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

-19.5 -19.0 -18.7

droSim1

-18.7 -18.2

droSec1

-18.7 -18.2

droYak2

-7.0 -6.7 -6.5 -6.3 -6.3 -6.2

droEre2

-9.9 -9.7 -9.6 -9.4 -9.2 -9.2

droAna3

-7.5 -7.0

dp4

-7.6 -7.5 -7.4

droPer1

-4.1 -4.0 -3.7 -3.6 -3.4 -3.3

droWil1

-8.3 -8.2 -7.8 -7.8 -7.8 -7.7

droVir3

-2.7 -2.6 -2.5 -2.3 -2.1 -2.0

droMoj3

-1.5 -1.0 -1.0 -0.9 -0.8 -0.8

droGri2

-6.3

Generated: 01/05/2013 at 05:09 PM