Secondary structure and small RNA-seq evidence for dme-mir-303

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:4260197-4260296 - AAAACC-AAATTGATATCTTGGTTTAGGTTTCAC-AGGAAACTGGTTTAATAACGAAAA----------CTAGTTTCCTCTAAAATCCTAATCAAGACATCATGTGTCGTCG
droSim1 chrX:3275244-3275342 - AAAACC-AATGTGATCTCTTGCTTTGGCATT-AA-AGGAAGCTAGTTTAATTACGAAAA----------CTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG
droSec1 super_4:2464323-2464421 + AAAACC-AATGTGATCTCTTGCTTTGGCTTT-AA-AGGAATCTAGTTTGATTACGAAAA----------CTAGTTTCCTCTAAGGTTTTAAACATTACATCATGTGTCGTCG
droYak2 chrX:4177737-4177835 + GAACTCAAATAATCTGCCTTGCTTAGAATTTTAA-GAGCAAAAAGTTTGTTTACAAAAA----------CTATTTACCCCTAAAATTCTAATCTAGTCAGCATTAT--TTCG
droEre2 scaffold_4690:1630987-1631073 - GAACCA-AAAAATGTGCTTTGTTTAGAATTTTAGCGAGGAATCATTACAAATATGGATGTGAACTTAAAGTACTCACTGCAAG------------------------AAACG
droAna3 Unknown ----------------------------------------------------------------------------------------------------------------
dp4 Unknown ----------------------------------------------------------------------------------------------------------------
droPer1 Unknown ----------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181150:2098814-2098829 + AAA------------------------------------------------------------------------------------------------TCATTCGTCAACT
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------
droMoj3 Unknown ----------------------------------------------------------------------------------------------------------------
droGri2 Unknown ----------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:4260197-4260296 - AAAACCAAATTGATAT--CTTGGTTTAGGTTTCACAGGAAACTGGTTTAATAACGAAAACTAGTTTCCTCTAAAATCCTAATCAAGACATCATGTGTCGTCG
droSim1 chrX:3275244-3275342 - AAAACCAATGTGATCT--CTTGCTTTGGCATT-AAAGGAAGCTAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG
droSec1 super_4:2464323-2464421 + AAAACCAATGTGATCT--CTTGCTTTGGCTTT-AAAGGAATCTAGTTTGATTACGAAAACTAGTTTCCTCTAAGGTTTTAAACATTACATCATGTGTCGTCG
droYak2 chrX:4177737-4177835 + GAACTCAA-ATAATCTGCCTTGCTTAGAATTTTAAGAGCAAAAAGTTTGTTTACAAAAACTATTTACCCCTAAAATTCTAATCTAGTCAGCATTAT--TTCG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAAACCAATGTGATCTCTTGCTTTGGCA-TTAAAGGAAGCTAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCGSizeHit CountTotal NormTotalGSM343915
Embryo
......................TTGGCA-TTAAAGGAAGCTAGT........................................................2111.0011
......................TTGGCA-TTAAAGGAAGCTAGTT.......................................................2211.0011
dp4
----------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-27.0 -26.5 -26.5 -26.5 -26.2 -26.2

droSim1

-19.9 -19.2

droSec1

-19.5 -19.4

droYak2

-10.9 -10.8 -10.4 -10.3 -10.1

droEre2

-7.1 -7.0 -6.8 -6.7 -6.6 -6.6

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:15 PM