Secondary structure and small RNA-seq evidence for dme-mir-193

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:21567099-21567236 + TTTGATCG-----C-----------------AATCCGTGTGTGCCCTTATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droSim1 chr3L:20903305-20903442 + TTCGATCG-----C-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droSec1 super_11:1487328-1487465 + TTCGATCG-----C-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droYak2 chr3L:18945598-18945735 - TTTGATCG-----G-----------------AATCCGTGAGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droEre2 scaffold_4784:21221186-21221323 + TTTAATCG-----G-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTACATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droAna3 scaffold_13337:17070826-17070956 - CCGAATCG-----A-----------------AATCTGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATTGCCA--TATTCATAAATTCTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTA------------
dp4 chrXR_group6:2746028-2746170 - CTCAATTG-----G-----------------AATATTTGTGTGCACCCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGCTATACAGCCG--TATTAATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGGCTTAACAATAA
droPer1 super_9:1042494-1042636 - CTCAATTG-----G-----------------AATATTTGTGTGCACCCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGCTATACAGCCG--TATTAATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGGCTTAACAATAA
droWil1 scaffold_180727:1082196-1082335 - TTTAATTA-----A---------TC------AATCTGTGTGTGCGCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTACA-AGTCAAAAATTTATT-ATCATCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGACGAAAT-----
droVir3 scaffold_13049:17910638-17910773 + CTTAATGG-----T-----------------TGTAAGCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATATATATATG--TAT-CGTAAATCTTCTACTGGCCTACTAAGTCTCAATATAATGGGAGTAAAAACCTCAG-TATAAC-----
droMoj3 scaffold_6680:23178993-23179110 + ------------------------------------GCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATAAATA------TTATCATAAGTTCTCTACTGGCCTACTAAGTCTCAATATAATGGGAGTAAACACCTCAG-TTCAA------
droGri2 scaffold_10030:24062-24212 - TATAACTATCGAGGAAATTTACATAAATGTGCTAAAGCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATAAAGACCTT--TA-TCGTAAATCTTCTACTGGCCTACTAAGTCCCAATATAATGGGAGTAAAACCCTCA-------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:21567099-21567236 + TTTGATCG-----C-----------------AATCCGTGTGTGCCCTTATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droSim1 chr3L:20903305-20903442 + TTCGATCG-----C-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droSec1 super_11:1487328-1487465 + TTCGATCG-----C-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droYak2 chr3L:18945598-18945735 - TTTGATCG-----G-----------------AATCCGTGAGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droEre2 scaffold_4784:21221186-21221323 + TTTAATCG-----G-----------------AATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTACATAGCCA--TATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----
droAna3 scaffold_13337:17070826-17070956 - CCGAATCG-----A-----------------AATCTGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATTGCCA--TATTCATAAATTCTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTA------------
dp4 chrXR_group6:2746028-2746170 - CTCAATTG-----G-----------------AATATTTGTGTGCACCCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGCTATACAGCCG--TATTAATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGGCTTAACAATAA
droPer1 super_9:1042494-1042636 - CTCAATTG-----G-----------------AATATTTGTGTGCACCCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGCTATACAGCCG--TATTAATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGGCTTAACAATAA
droWil1 scaffold_180727:1082196-1082335 - TTTAATTA-----A---------TC------AATCTGTGTGTGCGCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTACA-AGTCAAAAATTTATT-ATCATCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGACGAAAT-----
droVir3 scaffold_13049:17910638-17910773 + CTTAATGG-----T-----------------TGTAAGCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATATATATATG--TAT-CGTAAATCTTCTACTGGCCTACTAAGTCTCAATATAATGGGAGTAAAAACCTCAG-TATAAC-----
droMoj3 scaffold_6680:23178993-23179110 + ------------------------------------GCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATAAATA------TTATCATAAGTTCTCTACTGGCCTACTAAGTCTCAATATAATGGGAGTAAACACCTCAG-TTCAA------
droGri2 scaffold_10030:24062-24212 - TATAACTATCGAGGAAATTTACATAAATGTGCTAAAGCGTGTGCCCTCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGATAAAGACCTT--TA-TCGTAAATCTTCTACTGGCCTACTAAGTCCCAATATAATGGGAGTAAAACCCTCA-------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTCGATCGCAATCCGTGTGTGCCCCCATTATGGTTGGGATTTTTTAGATCAGCAGTTATTGCTATATAGCCATATTTATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACAGGTTCGAC-----SizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTCAATTGGAATATTTGTGTGCACCCATTATAGTTGGGATTTTTTAGATCAGCAGTTATTGCTATACAGCCGTATTAATAAATCTTCTACTGGCCTACTAAGTCCCAACATAATGAGAGTAAAAACCACTGGCTTAACAATAASizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
.................................TTGGGATTTTTTAGATCAGC..........................................................................................2011074.00107401074
.................................TTGGGATTTTTTAGATCAGCAG........................................................................................2211000.0010001999
...............................AGTTGGGATTTTTTAGATCAGC..........................................................................................221754.007540754
...............................AGTTGGGATTTTTTAGATCAGCA.........................................................................................231477.004770477
...............................AGTTGGGATTTTTTAGATCAGCAG........................................................................................241454.004540454
.................................TTGGGATTTTTTAGATCAGCA.........................................................................................211434.004340434
...............................AGTTGGGATTTTTTAGATCAG...........................................................................................211381.003810381
................................GTTGGGATTTTTTAGATCAGC..........................................................................................211275.002750275
..................................TGGGATTTTTTAGATCAGCAGT.......................................................................................221213.002130213
..................................TGGGATTTTTTAGATCAGCAG........................................................................................211152.001520152
.................................TTGGGATTTTTTAGATCAGCAGT.......................................................................................231107.001070107
...............................AGTTGGGATTTTTTAGATCA............................................................................................20165.0065065
.......................................................................................TACTGGCCTACTAAGTCCCAAC..................................22144.0044044
.................................TTGGGATTTTTTAGATCAG...........................................................................................19138.0038038
.......................................................................................TACTGGCCTACTAAGTCCCA....................................20128.0028028
..................................TGGGATTTTTTAGATCAGC..........................................................................................19124.0024024
.......................................................................................TACTGGCCTACTAAGTCCCAA...................................21123.0023023
..................................TGGGATTTTTTAGATCAGCAGTT......................................................................................23123.0023023
.................................TTGGGATTTTTTAGATCAGCAGTT......................................................................................24119.0019019
................................GTTGGGATTTTTTAGATCAG...........................................................................................20118.0018018
..................................TGGGATTTTTTAGATCAGCA.........................................................................................20114.0014014
.................................TTGGGATTTTTTAGATCA............................................................................................18113.0013013
...............................AGTTGGGATTTTTTAGATCAGCAGT.......................................................................................2518.00808
........................................................TATTGCTATACAGCCGTATTAAT................................................................2317.00707
........................................................................................ACTGGCCTACTAAGTCCCAACAT................................2316.00606
................................GTTGGGATTTTTTAGATCA............................................................................................1915.00505
...............................AGTTGGGATTTTTTAGATC.............................................................................................1914.00404
.......................................................................................TACTGGCCTACTAAGTCCC.....................................1913.00303
.......................................................TTATTGCTATACAGCCGTATT...................................................................2112.00202
...............................AGTTGGGATTTTTTAGATCAGCAGTT......................................................................................2612.00202
................................GTTGGGATTTTTTAGATCAGCA.........................................................................................2212.00202
........................................................................................ACTGGCCTACTAAGTCCCAACA.................................2212.00202
........................................................TATTGCTATACAGCCGTATTAA.................................................................2211.00101
.........................................................................................CTGGCCTACTAAGTCCCAACAT................................2211.00101
........................................................................................ACTGGCCTACTAAGTCCCAAC..................................2111.00101
...................................GGGATTTTTTAGATCAGCAGT.......................................................................................2111.00101
........................................................................................ACTGGCCTACTAAGTCCCA....................................1911.00101
........................................................TATTGCTATACAGCCGTATT...................................................................2011.00101

Secondary Structure

dm3

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droSim1

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droSec1

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droYak2

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droEre2

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droAna3

dG=-20.6,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-19.9,  p-value=0.009901

dp4

dG=-22.7,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droPer1

dG=-22.7,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droWil1

dG=-19.67,  p-value=0.009901 dG=-18.97,  p-value=0.009901 dG=-18.97,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droVir3

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

droMoj3

dG=-17.5,  p-value=0.009901 dG=-17.5,  p-value=0.009901 dG=-17.5,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.3,  p-value=0.009901

droGri2

dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901

Generated: 03/07/2013 at 04:53 PM