Secondary structure and small RNA-seq evidence for dme-mir-4975

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:2594652-2594793 - TAGAACTGGAAATCTGGGCAAATAA--AGCACGTTGCTCCCTGTTTACTTGGGTTTTCTG----------------------------TTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTGTACACAAGAAGATTCA
droSim1 chr2R:1414726-1414867 - TAGAACTGAAAGTCTCGGCAAATAG--AGCACGTTGCTCCCTGTTTACTCAGGTTCCCTG----------------------------TTCATTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGTAAAGATACAGATATCTCTGTATACTAGAAGATACA
droSec1 super_1:259050-259190 - TAGAACTGGAAGTCTCGGCAAATAA--AGCACGTTGCTCCCTGTTTACTCAGGTTCCCTG----------------------------TTCAGTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGT-AGGATACAGATATCTCTGTATACTAGAAGATACA
droYak2 chr2L:15337545-15337682 - TAGAAATGAAAATCTCGGCAAGTAA--AGCACGTTGCTCCATGTTTACTCAGGTTTGCTG----------------------------TTTATATCGCCTATCAAACGTTGAACTTGA---ATCACGATCAGTTGGTCAACATACATATATTTGT-CACACTAGGTGATCCA
droEre2 scaffold_4929:19950710-19950840 + TAGGACTGCAGATCCCGGCAACTAA--AGCACGTTGCTCCCAGTTTACTCAGGTTCGCTG----------------------------TTTATATCGCCTATCGAGCGTTGAACTTGAGGAGCCACGATCAGTTGGTCAGCATACATATA-----------AAGATGATCCA
droAna3 scaffold_13266:18414789-18414883 + AAGTCTA----ATTTCGGT------------------GCCTTGTTTACTTCGCTCTCCGGCGGAGAGCTGCAGTGCACGAGGTGTCTAATCGGCCAGCCCATAGAGCAATGAACTT--------------------------------------------------------
dp4 chr3:859167-859237 - TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTT-TCTGTTTACGTTACTTCTCGT----------------------------CCCGTCCCGTCT------------------------------------------------------------------------
droPer1 super_2:1035040-1035110 - TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTT-TCTGTTTACGTTACTTCTCGT----------------------------CCCGTCCCGTCT------------------------------------------------------------------------
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:2594652-2594793 - TAGAACTGGAAATCTGGGCAAATAA--AGCACGTTGCTCCCTGTTTACTTGGGTTTTCTG----------------------------TTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTGTACACAAGAAGATTCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TAGAACTGAAAGTCTCGGCAAATA--GAGCACGTTGCTCCCTGTTTACTCAGGTTCCCTGTTCATTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGTAAAGATACAGATATCTCTGTATACTAGAAGATACASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTT-CTGTTTACGTTACTTCTCGTCCCGTCCCGTCT------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-20.1 -19.7 -19.5 -19.4 -19.4 -19.3

droSim1

-22.0 -21.7 -21.6 -21.6 -21.4 -21.3

droSec1

-23.6 -23.4 -23.2 -23.1 -22.9 -22.9

droYak2

-19.4 -19.0 -19.0 -18.5 -18.5 -18.5

droEre2

-27.0 -26.9 -26.4 -26.3 -26.2 -26.2

droAna3

-25.3 -25.2 -25.2 -25.1 -25.0 -24.9

dp4

-6.2 -6.0 -5.4 -5.2

droPer1

-6.2 -6.0 -5.4 -5.2

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 05:26 PM