L:13379253-13379350 + AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droSec1 super_16:1746050-1746147 + AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droYak2 chr2L:10029706-10029801 + AGCAATAAGTTAGATGTGAGTATG------GCTATTTAAAT---------CAACC-GAAC--GT-ATGT-------ATGTTATATAG-----T-----TTG---CATT-----TTGTATTTGCAGTTTTATGATAGCAAA
droEre2 scaffold_4929:11847836-11847927 - AGCAATAAGTTAGACGTGAGTATG------GCTATCTAAAT---------CAGCC--------GAACGT-------GTATTCTAATG-----TTTG--------CACT-----TTGTATTTGCAGTTTTATGATAGCAAA
droAna3 scaffold_12943:1669999-1670103 + AGCGATAAGTTAGACGTGAGTATT-----GTCTCTGTCAAG---------TGTAT-------GGTACTAATATTTA----ACTAATT-----CTTGTATTAACTTGTT-----TTTAATTTCCAGTTTTATGATAGCAAT
dp4 chr4_group1:1879331-1879430 - AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCTTT-----TTAAAACAA-------TCATTTTCATA-----TACATATAT---ATTT-----TTGTGTGTTTAGTTTTATGATAGCAAC
droPer1 super_5:3326174-3326277 + AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCTTT-----TTAAAATAT----TTTATATTTTTATATATTACATATATTT------------TTTGGTGTTTAGTTTTATGATAGCAAC
droWil1 scaffold_180772:852551-852648 - AGCGATAAGTTAGATGTGAGTATA------T-TATATCTTTTGTCCCATT----------TTGGAATAT-------GTTTTTGAATA-----CCTT--------TTCT-----TTGGGATTTCAGTTTTATGATAGCAAC
droVir3 scaffold_12723:5236355-5236448 - AGTGATAAGTTAGACGTGAGTATT------ATCAACATATATGAATTATT----------T-TAAAATA-------ATAATC-------------GAAT-T---TAAT-----TTGTTATCCCAGTTTTATGATAGCAAC
droMoj3 scaffold_6500:16444108-16444197 + AGTGATAAGTTAGACGTGAGTATTACAGAGGCCCTATCAA------------------------AAT-A-------TC------ATT-----CGTGTATCT---AATATAATAT----TTTTCAGTTTTATGATAACAAC
droGri2 scaffold_15126:8263493-8263587 - AGTGATAAGTTAGACGTGAGTATTT-----ATTAAC--------------TTCATTCAAC--GTAATAT-------ACATACTAAAA-----TATGAA--------TACATCAT----TTTGCAGTCTTATGATAGCAAC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:13609973-13610070 + AGCAATAAGTTAGACGTGAGTATGGCTATACAAATCATCTGGAACGTAAGTTCTAATGTATGTATTGTATGTTGTATTTGCAGTTTTATGATAGCAAA
droSim1 chr2L:13379253-13379350 + AGCAATAAGTTAGACGTGAGTATGGCTATACAAATCATCTGGAACATACGTTCTAATGCATGTATTGTATGTTGTATTTGCAGTTTTATGATAGCAAA
droSec1 super_16:1746050-1746147 + AGCAATAAGTTAGACGTGAGTATGGCTATACAAATCATCTGGAACATACGTTCTAATGCATGTATTGTATGTTGTATTTGCAGTTTTATGATAGCAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AGCAATAAGTTAGACGTGAGTATGGCTATACAAATCAT--CTGGAACATACGTTCTAATGCATGTATTGTATGTTGTATTTGCAGTTTTATGATAGCAAASizeHit CountTotal NormTotalGSM343915
Embryo
................................................................TATTGTATGTTGTATTTGCAGT..............22111.001111
................................................................TATTGTATGTTGTATTTGCAG...............2115.0055
................................................................TATTGTATGTTGTATTTGCA................2011.0011
dp4
AGCGATAAGTTAGACGTGAGTATATCTTTGCCATCTCTTTTTAAAACAATCATTTTCATATACATATATATTTTTGTGTGTTTAGTTTTATGATAGCAACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-19.5,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.7,  p-value=0.009901

droSim1

dG=-18.7,  p-value=0.009901 dG=-18.2,  p-value=0.009901

droSec1

dG=-18.7,  p-value=0.009901 dG=-18.2,  p-value=0.009901

droYak2

dG=-7.0,  p-value=0.009901 dG=-6.7,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.3,  p-value=0.009901 dG=-6.3,  p-value=0.009901

droEre2

dG=-9.9,  p-value=0.009901 dG=-9.7,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-9.2,  p-value=0.009901 dG=-7.9,  p-value=0.009901

droAna3

dG=-7.5,  p-value=0.009901 dG=-7.0,  p-value=0.009901 dG=-6.1,  p-value=0.009901

dp4

dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-5.3,  p-value=0.009901

droPer1

dG=-4.1,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.6,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-2.6,  p-value=0.009901

droWil1

dG=-8.3,  p-value=0.009901 dG=-8.2,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.8,  p-value=0.009901

droVir3

dG=-2.7,  p-value=0.009901 dG=-2.6,  p-value=0.009901 dG=-2.5,  p-value=0.009901 dG=-2.3,  p-value=0.009901 dG=-2.1,  p-value=0.009901

droMoj3

dG=-1.5,  p-value=0.009901 dG=-1.0,  p-value=0.009901 dG=-1.0,  p-value=0.009901 dG=-0.9,  p-value=0.009901 dG=-0.8,  p-value=0.009901

droGri2

dG=-6.3,  p-value=0.009901

Generated: 03/07/2013 at 04:55 PM