Secondary structure and small RNA-seq evidence for dme-mir-3645

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:5516298-5516464 - AAACAAATCGATATGGTGAGTGC---AG-GC----------------TGTTTAT----------TGCGGCGCTGTTTACTGTTTACGATC------GCACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAG-----------------------------------------CACTCAAGTTTCCTTCATTGTTTTCCTTTCTTTCCCCTCTCTCTCTC------C---CCGCAGGCAGCTTATACCGAG
droSim1 chrX:4275639-4275796 - AAACAAATAGAAATGGTGAGTGC---AG-GC----------------TGTTTAT----------TGCGGCGCTGTTTACTGTTTACGATC------G---------TGCGCTATTCGGCGCCTTTGGAAGCCAG-----------------------------------------CACTCAAGTTTCCCTCATTGTTTTCCTTTCTTCCCCCCCTCTCTCTC------C---CCGCAGGCAGCTTACACCGAG
droSec1 super_4:1240682-1240837 + AAACAAATAGAAATGGTGAGTGC---AG-GC----------------TGTTTAT----------TGCGGCGCTGTTTACTGTTTACGATC------G---------TGCGCTATTCGGCGCCTTTGGAAGCCAG-----------------------------------------CACTCAAGTTTCCCTCATTGTTTTCCTTTCTTTCC-CCCTCTCTCA-------C---CCGCAGGCAGCATACACCGAG
droYak2 chrX:2953226-2953406 + AAACAAATCGATATGGTGAGTGC---AG-GC----------------TGTTTAT----------TGCGATGCTGTTTACTGTTTACAACCGCTTTCGCACTGGAAGT-CGGTTTTCGGCGCCTTGGAAAACCAA-----------------------------------------CACTCAAGTTTCCTTCTTTGTTTTCCTTTTCTCTCCCTCTCTCTCTTTCTCTCTCTGTCGCAGGCCGCTTACACCGAG
droEre2 scaffold_4690:2867616-2867787 - AAACAAATCGATATGGTGAGTGC---AG-GC----------------TGTTTAT----------TGCGGCGCTGTTTACTGTTTACGGTC------GCACCGCAAGT-CGCTTTTCGGCGCCTTGGAAAACCAA-----------------------------------------CACTCAAGTTTCCCTCTTTGTTTTCCTTTCTTCTCCCTCTCTCTCTCACTCTCT---TCGCAGGCAGCTTACACCGAG
droAna3 scaffold_13117:2022234-2022400 + AAACAAATCGATATGGTAAGTGCGTGAA-GTAGGCAACATGACACTTTGTATAT----------TTGACAACAATTGAATGTTTACGGG--------------ACCTC--CTATTTCCCGC-TTCGGCAGCAACGA-TG-----------ACGACGAC-----------------GACTCATGTTTTCCT--TTGTTTTGTTGTT---------------------------TTTCAGGCAGCTTACACCGAG
dp4 chrXL_group1a:8129365-8129509 - CAACAAATCGATATGGTAAGTGGGCTGA-AC----------------AGTA-AT------------TGATATCGTGGCCAATATATAGCCGCT-ACGTATCGTATG---------------------------------------------GCTTTTCCACTGAGTTTTGCTGGGAGCTAATGTGTTCTT--TTGTT--TGG-T------------------------T---TTACAGGCAGCTTACACCGAG
droPer1 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12928:4987995-4988105 + T---CAATCAATATGGTAAGTTGGCCAAAAT----------------TGTT-GTTGCT------TTT------------ACGACACGTACATT-GTTTAT--------------------------AGTGTGTTTATTCTTGCTACTTT--------------------------------------------------TGC-A------------------------T---TTACAGGCAGCTTACACCGAG
droMoj3 scaffold_6359:3485302-3485418 + -------TCAATATGGTAAGTTGGC-ACAGC----------------TGTT----------------------------------------------------------GCTATT-----TTTTAGAGAGCAAATA-ATATGTTTCGTTTGTTTTTACAATTG----------------------------------------TTGTCTTTTTCTCTTGTTA------T---TTACAGGCAGCATACACCGAG
droGri2 scaffold_14853:9687493-9687620 + CATTAAATCAACATGGTAAGTTGTATAA-AT----------------CTATTTTTGCAGCTATCTGCAGCATTGTGTGCACTATATACACATT-AAT----------------------------GAGTGTAATAA-TTTTGTTGTTTT--------------------------------------------------TGT-T------------------------T---TTACAGGCAGCTTACACCGAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:5516298-5516464 - AAACAAATCGATATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCGCACTGGAAGTGCGCTTTCCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCTTCATTGTTTTCCTTTCTTTCCCCTCTCTCTCTCCCCGCAGGCAGCTTATACCGAG
droSim1 chrX:4275639-4275796 - AAACAAATAGAAATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTCCTTTCTTCCCCCCCTCTCTCTCCCCGCAGGCAGCTTACACCGAG
droSec1 super_4:1240682-1240837 + AAACAAATAGAAATGGTGAGTGCAGGCTGTTTATTGCGGCGCTGTTTACTGTTTACGATCG---------TGCGCTATTCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTCCTTTCTTTCCCC-CTCTCTCAC-CCGCAGGCAGCATACACCGAG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAACAAATAGAAATGGTGAGTGCAGGCTGTTT----------ATTGCGGC------------GCTGTTTACTGTTTACG-ATCG---------TGCGCTAT----TCGGCGCCTTTGGAAGCCAGCACTCAAGTTTCCCTCATTGTTTTCCTTTCTTCCCCCCCTCTCTCTCCCCGCAGGCAGCTTACACCGAGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CAACAAATCGATATGGTAAGTG--GGCTGAACAGTAATTGATATCGTGGCCAATATATAGCCGCT-----------ACGTATCGTAT-------GGCTTTTCCACTGAGTTTTGCTGGGAGCTAAT------------------GTGTTCTT-----------TTGTTTGGTTTTACAGGCAGCTTACACCGAGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-36.0,  p-value=0.009901 dG=-35.4,  p-value=0.009901 dG=-35.2,  p-value=0.009901 dG=-35.1,  p-value=0.009901 dG=-35.0,  p-value=0.009901

droSim1

dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.0,  p-value=0.009901

droSec1

dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.0,  p-value=0.009901

droYak2

dG=-27.2,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-24.7,  p-value=0.009901

droEre2

dG=-29.2,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droAna3

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-17.5,  p-value=0.009901

dp4

dG=-22.7,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.0,  p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

dG=-11.8,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-9.4,  p-value=0.009901

droMoj3

dG=-11.3,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.7,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-6.1,  p-value=0.009901

droGri2

dG=-17.4,  p-value=0.009901 dG=-17.4,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-11.0,  p-value=0.009901

Generated: 03/07/2013 at 05:33 PM