Secondary structure and small RNA-seq evidence for dme-mir-4915

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:29757-29904 + GAAAATGCCACCCAGGTGAG-------AAAAAGTA----------GTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTA------AGC-------------------------------------------------------------------------------------------------------------------------------------AT---ATC----------------------ACGC--------AAGGAC------AAACATTAAGTTAAGGCCTAGTTCCTATTATACTAGGAATACTCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCTACTTATG--------CC---------------------------------TC----T-TATTCTTC-TTTT--CTCAGACCTCCGCCAAAGAA
droSim1 chrX:14351-14498 + GAAAATGCCACCCAGGTGAG-------AAAAAGTA----------GAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTA------AGC-------------------------------------------------------------------------------------------------------------------------------------AT---ATC----------------------GCGC--------AAGGAC------AAGTATTAAGTAAAGTTATAGTTCCTATTATACTAGGAATACTGCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTACTTATG--------CC---------------------------------TC----T-TATTCTTT-TTTT--CCCAGACCTCCGCCAAAGAA
droSec1 super_108:19641-19788 + GAAAATGCCACCCAGGTGAG-------AAAAAGTA----------GAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTA------AGC-------------------------------------------------------------------------------------------------------------------------------------AT---ATC----------------------ACGC--------AAGGAC------AAGTATTAAGTAAAGTTATAGTTCCTATTATACTAGGAATACTGCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCCTTATG--------CC---------------------------------TC----T-TATTCTTT-TTTT--CCCAGACCTCCGCCAAAGAA
droYak2 chrX:20604-20735 + GAAAATGCCACCCAGGTGAG-------AGAACTAA----------GTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATA------AAA-------------------------------------------------------------------------------------------------------------------------------------AT---ATC----------------------CTGC--------CAAGTTA-AA----------AGTGAAAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTATAATTGCATAG----------------------------------------------------------------------------------------------TTTTCCTACTAATG--------TC---------------------------------CC----TTTCTTCTTC-TTTT--CCCAGACCTCCGCCGAAGAA
droEre2 scaffold_4644:14892-15014 + GAAAATGCCGCCCAGGTGAG-------AAAATTTA----------GTC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATA------AGC-------------------------------------------------------------------------------------------------------------------------------------ATCTTATC----------------------CTGC--------AAAGAA---A----------AGTTAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTATA-------AG----------------------------------------------------------------------------------------------TTTCCCTACTAATG--------CC---------------------------------CC----T-TTTTCTTC-TTTT--CCCAGACCTCCGCCAAAGAA
droAna3 scaffold_12929:1781922-1782010 - AGAAATGCCACCCAGGTGAGTCTGTCTAGAGTTTG----------ATGGGATTGGAGTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA----------ATT-------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT-G----GA----TTGT-GATT--TTCAGACCTCCGCCAAAGAA
dp4 chrXL_group1a:594378-594471 + GAAAATGCCACCCAGGTGAGT-------GTCCGAG----------GT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCTTC--------------------------------------------------------------AATGGACTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGACCAATA--------TC-------------------GTC-----------TT----T-GA-TCCTT-TCCC--GGCAGACCTCCTCCAAAGAA
droPer1 super_157:12433-12452 + GAAAAAGCCACCCAGGTGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181150:2495748-2495847 + GAAAATGCCACCAAGGTGAGT-------GAGATAA----------GTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT--TTCCTTTTTTTCTC-----ACAGTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTAATTA-----------C---------------------------------CG----TTTCCACTTCTTATT--TTCAGGCCACCGCCTAAGGC
droVir3 scaffold_12928:440188-440807 + GAAAATGCCACCCAGGTAAATGCGCGTATGTT--GATTAACCAGACTTGCAATGGAATCAGGGAAAGGGGTCGTCTATCAGTGAGGCGAAATTAACAGAGCTA---------------------GGAAAATTTTGGAAGTTGCATAAATT-------------------------------------------------------------------------------CAAAAAGAATCCAAAGTGGAGAAGGATATTCACCTGAAGAGCCAGAAATTGTTGGGTTATTTAAACACTTGGGTTAAAATGGAGTTAA---------GAACAA--------------------------------------------------------------------GCGAAAAATATCAATTGGAAAATGGGCTTAAGACAATGCGCGACTACGAAATACCCTGGACAAAGCGC-GACTACGAAATACCCTG--------------------------------------------------------------GACAAAGCGCTGAGCTGTCCTTAAAAACATTCTAGCTTCCTTCTGTAAT------------ACACACACACACACACACACACATACATGCAGATTCTGTGCTTCAGTCACATAAATC------------------------------------------------------------------------------------------------------------------------------------------------------------ATGATAA----CATCGTAATACCCTCTACAAAGGGTATACGAATGATGTAATCTAGGATTGAAGCAAACCA---------TCTGAAAGG---TCTTTGGGCTTGACAAACAAATAGTTGGGCGAAACAGA-GAACAGTTTAGCTCCGCT------------------------------GTCGAGTTGTG--------ATTCCTGAGTGTTTTTTCTCT---TATTAATAGA-TC----AAT--TTGCT-TGCT--TGCAGACCGCCGCCAAAGAA
droMoj3 scaffold_6328:1398030-1398785 + GAAAATGCCACCCAGGTGAGT-------ATG-----------------GGATTAGCATTAGGGAAGGAATTTAAATTTGAATAGGAAAAAATTTGTAGACTCTATATA----------------------------------------CCCTATAGTAAATATTCTTAAGGGTCTAAACCAAACTCTTGTCGAATTCAATTTTTGATTTTCTTGTCTTTAATTTCTTGACTAAAATTACCCCAAGTCTATTAGTATCTGGAGTTTTAGGACTTGCATCTTGTATGTTAA-------------TAAAAATCGGACTAA---------AAATATCTTGAATGTCTGTCTCTTAACTTGGTCAAATCTAATCTGACTAAATCGTTAGATTATTTCCGTGTATTGGAACATACAACTATTGTATAATACGTCTATAAATACCCTTTACTTCGTTACATCAAGATGAAAGCTGATTTTAAGAAATAATTTGATTGATTCCACATTAAAA----------ATT---------------------------------------GCCGAGTTGTGACTCCAAACTAAATTG-----TT--------------------------------------------------------------------------------AGATAAGGTAGATAGATAAATGGA-----------------------------------------AAGGCCTATAGGTCTATCGTAAAT--GCCCCACCCATGCTGATCAGAA------------------ATGTGTATTTGTATAAACAATATGATAAATGTTTTCATAATATAA--TTCGAGTGCTAGACAAATGATAAGTCAAAGGAA--GGGCAAATGATA-------AGTGAAAGGAAACCTTGGGGCTTTACTAAT-----------CGATATAGTTGACTGGTTTAGTTCAGCTATGGAGTATATAGTAGTATAGTTACTG----CTGGCCACACACTATGGC---------------------GTC-----------TCACTCA-CA-TCCCA-TCCCATTGCAGACCGCCGCCAAAGAA
droGri2 scaffold_15203:6868729-6869248 + GAAAATGCCACCCAGGTGAGT-------GGC-------------------ATTGTAGTTG-----------------------------------------CGACACAGTTGCCAGTAGCGCTAACTTATTTT-----------------------------------------------------TATTC-------------GACT-------------------------------------------TCTTTGTCCGCTTGAAGAGTAAC-----------------------------TCTAACAAATTTAAAAACCCATTTATCAA--------------------------------------------------------------------ACGCGACGCGACGAATCAGAAACAGGCTTCAATTTATGCAGAGCTCTGCAGCATCTCTTC----------------------TAGA--------AGAGAA---GAGATACAGAGAGAAAAGGCGTGGT-----------------------------------CGATCTTTAAAAGAGGTTCCCTTCCTTCAATCTCTCAAATTGTAGCAGATATGCAGTTTTATTGATTTACACTTTCAGA--------------AATATCGCTTTTGGCGATTAGGGCGGTGGGTGTGTGGGCGTTGCCGTTGCCAGTTACCGTTTATATACCTTGCAACTCAAAAGCTTTTATGGGCGGCGGAGATGGGCATCGCTGATGCCGATCTTTGAAAGACATCGCGAAATATTTGTGTTCAT------------------------------------------------------------------------------TTAACAACTGCATTA----------------------------------------------------------------------------------------------TTTTTG----------------T-----------------------TTTTTTTTGAT-T----TG----TTGT-TATC--TGCAGACCGCCGCCAAAGAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:29757-29904 + GAAAATGCCACCCAGGTGAGAAAAAGTAGTAAATTAAGCATATCACGCAAGGACAAACATTAAGTTAAGGCCTAGTTCCTATTATACTAGGAATACTCAATCCTACTTATGCCTCTTATTCTTCTTTTCTCAGACCTCCGCCAAAGAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAAAATGCCACCCAGGTGAGAAAAAGTAGAAAATTAAGCATATCGCGCAAGGACAAGTATTAAGTAAAGTTATAGTTCCTATTATACTAGGAATACTGCATT--CTACTTA-------TGCCTCTTATTCTTTTTTTCCCAGACCTCCGCCAAAGAASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GAAAATGCCACCCAGGTGAGT--------------------------------------------------------------GTCCGAGGTGCCTTCAATGGACTACTGACCAATATCGTCTTTGATCCT-TTCCCGGCAGACCTCCTCCAAAGAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.8,  p-value=0.009901

droSim1

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.2,  p-value=0.009901

droSec1

dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-18.7,  p-value=0.009901 dG=-18.7,  p-value=0.009901 dG=-18.6,  p-value=0.009901

droYak2

dG=-10.8,  p-value=0.009901 dG=-10.7,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.4,  p-value=0.009901

droEre2

dG=-6.9,  p-value=0.009901 dG=-6.6,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.3,  p-value=0.009901 dG=-6.2,  p-value=0.009901 dG=-4.1,  p-value=0.009901

droAna3

dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.4,  p-value=0.009901

dp4

dG=-11.6,  p-value=0.009901 dG=-11.6,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.9,  p-value=0.009901

droPer1

dG=0.0,  p-value=1.0

droWil1

dG=-7.5,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.1,  p-value=0.009901 dG=-6.8,  p-value=0.009901

droVir3

dG=-131.1,  p-value=0.009901 dG=-131.1,  p-value=0.009901 dG=-131.1,  p-value=0.009901 dG=-131.1,  p-value=0.009901 dG=-131.1,  p-value=0.009901

droMoj3

dG=-156.6,  p-value=0.009901 dG=-156.6,  p-value=0.009901 dG=-156.5,  p-value=0.009901 dG=-156.5,  p-value=0.009901 dG=-156.5,  p-value=0.009901

droGri2

dG=-131.8,  p-value=0.009901 dG=-131.8,  p-value=0.009901 dG=-131.8,  p-value=0.009901 dG=-131.8,  p-value=0.009901 dG=-131.8,  p-value=0.009901

Generated: 03/08/2013 at 01:17 AM