Secondary structure and small RNA-seq evidence for dme-mir-1015

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:20164939-20165032 + TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1 chr3R:19998542-19998635 + TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1 super_0:20503496-20503589 + TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGTCTGAGTG-------AGACTTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2 chr3R:26340571-26340664 - TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGACTGGGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2 scaffold_4820:7895693-7895786 - TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGGCTGAGTG-------AGGACTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC
droAna3 scaffold_13088:204245-204339 + TCATGGGCTACGACAGTGAGTG-----ATGCTCCAGATAGGTTGGCTTAGGAAGTC------ATTAA------------AGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC
dp4 chr2:18646206-18646298 - TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC
droPer1 super_3:1376406-1376498 - TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC
droWil1 scaffold_181108:4541725-4541808 - TAATGGGTTATGACAGTAAGTTAGC---TGGTAAAGTTGATTTCT------------------TTTA------------ACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC
droVir3 scaffold_13047:3497490-3497590 + TTGTGGGCTACGAAAGTAAGTA------TTTACTTGATAACTCG------TT-------AAACCTAAAG--TCTGTTAACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA
droMoj3 scaffold_6540:20508341-20508431 + TAATGGGCTACGATGGTAAATG--CTGATGTTCATGAATATTTATCCAAGTA-------ATTT------------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA
droGri2 scaffold_14906:156637-156731 + TGGTGGGCTATGATAGTGAGTT--G--ATTCTATT---------------GTAATAATCA------AATCGTTTTTGTTATTTTATAAACA---TGCCATTTTAACAGTCAAGATACTCAAGA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:20164939-20165032 + TCATGGGCTACGACGGTGAGTGATGCTCCAGTTAGCTTGGCTGAGTGAGG-ATTTAAGTCCTGGGACATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1 chr3R:19998542-19998635 + TCATGGGCTACGACGGTGAGTGATGCTCCAGTTAGCTTGGCTGAGTGAGG-ATTTAAGTCCTGGGACATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1 super_0:20503496-20503589 + TCATGGGCTACGACGGTGAGTGATGCTCCAGTTAGCTTGTCTGAGTGAGA-CTTTAAGTCCTGGGACATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2 chr3R:26340571-26340664 - TCATGGGCTACGACGGTGAGTGATGCTCCAGATAGCTTGACTGGGTGAGG-ATTTAAGTCCTGGGACATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2 scaffold_4820:7895693-7895786 - TCATGGGCTACGACGGTGAGTGATGCTCCAGATAGCTTGGCTGAGTGAGG-ACTTAAGTCCTGGGACATCTCTCTTGCAGTCAAAATCCTAAAAC
droAna3 scaffold_13088:204245-204339 + TCATGGGCTACGACAGTGAGTGATGCTCCAGATAGGTTGGCTTAGGAAGTCATTAAAGCCCTGGGATGTCTCTCTTGCAGTTAAGATCCTGAAAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCATGGGCTACGACGGTGAGTGATGCTCCAGTTAGCTTGGCTGAG--TGAGGATT--TAAGTCCTGGGACATCT----CTCTTGCAGTCAAGATCCTAAAAGSizeHit CountTotal NormTotalGSM343915
Embryo
.............................................................TCCTGGGACATCT----CTCTTGCAG...............2211.0011
...........................................................AGTCCTGGGACATCT----CTCTTGC.................2211.0011
.............................................................TCCTGGGACATCT----CTCTTGCAGT..............2311.0011
...............GTGAGTGATGCTCCAGTTAGCT.................................................................2211.0011
dp4
TGATGGGCTACGATGGTAAG---------AGCTAGCCACACAAATTATTAGTATTTCTATTTCTCAAAATATTTCTTTCTTTTGCAGTCAAGATACTAAAGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-18.8,  p-value=0.009901 dG=-18.4,  p-value=0.009901 dG=-17.9,  p-value=0.009901 dG=-17.9,  p-value=0.009901 dG=-17.0,  p-value=0.009901

droSim1

dG=-18.8,  p-value=0.009901 dG=-18.4,  p-value=0.009901 dG=-17.9,  p-value=0.009901 dG=-17.9,  p-value=0.009901 dG=-17.0,  p-value=0.009901

droSec1

dG=-20.0,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.1,  p-value=0.009901

droYak2

dG=-17.8,  p-value=0.009901 dG=-17.7,  p-value=0.009901 dG=-17.4,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.0,  p-value=0.009901

droEre2

dG=-18.9,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.2,  p-value=0.009901

droAna3

dG=-16.7,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-15.8,  p-value=0.009901

dp4

dG=-4.9,  p-value=0.009901 dG=-4.2,  p-value=0.009901

droPer1

dG=-4.9,  p-value=0.009901 dG=-4.2,  p-value=0.009901

droWil1

dG=-8.3,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.3,  p-value=0.009901

droVir3

dG=-2.5,  p-value=0.009901 dG=-2.3,  p-value=0.009901 dG=-1.5,  p-value=0.009901

droMoj3

dG=-3.5,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.7,  p-value=0.009901 dG=-2.6,  p-value=0.009901

droGri2

dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.5,  p-value=0.009901

Generated: 03/07/2013 at 04:48 PM