Secondary structure and small RNA-seq evidence for dme-mir-4946

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:18867030-18867176 - TAAAAATAAAA----AAATG-------------CTC-----------------GATTGCTGCAA-----------------------------------------CTAAGAAACA--AATATTTTCAGTTGTTCAT----TGCAAATTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCTAGGCTTATCAGCT-GCAATGCCTCTATGAAGGG
droSim1 chr2L:18557325-18557471 - TAAAAATAACA----AAACG-------------CTC-----------------ATTTGCTGCAA-----------------------------------------ATAAGAAACA--AATATTTTCAGTTGTTCAT----TGCAAGTTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCCAGGCTTATCAGCT-GCAATCCCCCCAAGAAGGG
droSec1 super_7:2494148-2494294 - TAAAAATAACA----AAACG-------------TTC-----------------ATTTGCTGATA-----------------------------------------ATAAGAAACA--AATATCTTAAGATGTTCAT----TGCAAATTAATTTA---TGTACATTGCTAT---------------GAAATCAATTGAAAATATAAT---TGTA--------------------TCCTAGGCTTATCAGCT-GCAATCCCCCCAAGAAGGG
droYak2 chr2R:5382904-5383074 - TAAAAATAACA----AAGCA-------------TAT-------------TAGCATATGCTGCAA-----------------------------------------ACAATAAATA--AATATTTTCAGCTGTGCAT----TGCAAATTAATGTA---TTTACATAGCTAT---------------GAAAGCAATTGAAACGACAAT---TGCAGGTCATTTTTATTGCACACATCCTAGGCTTATCAGTG-GCAATGCCCCTACGAAGAG
droEre2 scaffold_4845:5409251-5409398 + TACAAGTAACA----AAGTG-------------CTA-----------------ATTCGCTGCAA-----------------------------------------ATAGGAAATA--AATATTTTCAT------------------------TATTAT-CACATTGCCA----------------GAAACCAATTGAAAAGATAAT---TGTAGGCCACTTTTGTTGCACGCATCCTAGGCTTATCAGCT-GATATGCCCCCACGAAGGG
droAna3 scaffold_13334:1096999-1097137 - TAAATATTTTT----AAGTA-------------ATT-----------------AATTG-----------GGCTACTG----------------------------GCTTTAAAAAATAATATTTTCAAATGTTATT----GGTAATTTAATTTT---TTTATAATTTT-TAAA------------TACATTTTTTTAAACTAAAATCCTTGTT--------------------TTCT----------------GCTTCCTTT--TCAGCT
dp4 chrXR_group6:8932576-8932713 + TTAAAATAAAA----ACATT--------------TC-----------------ATATTTAAATT-ACAAGGTTTTAT----------------------------ATTTTAAATA--AATAT------------ATTTCCCACAAATTAAAGAT---AATATATTTATTT---------------TAAAGTAATTTATAATTAAAT---TGAA--------------------TATGGGCCCTA----C---------TACAAAGACTTT
droPer1 super_1:5889084-5889218 + GATAGGTT---------------------------T-----------------TTGCAACACAA-----------------------------------------AAAATAAACA--AAGATTAGTTTCCAGTTAT----TAAATATTAATATA---TATATTTGAAGCA---------------GAAATATGTATATTTTAGAAT---CGTT--------------------TCTGTGGGGTTTTCATT-GCAATACCTTT--TATGAA
droWil1 scaffold_180698:8557325-8557469 - ACCAAAGAGAA----ATATCTCAAACTCAAACTCACAAACAAGACACATCAGCGC--------------------------------GCAAGAGCAACAACGCAAAGAACAAT--------------------------------------------TAAACAATTCTAT---------------TAAATTGATCGAAAATATAAA---CATT--------------------TCA-CAGCATAACAACA-ACAAA-----AGAAAAGGA
droVir3 scaffold_12855:7203873-7204022 + TGAAAATGAAT----AAATA-------------TAT-------------------ATGCTCCAATTAAAATTGAAACTACTATCCGAT--------------------------------------CGAAGGTCTT-TG-TTCAAATTCATTTG---A--GGGGTTTTTC---------------GCACTTTTTGGAAAATCCATC---ACTC--------------------CCCGATGGAAATGGGCT-TCAATGACTTAGTGGGTGG
droMoj3 scaffold_6500:29247639-29247782 - GGCCAATTAAC----AAACG-------------CAC-------------------GTGCAGCAG-----------------------------------------CTACAACAGC--ATCGTGTGCACACATACAT----TCAAACT-TCTTCT---GGAACATTCTTTTAATCACATCAGCTGTTAGTTTGGTTTAGTTTTGGTA---GATG--------------------G---------CGCTGCA-G------CACTGAATCTAT
droGri2 scaffold_14853:9426729-9426870 + TCCACAAAGATATCAAAATC--------------TC-----------------AGATACTGCTT-GAAAGTTGACAT---------------------------------------------TT-----CCCTCAT----AGAATA-TCCTTTA---TGTACAGTAATAT---------------GAGT--GTTTGTATTTGAAGTCT-TCTT--------------------TTTCATCGTCATTTATCTCCATCCTCTCTTTGACTGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:18867030-18867176 - TAAAAATAAAAAAATGCTCGATTGCTGCAACTAAGAAACAAATATTTTCAGTTGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATGCCTCTATGAAGGG
droSim1 chr2L:18557325-18557471 - TAAAAATAACAAAACGCTCATTTGCTGCAAATAAGAAACAAATATTTTCAGTTGTTCATTGCAAGTTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCCAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG
droSec1 super_7:2494148-2494294 - TAAAAATAACAAAACGTTCATTTGCTGATAATAAGAAACAAATATCTTAAGATGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TAAAAATAACAAAACGCTCATTTG-----------CTGCAAATAAGAAACAAATATTTTCAGTTGTTCATTGCAAGTTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCCAGGCTTATCAGCTGCAATCCCCCCAAGAAGGGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTAAAATAAAAACATTTCATATTTAAATTACAAGGTTTTATATTTTAAATAAATATATT--------TCCCACAAATTAAAGATAATATATTTATTTTAAAGTAATTTATAATTAAATTGAATATGGGCCCT------------ACTACAAAGACTTTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-18.4,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.8,  p-value=0.009901

droSim1

dG=-19.9,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901

droSec1

dG=-7.8,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-6.9,  p-value=0.009901

droYak2

dG=-17.6,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-11.6,  p-value=0.009901

droEre2

dG=-3.1,  p-value=0.009901 dG=-2.4,  p-value=0.009901 dG=-2.1,  p-value=0.009901

droAna3

dG=-4.2,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.5,  p-value=0.009901

dp4

dG=-6.6,  p-value=0.009901 dG=-6.6,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-4.9,  p-value=0.009901

droPer1

dG=-9.3,  p-value=0.009901 dG=-9.2,  p-value=0.009901 dG=-8.9,  p-value=0.009901 dG=-8.6,  p-value=0.009901 dG=-8.5,  p-value=0.009901

droWil1

dG=-1.3,  p-value=0.009901 dG=-0.3,  p-value=0.009901

droVir3

dG=-10.7,  p-value=0.009901 dG=-10.7,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-10.3,  p-value=0.009901

droMoj3

dG=-8.4,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.0,  p-value=0.009901 dG=-8.0,  p-value=0.009901 dG=-7.7,  p-value=0.009901

droGri2

dG=-6.8,  p-value=0.009901 dG=-6.8,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.5,  p-value=0.009901 dG=-6.4,  p-value=0.009901

Generated: 03/07/2013 at 05:44 PM