Secondary structure and small RNA-seq evidence for dme-mir-307b

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:5508724-5508873 + TT--------CACTGGTGCCAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droSim1 chr2R:4140592-4140741 + TT--------CACTGGTGCCAGTTAGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droSec1 super_1:3126024-3126173 + TA--------CACTGGTGCCAGTTAGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droYak2 chr2L:18140614-18140763 + CT--------CACTGGTGCCAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droEre2 scaffold_4929:8848853-8848999 - TA--------TTTTG----TAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGCTTCACTT
droAna3 scaffold_13266:12795452-12795608 + TTAA------CATT----CTAGTTAGTCTTGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAAGGCTGC--TAACTTTC----------------GTTTCGGAT--TGGGGTTCACTG
dp4 chr3:14135673-14135829 + TA--------TTCTTTTGTCCG---GCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCGACCCGAACTTTTTCTCAGTTTTCA-----------------GTTTTCACT-
droPer1 super_4:1183038-1183202 - TGAATCACTATTCTGTTGTCCG---GCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCGACCCGAACTTTTTCTCAGTTTTCA-----------------GTTTTCACT-
droWil1 scaffold_180701:3433631-3433773 + GTAATAAAT---C---TTTCATTGAACTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATTATAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGGCAAAAT-GT-GT--TAAG----------------------------------TTCTATAA-
droVir3 scaffold_12875:5789437-5789575 + ---------------------GTTGGCTTAGTGGATACTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATCG-AACTAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GTT----------------------CGGTTTATTTT---GTCACTTTTGCACT-
droMoj3 scaffold_6496:24271651-24271794 - TC--------TATTGGT-----TTAGCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCGAATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-TCT----TAGTTTT-----------CT--------T---G--TTGTTTTTATT-
droGri2 scaffold_15112:722926-723081 + TC--------GCCTGTCGCCTGTTTTC-TTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GTT---------------TAGTTCTT---TTATTTTTATT--TAATTTTTTCT-

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:5508724-5508873 + TT--------CACTGGTGCCAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droSim1 chr2R:4140592-4140741 + TT--------CACTGGTGCCAGTTAGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droSec1 super_1:3126024-3126173 + TA--------CACTGGTGCCAGTTAGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droYak2 chr2L:18140614-18140763 + CT--------CACTGGTGCCAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGTTTCACT-
droEre2 scaffold_4929:8848853-8848999 - TA--------TTTTG----TAGTTAGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCTGC--TAACTTTGCA-------------------------TCGGCTTCACTT
droAna3 scaffold_13266:12795452-12795608 + TTAA------CATT----CTAGTTAGTCTTGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAAGGCTGC--TAACTTTC----------------GTTTCGGAT--TGGGGTTCACTG
dp4 chr3:14135673-14135829 + TA--------TTCTTTTGTCCG---GCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCGACCCGAACTTTTTCTCAGTTTTCA-----------------GTTTTCACT-
droPer1 super_4:1183038-1183202 - TGAATCACTATTCTGTTGTCCG---GCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GCGACCCGAACTTTTTCTCAGTTTTCA-----------------GTTTTCACT-
droWil1 scaffold_180701:3433631-3433773 + GTAATAAAT---C---TTTCATTGAACTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATTATAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGGCAAAAT-GT-GT--TAAG----------------------------------TTCTATAA-
droVir3 scaffold_12875:5789437-5789575 + ---------------------GTTGGCTTAGTGGATACTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATCG-AACTAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GTT----------------------CGGTTTATTTT---GTCACTTTTGCACT-
droMoj3 scaffold_6496:24271651-24271794 - TC--------TATTGGT-----TTAGCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCGAATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-TCT----TAGTTTT-----------CT--------T---G--TTGTTTTTATT-
droGri2 scaffold_15112:722926-723081 + TC--------GCCTGTCGCCTGTTTTC-TTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATCG-AAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAAT-GTT---------------TAGTTCTT---TTATTTTTATT--TAATTTTTTCT-

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTCACTGGTGCCAGTTAGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCGAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAATGCTGC--TAACTTTGCATCGGT--------TTCACTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATTCTTTTGTCCG---GCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATCGAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAGACAAAATGCGACCCGAACTTTTTCTCAGTTTTCAGTTTTCACTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-26.8,  p-value=0.009901

droSim1

dG=-26.8,  p-value=0.009901

droSec1

dG=-26.8,  p-value=0.009901

droYak2

dG=-26.8,  p-value=0.009901

droEre2

dG=-26.8,  p-value=0.009901

droAna3

dG=-26.8,  p-value=0.009901

dp4

dG=-26.8,  p-value=0.009901

droPer1

dG=-26.8,  p-value=0.009901

droWil1

dG=-26.7,  p-value=0.009901

droVir3

dG=-26.8,  p-value=0.009901

droMoj3

dG=-26.8,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-25.8,  p-value=0.009901

droGri2

dG=-26.8,  p-value=0.009901

Generated: 03/07/2013 at 05:12 PM