Secondary structure and small RNA-seq evidence for dme-mir-4940

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:9137677-9137812 + CCAGACTCAGACGGACTTA----TCGCAA----CTTATCGAT------CGGGTGGCGGATATA----------GATCA-----------------TTGGTT---------------------------------------------------------------------------------------------------------------ATCCCTTAATTAAAGC--------AAACAAGATTTGTTTCGGCCGCCC--GATTTTACATACAACGAC-----------------ACGAATAGCAGG-----------------------------ATAT-AG
droSim1 chr3L:8545595-8545743 + CCTGACTCAGACGGACTTA----TCGCAG----CTTATCGAT------CGGGTGGCGGATATA----------GATCATAGCAAGCCCTATCGAATTGGTT---------------------------------------------------------------------------------------------------------------ATACCT--ATTAAAGC---------AACTAGGTTTGTTTCGGCCGCCC--GATTTTACATACAACGAC-----------------ACAA-TAGCAGG-----------------------------ATAT-AG
droSec1 super_0:1396669-1396817 + CCTGACTCAGACGGACTTA----TCGCAG----CTTATCGAT------CGGGTGGCGGATATA----------GATCATAGCAACCCCTATCGAATCGGTT---------------------------------------------------------------------------------------------------------------ATACCT--ATTAATGC---------AACTAGGTTTGTTTCGGCCGCCC--GATTTAACATACAACGAC-----------------ACAA-TAGCAGG-----------------------------ATAT-AG
droYak2 chr3L:2783249-2783373 - CCAGACTCAGACGGACTA-------GCAA----CTTCGCGAT------CGGGTGGCGGCTGTA----------GATT-------------------------------------------------------------------------------------------------------------GT-----------------CCTTGT---------ATCAAAGG--------AAAAGAGATTTCTTTTGGCCACCC--GATTCAAAATACAACGAC-----------------ACAA-TAGCAGG-----------------------------ATAT-AG
droEre2 scaffold_4784:4908876-4909031 - CCTGACTCAGACGGACTA-------GCAA----CTTATCGAT------CGGGTGGCGGATATACCCGTGCACAGATTGTAGCACACCCTATCGAATTGGAA---------------------------------------------------------------------------------------------------------------TTCCCC--ATTAAAAC--------TGAGTGGGCTTATATCGGCCGCCC--GATT-CACATACAACGAC-----------------ACAA-TAGCAGG-----------------------------ATAT-AG
droAna3 scaffold_13337:19535893-19536018 + CACTGCGATCTCGAGTACT----TT-GATCTCTCTTCTCAGGGCCCC-AAAAAGTATGCTAT-------------------------------------------------------------------------------------------------------------GA-------AAT-ATTTCGTTTGC--------------------------TAAAGTG--------TTTCAAGGATTCTTTTGCGAGCCC--ACCT------------CA-----------------AGGA-TGTCAAA-----------------------------CTCT-AG
dp4 chrXR_group5:393309-393508 - C-AGACTTAGACGGACTTCAATCTAGCAG----TTTAACGAT------CGGGAAACGGGAATA----------AACCAAAGT---------------------------------------------------CGGCAGCCTATCCATCAAAATTCCAATATAATCACAACAGAAA-----TC-CAATTTGTTGC----------------------------------------------TGGTTTATTTACGTTTCTC--GAGC-CACATACAACGAC-----------------ACAA-CAGCAGGTCTTCAGATAACTCATATGAAATATACTTATGC-GG
droPer1 super_9:3484001-3484112 - GCATACATAGGCATCGCA----------T----CC---------------------------------------------------------------------------------------------------------------ATCGGGGTCAC---------CCGGTGGAGGATAAA-TTTTGC-----------------GGTGGTAACCCCGCAACACAAGC--------A--------------------------CTCACACACACAGCGAC-----------------CCAA-ACACGTG-----------------------------CAATAAC
droWil1 scaffold_181096:6035694-6035827 - TCAGGCCTAAAATTAGTTG----CCATAA----CT-CTCATT------TATATAGTAGATTTG----------ATGCTTTTT-----------------------------------------------TGTT----------------------------------------------------------TTTT---------------------------TAATAT---------ATTAAAATTTTTATTA-------------ATGCATTTCA--GTGTAAAAATTAAAATGACACATTTTTCCTT-----------------------------ACGT-AA
droVir3 scaffold_13246:101577-101715 - CAGG---CAGACGAAAGTA----TCTC-----------CGAC--CC--CATGAAGTGTATATA------------TTC-----------------TTGATCAGCATCAATAGCTGAGTCGATGTAGCCATGTCCGTCTGCC----------------------------------------------------------------------------------------------------------TGTCCGTCCGTCC--GTCCGTATGTATGA--ACGCA--------------AGGA-TCTCAGA-----------------------------ACCT-TT
droMoj3 scaffold_6540:2381798-2381917 - GTAGATTCAGTTGTACTTT----ATAGAA----TT--TCGAT-----TTA---------------------------------------------------------------------------------------------------------------------TGTTAA-------AAT-TCATCCCTTAC---------------------------CAATAT---------ATATGTGTT-TTTTCAAATGCATGCATTT-TAATGGTATCAAC-----------------ACAATTTGAAAG-----------------------------TCTC-AT
droGri2 scaffold_15074:3698733-3698860 + CTGAACATAACTGAATAAA----TT--------------------------------------------------------------------------------------------------------------------------------------------CACAACAT-------ATT-TAGTCAGTTACTTATGTATATACT----------TGATACAATTGTGCAAACATGCAAAATTCCAATTAAATGTCA--CAATATATAAAAACTG----------------------A-TGCGAGA-----------------------------AGAT-TG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:9137677-9137812 + CCAGACTCAGACGGACTTATCGCAACTTATCGATCGGGTGGCGGATATAGATCA-----------------TTGGTTATCCCTTAATTAAAGCAAACAAGATTTGTTTCGGCCGCCCGATTTTACATACAACGACACGAATAGCAGGATATAG
droSim1 chr3L:8545595-8545743 + CCTGACTCAGACGGACTTATCGCAGCTTATCGATCGGGTGGCGGATATAGATCATAGCAAGCCCTATCGAATTGGTTATACCT--ATTAAAGCA-ACTAGGTTTGTTTCGGCCGCCCGATTTTACATACAACGACAC-AATAGCAGGATATAG
droSec1 super_0:1396669-1396817 + CCTGACTCAGACGGACTTATCGCAGCTTATCGATCGGGTGGCGGATATAGATCATAGCAACCCCTATCGAATCGGTTATACCT--ATTAATGCA-ACTAGGTTTGTTTCGGCCGCCCGATTTAACATACAACGACAC-AATAGCAGGATATAG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CCTGACTCAGACGGACTT--A--TCGCAGCTTATCGATCGGGTGGCGGATATAGATCATAGCAAGCCCTATCGAATTGGTTATACCT--ATTAAAGCA-ACTAGGTTTGTTTCGGCCGC------------------------------------------------------------------CCGATTTTACATACAACGACAC-AATAGCAGG-----------------------------ATATAGSizeHit CountTotal NormTotalGSM343915
Embryo
................................................................................................CA-ACTAGGTTTGTTTCGGCCGC------------------------------------------------------------------C..................................................................2311.0011
dp4
C-AGACTTAGACGGACTTCAATCTAGCAGTTTAACGATCGGGAAACGGGAATAAACCAAAGT--------------------------------------------------CGGCAGCCTATCCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGCTGGTTTATTTACGTTTCTCGAG-CCACATACAACGACAC-AACAGCAGGTCTTCAGATAACTCATATGAAATATACTTATGCGGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-28.2,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.2,  p-value=0.009901

droSim1

dG=-29.2,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droSec1

dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.9,  p-value=0.009901

droYak2

dG=-24.5,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-22.9,  p-value=0.009901

droEre2

dG=-36.9,  p-value=0.009901 dG=-36.5,  p-value=0.009901 dG=-36.4,  p-value=0.009901 dG=-36.3,  p-value=0.009901 dG=-36.3,  p-value=0.009901 dG=-31.2,  p-value=0.009901

droAna3

dG=-15.8,  p-value=0.009901

dp4

dG=-28.4,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-26.79,  p-value=0.009901

droPer1

dG=-20.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-17.8,  p-value=0.009901

droWil1

dG=-1.5,  p-value=0.009901 dG=-1.4,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-1.1,  p-value=0.009901

droVir3

dG=-11.5,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.8,  p-value=0.009901

droMoj3

dG=-4.4,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.6,  p-value=0.009901 dG=-3.4,  p-value=0.009901

droGri2

dG=-7.6,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-6.7,  p-value=0.009901

Generated: 03/07/2013 at 05:37 PM