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

-31.6 -31.2 -30.8

droSim1

-32.6 -32.2 -31.8 -31.7 -31.7 -31.7

droSec1

-30.6 -30.5 -30.5 -30.4 -30.3 -30.2

droYak2

-28.3 -27.7 -27.5 -27.3 -27.3

droEre2

-39.9 -39.5 -39.4 -39.3 -39.3 -39.1

droAna3

-20.4 -19.8

dp4

-28.8 -28.8 -28.6 -28.6 -28.0 -28.0

droPer1

-26.8 -26.2 -26.0 -26.0 -25.9 -25.8

droWil1

-9.2 -8.9 -8.4 -8.2 -8.2 -8.2

droVir3

-16.9 -16.8 -16.6 -16.6 -16.6 -16.5

droMoj3

-11.1 -10.9 -10.5 -10.4 -10.3

droGri2

-12.0 -11.3 -11.2

Generated: 01/05/2013 at 05:21 PM