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

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:19558216-19558323 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGCCCAGCGAGA
droSim1 chr3L:18890412-18890519 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droSec1 super_29:261369-261476 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droYak2 chr3L:20989402-20989507 - CTCT--------ATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droEre2 scaffold_4784:19355664-19355769 + CTCT--------ATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droAna3 scaffold_13337:17332424-17332537 - ATCTTATATAACACTATGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
dp4 chrXR_group8:7634812-7634919 + TTCT------TCAATCAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
droPer1 super_48:412952-413059 + TTCT------TCAATCAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
droWil1 scaffold_180727:842215-842322 + CCCTCGC---ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATACATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTTCATC---A
droVir3 scaffold_13049:13137002-13137114 + CGACCAGCCAGGATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTGCTCAACGTA-
droMoj3 scaffold_6680:14226499-14226603 - A---------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTGCTCAGCGTAA
droGri2 scaffold_15110:23882734-23882841 + TGCC------GCATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTCTTCAACGTAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:19558216-19558323 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGCCCAGCGAGA
droSim1 chr3L:18890412-18890519 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droSec1 super_29:261369-261476 + CTCT------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droYak2 chr3L:20989402-20989507 - CTCT--------ATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droEre2 scaffold_4784:19355664-19355769 + CTCT--------ATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAA
droAna3 scaffold_13337:17332424-17332537 - ATCTTATATAACACTATGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
dp4 chrXR_group8:7634812-7634919 + TTCT------TCAATCAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
droPer1 super_48:412952-413059 + TTCT------TCAATCAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAA
droWil1 scaffold_180727:842215-842322 + CCCTCGC---ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATACATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTTCATC---A
droVir3 scaffold_13049:13137002-13137114 + CGACCAGCCAGGATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTGCTCAACGTA-
droMoj3 scaffold_6680:14226499-14226603 - A---------ATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTGCTCAGCGTAA
droGri2 scaffold_15110:23882734-23882841 + TGCC------GCATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGTGTCTCTTCAACGTAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTCTATATACAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGACCAGCGAAASizeHit CountTotal NormTotalGSM343915
Embryo
........................TCTTTGGTTATCTAGCTGTATG..............................................................22155214.005521455214
........................TCTTTGGTTATCTAGCTGTATGA.............................................................23121390.002139021390
...............................................................TAAAGCTAGCTTACCGAAGTTA.......................2211825.0018251825
........................TCTTTGGTTATCTAGCTGTAT...............................................................211902.00902902
...............................................................TAAAGCTAGCTTACCGAAGTT........................211511.00511511
..............................................................ATAAAGCTAGCTTACCGAAGTTA.......................231375.00375375
...............................................................TAAAGCTAGCTTACCGAAGTTAA......................231301.00301301
..............................................................ATAAAGCTAGCTTACCGAAGTT........................221247.00247247
..........................TTTGGTTATCTAGCTGTATG..............................................................201137.00137137
..............................................................ATAAAGCTAGCTTACCGAAGTTAA......................24178.007878
..........................TTTGGTTATCTAGCTGTATGA.............................................................21153.005353
.........................CTTTGGTTATCTAGCTGTATG..............................................................21142.004242
........................TCTTTGGTTATCTAGCTGTA................................................................20138.003838
...........................TTGGTTATCTAGCTGTATG..............................................................19118.001818
.........................CTTTGGTTATCTAGCTGTATGA.............................................................22112.001212
...........................TTGGTTATCTAGCTGTATGA.............................................................20110.001010
........................TCTTTGGTTATCTAGCTGTATGAG............................................................2418.0088
................................................................AAAGCTAGCTTACCGAAGTTA.......................2114.0044
........................TCTTTGGTTATCTAGCTGT.................................................................1914.0044
dp4
TTCTTCAATCAGGGTGCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGCGTCTGTCCAGCGAAASizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
........................TCTTTGGTTATCTAGCTGTATG..............................................................22139978.0039978376182360
........................TCTTTGGTTATCTAGCTGTATGA.............................................................23125244.0025244228462398
........................TCTTTGGTTATCTAGCTGTAT...............................................................2116922.00692225204402
...............................................................TAAAGCTAGCTTACCGAAGTTA.......................2212318.0023181801517
...............................................................TAAAGCTAGCTTACCGAAGTT........................211767.00767302465
..............................................................ATAAAGCTAGCTTACCGAAGTTA.......................231608.0060852088
..............................................................ATAAAGCTAGCTTACCGAAGTT........................221279.0027918099
........................TCTTTGGTTATCTAGCTGTA................................................................201222.0022268154
...............................................................TAAAGCTAGCTTACCGAAGTTAA......................231184.001841768
........................TCTTTGGTTATCTAGCTGT.................................................................191156.0015615141
..........................TTTGGTTATCTAGCTGTATG..............................................................20191.0091847
..............................................................ATAAAGCTAGCTTACCGAAGTTAA......................24169.0069645
..........................TTTGGTTATCTAGCTGTATGA.............................................................21162.0062539
.........................CTTTGGTTATCTAGCTGTATG..............................................................21130.0030300
.........................CTTTGGTTATCTAGCTGTATGA.............................................................22128.0028235
..............................................................ATAAAGCTAGCTTACCGAAGT.........................21120.0020416
...............................................................TAAAGCTAGCTTACCGAAGT.........................20119.0019217
..........................TTTGGTTATCTAGCTGTAT...............................................................19114.001459
...........................TTGGTTATCTAGCTGTATGA.............................................................20111.001192
..............................................................ATAAAGCTAGCTTACCGAAG..........................2019.00954
...........................TTGGTTATCTAGCTGTATG..............................................................1918.00880
................................................................AAAGCTAGCTTACCGAAGTTA.......................2116.00651
........................TCTTTGGTTATCTAGCTGTATGAG............................................................2416.00660

Secondary Structure

dm3

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droSim1

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droSec1

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droYak2

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droEre2

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droAna3

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

dp4

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droPer1

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droWil1

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droVir3

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droMoj3

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

droGri2

dG=-24.0,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901

Generated: 03/07/2013 at 07:28 PM