Secondary structure and small RNA-seq evidence for dme-mir-974

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19445696-19445826 + AG----GTCC-AGGTAAGCTCAA-TTGTCACCGGTCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTTCCAA-GAGCAAATATAACTTCATTGGAA-GCTAAGTGGATTTGCCCA-AAT-------CAGCTTGGTATTTAT
droSim1 chrX:15011423-15011546 + GT----A---------AACTCAA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CACCTTGGTATTTAT
droSec1 super_8:1728102-1728227 + AG----G-------TAAACTCGA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CTCCTTGGTATTTAT
droYak2 reseq:-1--1 * GA----AAAC-AGAACCACTGAC-TTAGCACTGGTCATGGCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGACTTGTCCA-AGA-------CAGC-----------
droEre2 scaffold_4690:9682437-9682562 + GA----AAAC-AGAACCACTAAC-TCAGCACTGGGCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGATTTGCCCA-AGC-------CAACTTGCTG-----
droAna3 scaffold_13417:2478487-2478598 - GG----TTGC-A---ATCCTGGC-TTGGGGTAGGTCATCTCCTCTAAGCGAGCAAAGAAGTAGTATTTGTTTGCTTTTAATGGTCAAATATAACTTTTTTGGAA-GCTACGAGGAGTTGTCC---------------------------
dp4 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7946609-7946719 + AT-----------------TCATTTTTCCAATGGCCATATCCTCTAAGCGAGCAAGAAAGTGGTATTTGTC--TTTGGAA-ATTCAAATATAACTTTTTTGGAA-GCTACAAGGCAATGTCCACAAT-------CAAC-----------
droVir3 scaffold_13042:917533-917679 - ATCCGAATATGAGATTTACCA-ATTATTAACTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTATTTGCGTGAATCTGA-TATCAAATAAGACTTTTTTGGTTCGCTATGAGGTATTGTTCA-TAAATAAACACGTCTGCCTATATAC
droMoj3 scaffold_6328:2908489-2908614 - TC----A---------------ATCAGACGCTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTTT-TGCGTGCATCTGA-TATCAAATAAAACTTTTTTGGTT-GCTGCGAGGTATTGTTGA-AATGTAAACGTTGCTCGCTCTCTAC
droGri2 scaffold_15081:2051206-2051247 - CA----------------------------AAGGACATCTTCTGTAAGCGAGCAAAAATATAATATTTGT-------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19445696-19445826 + AG----GTCC-AGGTAAGCTCAA-TTGTCACCGGTCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTTCCAA-GAGCAAATATAACTTCATTGGAA-GCTAAGTGGATTTGCCCA-AAT-------CAGCTTGGTATTTAT
droSim1 chrX:15011423-15011546 + GT----A---------AACTCAA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CACCTTGGTATTTAT
droSec1 super_8:1728102-1728227 + AG----G-------TAAACTCGA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CTCCTTGGTATTTAT
droYak2 reseq:-1--1 * GA----AAAC-AGAACCACTGAC-TTAGCACTGGTCATGGCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGACTTGTCCA-AGA-------CAGC-----------
droEre2 scaffold_4690:9682437-9682562 + GA----AAAC-AGAACCACTAAC-TCAGCACTGGGCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGATTTGCCCA-AGC-------CAACTTGCTG-----
droAna3 scaffold_13417:2478487-2478598 - GG----TTGC-A---ATCCTGGC-TTGGGGTAGGTCATCTCCTCTAAGCGAGCAAAGAAGTAGTATTTGTTTGCTTTTAATGGTCAAATATAACTTTTTTGGAA-GCTACGAGGAGTTGTCC---------------------------
droWil1 scaffold_181096:7946609-7946719 + AT-----------------TCATTTTTCCAATGGCCATATCCTCTAAGCGAGCAAGAAAGTGGTATTTGTC--TTTGGAA-ATTCAAATATAACTTTTTTGGAA-GCTACAAGGCAATGTCCACAAT-------CAAC-----------
droVir3 scaffold_13042:917533-917679 - ATCCGAATATGAGATTTACCA-ATTATTAACTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTATTTGCGTGAATCTGA-TATCAAATAAGACTTTTTTGGTTCGCTATGAGGTATTGTTCA-TAAATAAACACGTCTGCCTATATAC
droMoj3 scaffold_6328:2908489-2908614 - TC----A---------------ATCAGACGCTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTTT-TGCGTGCATCTGA-TATCAAATAAAACTTTTTTGGTT-GCTGCGAGGTATTGTTGA-AATGTAAACGTTGCTCGCTCTCTAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
--------GTAAACTCAATTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCGTTTCCAAGAACAAATATAACTTCTTTGAAAGCTAGGTGGATTTGCCCAAGTCACCTTGGTATTTATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-----------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-26.7 -26.4

droSim1

-33.3 -33.2 -33.2 -33.1 -33.0 -33.0

droSec1

-33.3 -33.2 -33.2 -33.1 -33.0 -33.0

droYak2

-28.9 -28.8 -28.7 -28.6 -28.5 -28.4

droEre2

-39.2 -39.1 -38.5 -38.4

droAna3

-34.6

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-25.7 -25.4 -25.4 -24.7

droVir3

-34.1 -34.1 -34.1 -34.1 -33.8 -33.8

droMoj3

-26.5 -26.2 -26.1 -25.9 -25.9 -25.8

droGri2

-0.1 0.0 0.1 0.1 0.2 0.5

Generated: 01/05/2013 at 05:33 PM