Secondary structure and small RNA-seq evidence for dme-mir-4943

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:16528359-16528506 - ATTTTAAACAACTA-TTTCGG-------ATCGTTTG---------------AATGACCAATTTTGT-------------CTTTTATTTTCTCT--G--------------T-G-----TTTT-----CAGTTAATG-AAAGAT-AG-TGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droSim1 chr2L_random:601476-601603 - ATTT------------------------ATTT-TTG---------------AATGACCAATTTTGT-------------CTT---TCTTCTCT--G--------------T-C-----GTTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droSec1 super_7:174891-175018 - ATTT------------------------ATTT-TTG---------------AATGACCAATTTTGT-------------CTT---TCTTCTCT--T--------------T-C-----TTTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droYak2 chr2R:4574442-4574584 + ATTTTATAAAACTA-TGGGGG-------ATAC-TTA---------------GATAATTAATTTTGT-------------CAT---TGTTCTTT--G--------------T-C------TTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droEre2 scaffold_4845:19592406-19592554 - ATTTTATGCAACTA-TTGTGT-----GTATCT-TTA---------------AATGACTAATTTTGT-------------CAT---TCTTCTCT--G------TTT-----T-T-----TTTT-----CAGTTAATG-AATAGT-AG-CAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droAna3 scaffold_12916:16031637-16031788 + ATGTT------------------------TAA-ATG---------------ATTAAAAAATTATGTTCAACTAATTATTAA-------TTTAT--A------TTTT-ATTGTCTTCCCATTA-----CAGTTAATGAAAAAGT-AATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCCC---------AAGAAGACCATGTTGATTG
dp4 chr4_group3:8251613-8251715 - TT-----------------------------------------------------------------------------------TGTTCCTTTTC--------------T-C-----TTTA-----CAGTTATTTGCCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAA---------CAGAAGACGATGTTGATTG
droPer1 super_1:9700572-9700674 - TT-----------------------------------------------------------------------------------TGTTCCTTTTC--------------T-C-----TTCA-----CAGTTATTTGCCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAA---------CAGAAGACGATGTTGATTG
droWil1 scaffold_180772:4810613-4810759 - AAGTTTACCAATTAATAGCAA-------ATTG-TTGGTATTTCCATTTTAAAATTGCTAACATTTA---------CCTTAA-------TTTCT--C------TTCT-TTTC-T-----TTTT-----CAAT---------TCC-AG-CTTACGTTGCTATAAATGAGAAAGGATCAA------------GATCAA---------ACGAAAAGGATGTTGATTG
droVir3 scaffold_13052:1601321-1601473 - ATATTGCGCAACCA-TTCTGGTCCGAATTTCA-TTG---------------AGTCAGTCATTTTGG----GTAACTCTT------------GA--GTTTATTTCTTAATTGTC------TTTCGCTGAAATTGTGCAATAAAT-AA-CA---ATTT---------------TACCATCAGCATTAGCCAGCACAC---------ACACGCACGCTATCGGTTT
droMoj3 scaffold_6500:21042727-21042874 - AATTA------------------------TAA-TTG---------------AACACTTGA-TGCGATTGCCAAATTTTTGAT---TTTTGGTTCTA--------------T-T-----TTTA-----GAGTTACAG-CTAAAT-GA-AA---ACTATACCAATTATAAAATCAAAAGGGCTACACAAGAACATTTATGATTTCAAAGAAAAGTGTTTCATTTG
droGri2 scaffold_14822:853797-853916 - GCATG-----------------------------------------------ATGACTTGTGGTCT-------------CTA---TTCTATAT--G--------------C-T-----GGTT-----GAGTTTGTG-AATGGTCAG-TTGCCGTGGCGAAAGATAAAAGACAAG--GAACAGGTTGGATTGACCA---------AAGAGAAATATGATCATAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:16528359-16528506 - ATTTTAAACAACTATTTCGGATCGTTTGAATGACCAATTTTGTCTTTTATTTTCTCTGTGTTTTCAGTTAATGAAAGATAGTGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATTT---------ATT--------TTTGAATGACCAATTTTGTCTT---TCTTCTCTGTCGTTTCAGTTAAT-GAAAAGTAGTAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTT--------------------------------------GTTCC---TTTTCTCT----TTACAGTTATTTGCCAAGCAG-AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAACAGAAGACGATGTTGATTGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.............................................................................................................GAGACACAGTCGACAGAC......................1811.00110

Secondary Structure

dm3

dG=-19.5,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droSim1

dG=-10.8,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.0,  p-value=0.009901

droSec1

dG=-13.4,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-10.9,  p-value=0.009901

droYak2

dG=-8.1,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-7.2,  p-value=0.009901

droEre2

dG=-10.2,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.5,  p-value=0.009901 dG=-9.3,  p-value=0.009901 dG=-8.7,  p-value=0.009901

droAna3

dG=-3.7,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-3.3,  p-value=0.009901

dp4

dG=-8.8,  p-value=0.009901 dG=-8.7,  p-value=0.009901 dG=-8.4,  p-value=0.009901 dG=-8.4,  p-value=0.009901 dG=-8.3,  p-value=0.009901

droPer1

dG=-8.8,  p-value=0.009901 dG=-8.8,  p-value=0.009901 dG=-8.7,  p-value=0.009901 dG=-8.5,  p-value=0.009901 dG=-8.2,  p-value=0.009901

droWil1

dG=-11.2,  p-value=0.009901 dG=-10.8,  p-value=0.009901

droVir3

dG=-8.5,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901

droMoj3

dG=-9.8,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-9.5,  p-value=0.009901 dG=-9.5,  p-value=0.009901 dG=-9.4,  p-value=0.009901

droGri2

dG=-12.7,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-9.3,  p-value=0.009901

Generated: 03/07/2013 at 05:39 PM