Secondary structure and small RNA-seq evidence for dme-mir-284

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:8377222-8377351 - ATAATCGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCTCAACAATG
droSim1 chr3R:13050845-13050974 + ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droSec1 super_0:13609227-13609356 + ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droYak2 chr3R:12662228-12662357 - ATAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droEre2 scaffold_4770:13275536-13275665 + TTAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droAna3 scaffold_12911:3307955-3308116 - ACAAAAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGAACTGCTTCAGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGTACAGCA---GAAAGAGCCGTGAACCGTGTTCAATATGCCACGACAATG
dp4 chr2:2484958-2485100 - ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droPer1 super_7:2652948-2653090 - ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droWil1 scaffold_181130:2186197-2186330 - GTGTGTGACAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTTAGGGGAAAGGCTTGAGCATTGCATACTAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCTCAACGTT--------------------------------CAACAGTG
droVir3 scaffold_12855:584465-584599 + ATAAATGGAAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAAGGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGGACAACGTTGGAAAG------------TGTC------------------
droMoj3 scaffold_6540:12381805-12381927 - TGTAT---TAATTGCGTTGCAGTTCCTGGAATAAAGTTGACTGTGTCGCCTGTAAGGGG-AAGGCTTTTGCATTGCTTACAAAGTCAGCAACTTGATTCCAGCAACTGCGGCCCAAGCT---------------------------------------CAACGTGG
droGri2 scaffold_14906:1700701-1700824 + ATA--TGGAAATTGGGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAGAGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCTCAAACT---------------------------------------CAACGTTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:8377222-8377351 - ATAATCGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCTCAACAATG
droSim1 chr3R:13050845-13050974 + ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droSec1 super_0:13609227-13609356 + ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droYak2 chr3R:12662228-12662357 - ATAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droEre2 scaffold_4770:13275536-13275665 + TTAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droAna3 scaffold_12911:3307955-3308116 - ACAAAAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGAACTGCTTCAGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGTACAGCA---GAAAGAGCCGTGAACCGTGTTCAATATGCCACGACAATG
dp4 chr2:2484958-2485100 - ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droPer1 super_7:2652948-2653090 - ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droWil1 scaffold_181130:2186197-2186330 - GTGTGTGACAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTTAGGGGAAAGGCTTGAGCATTGCATACTAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCTCAACGTT--------------------------------CAACAGTG
droVir3 scaffold_12855:584465-584599 + ATAAATGGAAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAAGGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGGACAACGTTGGAAAG------------TGTC------------------
droMoj3 scaffold_6540:12381805-12381927 - TGTAT---TAATTGCGTTGCAGTTCCTGGAATAAAGTTGACTGTGTCGCCTGTAAGGGG-AAGGCTTTTGCATTGCTTACAAAGTCAGCAACTTGATTCCAGCAACTGCGGCCCAAGCT---------------------------------------CAACGTGG
droGri2 scaffold_14906:1700701-1700824 + ATA--TGGAAATTGGGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAGAGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCTCAAACT---------------------------------------CAACGTTG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGCAAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGATATTCCGCAACAATG-----------------SizeHit CountTotal NormTotalGSM343915
Embryo
..................................................................................GTCAGCAACTTGATTCCAGCAA...........................................22175.007575
..................................................................................GTCAGCAACTTGATTCCAGCA............................................21124.002424
........................CCTGGAATTAAGTTGACTGTGTAGC..................................................................................................25123.002323
........................CCTGGAATTAAGTTGACTGTGTAGCC.................................................................................................26118.001818
........................CCTGGAATTAAGTTGACTGTGTAG...................................................................................................2413.0033
.....GGGTAATTGCGTTGCAGTT...........................................................................................................................1912.0022
.....................................................................................AGCAACTTGATTCCAGCAA...........................................1911.0011
........................CCTGGAATTAAGTTGACTGTGTAGCCT................................................................................................2711.0011
..........................................................................CTCCTGAAGTCAGCAACTTGATTCCA...............................................2611.0011
dp4
ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGCAAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAG----CACAACGCTGAATGGTGCTCAAAATACSizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
..................................................................................GTCAGCAACTTGATTCCAGCAA...........................................2211410.0014102441166
........................CCTGGAATTAAGTTGACTGTGTAGCC.................................................................................................261994.00994127867
..................................................................................GTCAGCAACTTGATTCCAGCA............................................211981.0098153928
........................CCTGGAATTAAGTTGACTGTGTAGC..................................................................................................251490.0049067423
........................CCTGGAATTAAGTTGACTGTGTAG...................................................................................................241204.002043201
.....AGGCAATTGCGTTGCAGTT...........................................................................................................................191157.001576151
........................CCTGGAATTAAGTTGACTGTGT.....................................................................................................22193.0093192
........................CCTGGAATTAAGTTGACTGTG......................................................................................................21159.0059059
........................CCTGGAATTAAGTTGACTGTGTA....................................................................................................23150.0050149
..................................................................................GTCAGCAACTTGATTCCAGC.............................................20131.0031031
........................CCTGGAATTAAGTTGACTGTGTAGCCT................................................................................................27121.0021021
........................CCTGGAATTAAGTTGACTGT.......................................................................................................2018.00808
.....................................................................................AGCAACTTGATTCCAGCAA...........................................1918.00835
.....................................................................................AGCAACTTGATTCCAGCA............................................1817.00716
..................................................................................GTCAGCAACTTGATTCCAG..............................................1914.00404
........................CCTGGAATTAAGTTGACTG........................................................................................................1913.00303
.........................CTGGAATTAAGTTGACTGTGTAGC..................................................................................................2413.00312
...................................................................................TCAGCAACTTGATTCCAGCAA...........................................2112.00211
...AGAGGCAATTGCGTTGCAGTT...........................................................................................................................2112.00211
.........................CTGGAATTAAGTTGACTGTGTAG...................................................................................................2312.00202
..CAGAGGCAATTGCGTTGCAGTT...........................................................................................................................2211.00101
.........................CTGGAATTAAGTTGACTGTGTAGCC.................................................................................................2511.00101
....................AGTTCCTGGAATTAAGTTGA...........................................................................................................2011.00101
................................................................................AAGTCAGCAACTTGATTCCAGCA............................................2311.00110
.....AGGCAATTGCGTTGCAGT............................................................................................................................1811.00101
....................................................................................CAGCAACTTGATTCCAGCA............................................1911.00101
.....AGGCAATTGCGTTGCAGTTC..........................................................................................................................2011.00101

Secondary Structure

dm3

dG=-32.3,  p-value=0.009901 dG=-32.3,  p-value=0.009901 dG=-32.3,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-32.1,  p-value=0.009901

droSim1

dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.5,  p-value=0.009901 dG=-32.1,  p-value=0.009901

droSec1

dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.5,  p-value=0.009901 dG=-32.1,  p-value=0.009901

droYak2

dG=-35.5,  p-value=0.009901 dG=-32.1,  p-value=0.009901

droEre2

dG=-35.5,  p-value=0.009901 dG=-32.1,  p-value=0.009901

droAna3

dG=-34.1,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.3,  p-value=0.009901 dG=-32.1,  p-value=0.009901

dp4

dG=-35.0,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901

droPer1

dG=-35.0,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901

droWil1

dG=-33.4,  p-value=0.009901 dG=-33.3,  p-value=0.009901 dG=-33.0,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.7,  p-value=0.009901

droVir3

dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.5,  p-value=0.009901

droMoj3

dG=-32.7,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.3,  p-value=0.009901 dG=-32.3,  p-value=0.009901

droGri2

dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.1,  p-value=0.009901

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