Secondary structure and small RNA-seq evidence for dme-mir-4947

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:24834459-24834589 - TAAAGTAATAATATGAAAGCGACCCACCCAT--TC------------------------------------------------CCCTTCCGCCCATATTTATCCTT------------------------CGTCTACTGTTTCATCG----CAGGATTTAAGTGGGCGGAGCACGGAAT-----------TCGGGGGCGTGGCGC-----A--CTGGGTAGCGGGTA
droSim1 chr3R:24520998-24521128 - TAAAGTAATAATATGAAAGCGACCCACCCAT--TC------------------------------------------------GCCGCCCGCCCACTTTTATCCTT------------------------CGTCTACTGTTTCATCG----CAGGATTTAAGGGGGCGGAGCACGGAAT-----------TCGGGGGCGTGGCGC-----A--CTGGGTAGCGGGTA
droSec1 super_4:3696490-3696620 - TAAAGTAATAATATGAAAGCGACCCACCCAT--TC------------------------------------------------GCCGCCCGCCCACTTTTATCCTT------------------------CGTCTACTGTTTCATCG----CAGGATTTAAGGGGGCGGAGCACGGAAT-----------TCGGGGGCGTGGCGC-----A--CTGGGTAGCGGGTA
droYak2 chr3R:21664594-21664723 + TAAAGTAATAATATGAAAGCGACCGGCCCAC--C-------------------------------------------------CCTCGCCGCCCACTTTTATCCTT------------------------CGTCTACTGTTTCATCG----CAGGATTTAAGTGGGCGGAGCACGGAAT-----------TCGGGGGCGTGGCAC-----A--GTGGGTAGTGGGTA
droEre2 scaffold_4820:3199292-3199428 + TAAAGTAATAATATGAAAGCGACCGGCCCAC--C-------------------------------------------------CCTTTCCGCCCACTTTTATCCTT------------------------CGTCTACTGTTTCATCG----CAGGATTTAAGGGGGCGTAGCACGGAAT-----------TCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA
droAna3 scaffold_13340:19733656-19733776 + TAAAGTAATAATATAAAAGCGACCAGCCCCT--AC---------------TTCTACTCCACCCAACCA-------------------GCCTCCCGATCCTGGGCAG------------------------CGTTGGTTGTTTCAGAG----G--------------CGGCTTGAGGAAC-----------TCGGGGGCGTGCCGC-----T------------CCTA
dp4 chr3:722533-722667 - TAAAGAGATAATGACAAAGCAACCCATTAAAAGCCATCCCTTGACAACACTCCTCTCTCATCCC-------------------------------------------------------------------CTTCATATTCCCATCT----CCGAA---AAATGAGCGAAGAACGGAGA-----------GCAACGTTTTAATAA-----A--TTTGTAAACAGATT
droPer1 super_26:1114277-1114391 - GACGGTGGCCTTCC-------ACTTCCTCTT--CC------------------GCCGCCACCACACCCCCTTCCCACTGCCAA---------GC------A---CG------------------------CTCTTTTTATCGCAATT----G-------TTGTCGG-------CGGA------------------TTTTCGGCTT-----A--CATGCGAGGAGCTA
droWil1 scaffold_181096:10088805-10088934 + CAAAATGTCCTTGATG-----ACTGGC-------A-------------------------TTCACACACACACA---------CACACACACACACATTTAAACACATCCATATGTACATCCATGTATACATTTATCTAATACAGAT----G--------------CAGAGCTCGGA--------------------------AC-----T--TCAAGTATAAGGCA
droVir3 scaffold_13049:15807-15938 + TATG-TGGCAGTAGAAATTTCTCCCATAAATATAT-----------------------------GTAC---------------CCTTTCCGTCTTTATGTTTGTTT------------------------GGTTGAATGGATCGAAC----TACAAATCTAGAGATTAGAAATTGGAAA-----------TCCGTATTCTAGTA-----------ATGTATCCAGAA
droMoj3 scaffold_6500:17797597-17797712 + CACACACAC--------------ACACACAG--AC------------------------------------------------TTTGGCTACAAAATGTTAACTTG------------------------AGTTTGAAATTTTCCAG-----GGAATATGAGTGAGAGGCGAGCGAAAG-----------CAGTGAACAGAGTGA-----A--CAATGTATAAAGTA
droGri2 scaffold_14853:8203259-8203387 + CAAATTAACAACAAGAATTCTTTCCAGCTCC--CT-------------------------CTCTCTCTCTCTCTCTCTCTCTA---------AC----------TC------------------------CGTCTC-----TCATTTCCGAGAGAGAGCTAGTTACATTGCTGAGAGAGAAGTGAAGAGAGCCGAGC-----------------------TTTGTTA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:24834459-24834589 - TAAAGTAATAATATGAAAGCGACC----CACCCATTCCCCTTCCGCCCATATTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGTGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACT-------GGGTAGCGGGTA
droSim1 chr3R:24520998-24521128 - TAAAGTAATAATATGAAAGCGACC----CACCCATTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACT-------GGGTAGCGGGTA
droSec1 super_4:3696490-3696620 - TAAAGTAATAATATGAAAGCGACC----CACCCATTCGCCGCCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACT-------GGGTAGCGGGTA
droYak2 chr3R:21664594-21664723 + TAAAGTAATAATATGAAAGCGACC----GGCCCACCCCTCG-CCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGTGGGCGGAGCACGGAATTCGGGGGCGTGGCACAGT-------GGGTAGTGGGTA
droEre2 scaffold_4820:3199292-3199428 + TAAAGTAATAATATGAAAGCGACCGGCCCACCCCTT-----TCCGCCCACTTTTATCCTTCGTCTACTGTTTCATCGCAGGATTTAAGGGGGCGTAGCACGGAATTCGGGGGCGTGGCACAGTGGCTAGTGGATAGTGGGTA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TAAAGTAATAATATGAAAGCGACCCACCCAT--TCGCCGCCCGCCCACTTTTATCCTTCGTCT-----ACTGTTTCATCGCAGGATTTAAGGGGGCGGAGCACGGAATTCGGGGGCGTGGCGCACTGGGTAGCGGGTASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TAAAGAGATAATGACAAAGCAACCCATTAAAAGCCATCCCTTGACAACACTCCTCTCTCATCCCCTTCATATTCCCATCTCCGAA---AAATGAGCGAAGAACGGAGAGCAACGTTTTAATAAATTTGTAAACAGATTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-42.3 -41.6 -41.5

droSim1

-42.2 -41.4

droSec1

-42.2 -41.4

droYak2

-44.2

droEre2

-34.3 -34.0 -33.5 -33.4 -33.3

droAna3

-37.5 -37.3 -37.3 -37.1 -36.9 -36.8

dp4

-9.8 -9.8 -9.7 -9.5 -9.5 -9.4

droPer1

-15.5

droWil1

-6.7 -6.5 -6.3 -6.0 -6.0 -5.9

droVir3

-16.8 -16.8 -16.8 -16.8 -16.8 -16.4

droMoj3

-12.0 -12.0 -11.9 -11.9 -11.9 -11.9

droGri2

-38.0 -37.9 -37.8 -37.8 -37.7 -37.1

Generated: 01/05/2013 at 05:22 PM