Secondary structure and small RNA-seq evidence for dme-mir-313

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:16471680-16471780 - TCGTTCT--AGCCAACAA---TTTTCTGCTGCGGATGGGGGCAGTACTG--------------------------TTTTTTTAACATT--GAGTATTGCACTTTTCACAGCCCG-----AAAATGTTAGCAACTGC-CTT
droSim1 chr2R:15132971-15133071 - TCGATCT--AGCCAACAA---TTTTCTGCTGCGCATTGGGGCACTACTG--------------------------TTTTTTTTAAATT--GAGTATTGCACTTTTCACAGCCTT-----AAAATGTTAGCAACTGC-CTA
droSec1 super_1:14025885-14025985 - TCGATCT--AGCCAACAA---TTTTCTGCTGCGCATTGGGGCACTACTG--------------------------TTTTTTTTTAATT--GAGTATTGCACTTTTCACAGCCTT-----AAAATGTTAGCAACTGC-CTA
droYak2 chr2R:12724540-12724640 + TCTACGT--AGCCAACAA---TTTTCGGCTGTGGATTGGGCTAGTACTG--------------------------TGATTTTAGCATT--AAGTATTGCACATTCCCCAGCCTG-----AAAGTGTTAGTAACTGC-CAA
droEre2 scaffold_4845:10618281-10618381 - TCGATGT--AGCCAACAA---TTTTCGGCTGTGGAGTGGGCTAGTACTG--------------------------TGATTTTAACATT--GAGTATTGCACATTCCCCAGCCTG-----AAAGTGTTTGCATTTGC-CAA
droAna3 scaffold_13266:4132526-4132623 + TTT--GT--AGTCAGCAT---TTCCAGACTGTGGTTTGGGCAGATACTA--------------------------CATTTT--AGGAT--CAGTATTGCACATTCCCCAGCCTG-----GAAACGCTTGCGACAGA-CCT
dp4 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droPer1 super_4:2566453-2566554 + TTCGTGTTCGGTGGATAC---CTTCAAGCTGGGGGATGGG-CAATACTG--------------------------TGTTGTATTTGAA--CAGTATTGCACACCCACTGGCCTG-----AAAGTGCCTACTGCTGG-GTT
droWil1 scaffold_180700:3452993-3453102 + TTAATTATTTGTCCAAATTTAGTTCTGGCTGCGGTTTGTGCAAATTACT---T----------------------ATTTT--TTTGTA--AAGTATTGCACAACCTACAGCCTGGCACTAAATGGAGAAAAATCAT-CAA
droVir3 scaffold_12875:13669100-13669187 - T---------------------TTTCGGCTGTGGTCAGTGTCAATTCTT--------------------------TTTTTTTATTTTTACAAGTATTGCACTTTTCACGGCCGG-----AAAAATTGAGATTCCATTTAA
droMoj3 scaffold_6496:9090655-9090750 - TTT--TT--TGCATTCGT---TTTCCGGTTGTGAATTGTGTCAATTCTT--------------------------TTTATTTTAC-----AAGTATTGCACTTTTCACGGCCGG-----AAAAAGGATAAAATATT-TAA
droGri2 scaffold_15245:17564118-17564229 + TCATTAT--CCCGAACAA---CATCATTCCGCGCTCGGCTTTAGAATTTGTTCCTTATTTTGTGAGGATAATTTACAATTC--GAAGA--TAATAT-----------TGGC-AG-----GATATG-TTACAGTTCC-TCT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:16471680-16471780 - TCGTTC--TAGCCA-A--CAATTTTCTGCTGCGGATGGGGGCAGTA-CTGTTTTTTTAACATT--GAGTATTGCACTTTTCACAGCCCG-----AAAATGTTAGCAACT-GCCTT
droSim1 chr2R:15132971-15133071 - TCGATC--TAGCCA-A--CAATTTTCTGCTGCGCATTGGGGCACTA-CTGTTTTTTTTAAATT--GAGTATTGCACTTTTCACAGCCTT-----AAAATGTTAGCAACT-GCCTA
droSec1 super_1:14025885-14025985 - TCGATC--TAGCCA-A--CAATTTTCTGCTGCGCATTGGGGCACTA-CTGTTTTTTTTTAATT--GAGTATTGCACTTTTCACAGCCTT-----AAAATGTTAGCAACT-GCCTA
droYak2 chr2R:12724540-12724640 + TCTACG--TAGCCA-A--CAATTTTCGGCTGTGGATTGGGCTAGTA-CTGTGATTTTAGCATT--AAGTATTGCACATTCCCCAGCCTG-----AAAGTGTTAGTAACT-GCCAA
droEre2 scaffold_4845:10618281-10618381 - TCGATG--TAGCCA-A--CAATTTTCGGCTGTGGAGTGGGCTAGTA-CTGTGATTTTAACATT--GAGTATTGCACATTCCCCAGCCTG-----AAAGTGTTTGCATTT-GCCAA
droAna3 scaffold_13266:4132526-4132623 + TT--TG--TAGTCA-G--CATTTCCAGACTGTGGTTTGGGCAGATA-CTACATTTT--AGGAT--CAGTATTGCACATTCCCCAGCCTG-----GAAACGCTTGCGACA-GACCT
droPer1 super_4:2566453-2566554 + TTCGTGTTCGGTGG-A--TACCTTCAAGCTGGGGGATGGG-CAATA-CTGTGTTGTATTTGAA--CAGTATTGCACACCCACTGGCCTG-----AAAGTGCCTACTGCT-GGGTT
droWil1 scaffold_180700:3452993-3453102 + TTAATTATTTGTCCAAATTTAGTTCTGGCTGCGGTTTGTGCAAATTACTTATTT--TTTTGTA--AAGTATTGCACAACCTACAGCCTGGCACTAAATGGAGAAAAATC-ATCAA
droVir3 scaffold_12875:13669100-13669187 - T---------------------TTTCGGCTGTGGTCAGTGTCAATT-CTTTTTTTTTATTTTTACAAGTATTGCACTTTTCACGGCCGG-----AAAAATTGAGATTCCATTTAA
droMoj3 scaffold_6496:9090655-9090750 - TTT--T--TTGCAT-T--CGTTTTCCGGTTGTGAATTGTGTCAATT-CTTTTTATTTTAC-----AAGTATTGCACTTTTCACGGCCGG-----AAAAAGGATAAAATA-TTTAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCGATCTAGCCAACAATTTTCTGCTGCGCATTGGGGCACTACTGTTTTTTTTAAATTGAGTATTGCACTTTTCACAGCCTTAAAATGTTAGCAACTGCCTASizeHit CountTotal NormTotalGSM343915
Embryo
............................................................TATTGCACTTTTCACAGCCTTA...................221226.00226226
............................................................TATTGCACTTTTCACAGCCTTAA..................231180.00180180
............................................................TATTGCACTTTTCACAGCCTT....................21171.007171
.....................TGCTGCGCATTGGGGCACTACTG.........................................................23168.006868
.....................TGCTGCGCATTGGGGCACTACT..........................................................22165.006565
............................................................TATTGCACTTTTCACAGCCTTAAA.................24121.002121
.....................TGCTGCGCATTGGGGCACTAC...........................................................21120.002020
.....................TGCTGCGCATTGGGGCACTA............................................................20112.001212
............................................................TATTGCACTTTTCACAGCCT.....................2019.0099
....................CTGCTGCGCATTGGGGCACTACT..........................................................2319.0099
...........................................................GTATTGCACTTTTCACAGCCTT....................2216.0066
....................CTGCTGCGCATTGGGGCACT.............................................................2014.0044
.....................TGCTGCGCATTGGGGCACT.............................................................1913.0033
....................CTGCTGCGCATTGGGGCAC..............................................................1912.0022
...................TCTGCTGCGCATTGGGGCAC..............................................................2012.0022
...........................................................GTATTGCACTTTTCACAGCCTTA...................2312.0022
....................CTGCTGCGCATTGGGGCACTAC...........................................................2212.0022
....................CTGCTGCGCATTGGGGCA...............................................................1811.0011
.....................TGCTGCGCATTGGGGCACTACTGT........................................................2411.0011
...................TCTGCTGCGCATTGGGGCACTACT..........................................................2411.0011
....................CTGCTGCGCATTGGGGCACTACTG.........................................................2411.0011
dp4
-----------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-21.3 -21.0 -20.9 -20.9 -20.8 -20.6

droSim1

-10.7 -10.7 -10.7 -10.7 -10.2 -10.2

droSec1

-10.7 -10.7 -10.4 -10.4 -9.9 -9.9

droYak2

-25.2 -25.0 -24.6 -24.6 -24.5 -24.4

droEre2

-28.0 -27.8 -27.7 -27.5 -27.4 -27.2

droAna3

-22.1 -22.1 -21.9 -21.9 -21.8 -21.8

dp4

No secondary structure predictions returned

droPer1

-30.1 -29.2

droWil1

-27.0 -27.0 -27.0 -26.9 -26.9 -26.9

droVir3

-24.3 -23.5 -23.4 -23.3

droMoj3

-29.6 -28.8 -28.7 -28.6

droGri2

-12.7 -12.7 -12.7 -12.5 -12.5 -12.5

Generated: 01/05/2013 at 05:17 PM