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

-36.0 -35.4 -35.2 -35.1 -35.0 -35.0

droSim1

-33.1 -33.1 -33.0 -32.6 -32.1 -32.1

droSec1

-33.1 -33.1 -33.0 -32.6 -32.1 -32.1

droYak2

-27.2 -26.5 -26.2 -26.2

droEre2

-31.1 -30.6 -30.5 -30.3 -30.2 -30.1

droAna3

-27.7 -27.4 -27.3 -27.2 -27.2 -27.0

dp4

-26.0 -25.9 -25.9 -25.8 -25.7 -25.6

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

-11.3 -10.7

droMoj3

-12.7 -12.7 -12.6 -12.6 -12.5 -12.5

droGri2

-16.5 -16.4 -16.4 -16.3 -16.3 -16.3

Generated: 01/05/2013 at 05:19 PM