Secondary structure and small RNA-seq evidence for dme-mir-9c

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:16697909-16698030 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------------------------------------------TGATAT----
droSim1 zdv96e12.b1:15-131 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droSec1 super_7:344892-345054 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCCA-AAACAGCCACAAATACAGGAATGATTAATGATAT----
droYak2 chr2R:4405017-4405183 - CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAACCAA-AAACAGCCACAAATACAGGAATGATTAAAAATATCTTT
droEre2 scaffold_4845:19767520-19767683 + AT----------------------------TGC-ACCT---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCAAAAAACAGCCACAAATACAGGAATGATTTCTAATAT----
droAna3 scaffold_12916:15865465-15865583 - CA----------------------------CGC-ACTCCCTTTCA--------------TTA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
dp4 chr4_group3:8443145-8443295 + CT-CTCCCATTCGCTGTCTGTCGACTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droPer1 super_1:9894267-9894417 + CT-CTCCCATTCGCTGTCTGCCGCCTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droWil1 scaffold_181061:30518-30658 - CCTCCCCTCTTCACCATC-------------------T---TTTCCTCTCCCTCCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droVir3 scaffold_12963:12863840-12863951 - CA----------------------------CAC-ACAA---TTT---------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT---ACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droMoj3 scaffold_6500:7201331-7201445 + AT----------------------------TGCCACTC---TT----------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-C--ACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCG-------------------------------------------------
droGri2 scaffold_14978:830199-830317 + AT----------------------------TGC-AATT---TCTT--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCT---ATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCT----------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:16697909-16698030 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------------------------------------------TGATAT----
droSim1 zdv96e12.b1:15-131 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droSec1 super_7:344892-345054 + CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCCA-AAACAGCCACAAATACAGGAATGATTAATGATAT----
droYak2 chr2R:4405017-4405183 - CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAACCAA-AAACAGCCACAAATACAGGAATGATTAAAAATATCTTT
droEre2 scaffold_4845:19767520-19767683 + AT----------------------------TGC-ACCT---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCAAAAAACAGCCACAAATACAGGAATGATTTCTAATAT----
droAna3 scaffold_12916:15865465-15865583 - CA----------------------------CGC-ACTCCCTTTCA--------------TTA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
dp4 chr4_group3:8443145-8443295 + CT-CTCCCATTCGCTGTCTGTCGACTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droPer1 super_1:9894267-9894417 + CT-CTCCCATTCGCTGTCTGCCGCCTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droWil1 scaffold_181061:30518-30658 - CCTCCCCTCTTCACCATC-------------------T---TTTCCTCTCCCTCCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droVir3 scaffold_12963:12863840-12863951 - CA----------------------------CAC-ACAA---TTT---------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT---ACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droMoj3 scaffold_6500:7201331-7201445 + AT----------------------------TGCCACTC---TT----------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-C--ACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCG-------------------------------------------------
droGri2 scaffold_14978:830199-830317 + AT----------------------------TGC-AATT---TCTT--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCT---ATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCT----------------------------------------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CT---------------------------TGCACTATTTA--------TCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------SizeHit CountTotal NormTotalGSM343915
Embryo
..............................................................TCTTTGGTATTCTAGCTGTAG..........................................................................2117156.0071567156
..............................................................TCTTTGGTATTCTAGCTGTAGA.........................................................................2214089.0040894089
..............................................................TCTTTGGTATTCTAGCTGTAGAT........................................................................23129.002929
................................................................TTTGGTATTCTAGCTGTAGATT.......................................................................22120.002020
................................................................TTTGGTATTCTAGCTGTAGA.........................................................................20118.001818
..............................................................TCTTTGGTATTCTAGCTGTA...........................................................................20118.001818
................................................................TTTGGTATTCTAGCTGTAG..........................................................................19114.001414
..............................................................................................................TAAAGCTTTTATACCAAAGCT..........................2119.0099
...............................................................CTTTGGTATTCTAGCTGTAG..........................................................................2015.0055
...............................................................CTTTGGTATTCTAGCTGTAGA.........................................................................2114.0044
..............................................................................................................TAAAGCTTTTATACCAAAGCTC.........................2214.0044
.................................................................TTGGTATTCTAGCTGTAGA.........................................................................1913.0033
..............................................................TCTTTGGTATTCTAGCTGTAGATT.......................................................................2413.0033
.................................................................TTGGTATTCTAGCTGTAG..........................................................................1813.0033
..............................................................TCTTTGGTATTCTAGCTGT............................................................................1911.0011
................................................................TTTGGTATTCTAGCTGTAGAT........................................................................2111.0011
..............................................................................................................TAAAGCTTTTATACCAAAG............................1911.0011
dp4
CTCTCCCATTCGCTGTCTGTCGACTTCCATGCACTTTTTGTTCTCCTTTAATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..............................................................TCTTTGGTATTCTAGCTGTAG..........................................................................2117678.0076786709969
..............................................................TCTTTGGTATTCTAGCTGTAGA.........................................................................2213324.0033242969355
..............................................................TCTTTGGTATTCTAGCTGTA...........................................................................20176.00764729
..............................................................TCTTTGGTATTCTAGCTGTAGAT........................................................................23171.0071638
..............................................................TCTTTGGTATTCTAGCTGT............................................................................19126.0026818
..............................................................................................................TAAAGCTTTTATACCAAAGCT..........................21116.0016115
................................................................TTTGGTATTCTAGCTGTAGA.........................................................................20112.0012120
................................................................TTTGGTATTCTAGCTGTAG..........................................................................19110.001091
................................................................TTTGGTATTCTAGCTGTAGATT.......................................................................2218.00862
..............................................................TCTTTGGTATTCTAGCTGTAGATT.......................................................................2417.00752
...............................................................CTTTGGTATTCTAGCTGTAG..........................................................................2017.00761
...............................................................CTTTGGTATTCTAGCTGTAGA.........................................................................2116.00660
....................................................................................TTGTTTTTTGCACATTGTATATCATC...............................................2615.00550
..............................................................................................................TAAAGCTTTTATACCAAAGCTC.........................2214.00440
...............................................................CTTTGGTATTCTAGCTGTAGAT........................................................................2214.00440
................................................................TTTGGTATTCTAGCTGTAGAT........................................................................2114.00440
.................................................................TTGGTATTCTAGCTGTAGA.........................................................................1913.00330
...........................................TCCTTTAATTTTTGCTGTT...............................................................................................1912.00220
.................................................................TTGGTATTCTAGCTGTAG..........................................................................1812.00220
..............................................................TCTTTGGTATTCTAGCTG.............................................................................1812.00211
.............................................................................................................CTAAAGCTTTTATACCAAAGCT..........................2212.00220
....................................................................................TTGTTTTTTGCACATTGTATATC..................................................2311.00101
..............................................................................................................TAAAGCTTTTATACCAAAG............................1911.00110
............................................................................................................TCTAAAGCTTTTATACCAAAGC...........................2211.00110

Secondary Structure

dm3

dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droSim1

dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droSec1

dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droYak2

dG=-21.6,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.1,  p-value=0.009901

droEre2

dG=-21.6,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.1,  p-value=0.009901

droAna3

dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

dp4

dG=-22.3,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droPer1

dG=-22.3,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droWil1

dG=-22.3,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droVir3

dG=-21.5,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droMoj3

dG=-20.9,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.3,  p-value=0.009901

droGri2

dG=-20.9,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-20.2,  p-value=0.009901

Generated: 03/07/2013 at 07:30 PM