Secondary structure and small RNA-seq evidence for dme-mir-960

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:5641048-5641170 + TATC---G-----TA------------CCGCCCAC---------------------G---GGTTTTGTACCACATTCTGAGTATTCCAGATTGC-ATAGCTTTGTGCTAC------TATTGCTATACGGTCTGGGACACTTTTAACATGGTATCAA-ATCAG---------ATTCA----------------CCTAATAG
droSim1 chr2L:5434134-5434256 + CATC---G-----TC------------ACGCCCAC---------------------G---GGTTTTGTACCACATTCAGAGTATTCCAGGTTGC-ATAGCTTTGTGCTAC------TATTGCTGTACGATCTGGGACACTTTTAACATGGTATCAA-ATCTG---------ATTCC----------------CCCAAACG
droSec1 super_5:3718789-3718911 + CATC---G-----TA------------CCGCCCAC---------------------G---GGTTTTGTACCACATTCTGAGTATTCCAGATTGC-ATAGCTTTGTGCTAC------TATTGCTGTACGATCTGGGAGACTTTTAACATGGTATCAA-ATCTG---------ATTCC----------------CCCAAAGG
droYak2 chr2L:13552137-13552259 - CATC---G-----CT------------TCGCCCGC---------------------G---TGTTTTGTACCAGATTCTGAGTATTCCTGATTGC-ATAGCTTTGGCCTTT------GATTGCTATACGGTCTGGGACACTTTTAACGTGGTATCAA-ATCTG---------ATTCA----------------ACCGAAGG
droEre2 scaffold_4929:5729522-5729643 + CAAC---G-----CA------------CCGCCCGC---------------------G---TTTTTTGTGCCAGATTCAGAGTATTCCAGATTGC-ATAGCTTTGGGCTTT------GATTGCTATACGGTCTGGGACACTTTAAACGTGGCATCAA--TCCT---------ATTCA----------------ACTGATGG
droAna3 scaffold_12916:11084824-11084972 + TATC---G-----GCCAATAGGCCAATTAACCCGGACC---A------ATCAATATG---AGTTTTGTGCCAGATTCTGAGTATTCCTGATTGC-ATAGCTCTGTGTTGT------GACTGCTATACGGTCTGGGACACTTCTAACATGGCATCAA-ATCTG---------TGTCAAC--------------GGCAGCAG
dp4 chr4_group4:3182464-3182586 - TGTG---G-----GT------------GTGCGTGT---------------------GTGCGGGTGTGTGCTATATTCTGAGTATTGCCTCCTGTTGTAGTTGTGGAATATTGAAATATCAACTATACGGTTCGGAATCCTCTAAATATGGCAGCC--------------------A----------------CTAAAGAC
droPer1 super_10:2201395-2201525 - TATACACGTAAATGT------------GTGTGGGT---------------------GTGCGGGTGTGTTCTATATTCTGAGTATTGCCTCCTGTTGTAGTTGTGGAATATTGAAATATCAACTATACGGTTCGGAATCCTCTAAATATGGCAGCC--------------------A----------------CTAAAGAC
droWil1 scaffold_180708:8626131-8626297 - TAAG---A-----AT------------TAACTTTGAATTGGAAACGATATTGAAA-T---GAATTTATGCTAAATTCTGAGTATTCCTGATTGC-ATAGTGTGTATTTGA------TACTACTATACGGTCGGGGAAACTTTTAACATGGCCCAAA--TGATAAATGACAGTGACAATGAAAAAGAAAATACCAAAACAG
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6500:14018206-14018306 + TAA-----------------------------------------------------------------GTCATGCTTTGAGTATTCCTTATTGC-ATAGTTTAC--ATAT------AATTACTATACAGTCTGGAGCACTTAAAGTTGGGCATAGACAACCG---------AACAA----------------CTTAGGAG
droGri2 scaffold_15252:3146997-3147109 + TGTT---G-----AT------------TGGCCTTG---------------------G-------TTATGCTAAATTCCAAGTATTCCTTATTGC-ATAGTTTATAAT--T------GAATACTATACAATCTGGCGTTCTTAGAATTTGTCATAAG-AC-------------TTCA----------------CATAACAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:5641048-5641170 + TATC---G-----TA------------CCGCCCAC---------------------G---GGTTTTGTACCACATTCTGAGTATTCCAGATTGC-ATAGCTTTGTGCTAC------TATTGCTATACGGTCTGGGACACTTTTAACATGGTATCAA-ATCAG---------ATTCA----------------CCTAATAG
droSim1 chr2L:5434134-5434256 + CATC---G-----TC------------ACGCCCAC---------------------G---GGTTTTGTACCACATTCAGAGTATTCCAGGTTGC-ATAGCTTTGTGCTAC------TATTGCTGTACGATCTGGGACACTTTTAACATGGTATCAA-ATCTG---------ATTCC----------------CCCAAACG
droSec1 super_5:3718789-3718911 + CATC---G-----TA------------CCGCCCAC---------------------G---GGTTTTGTACCACATTCTGAGTATTCCAGATTGC-ATAGCTTTGTGCTAC------TATTGCTGTACGATCTGGGAGACTTTTAACATGGTATCAA-ATCTG---------ATTCC----------------CCCAAAGG
droYak2 chr2L:13552137-13552259 - CATC---G-----CT------------TCGCCCGC---------------------G---TGTTTTGTACCAGATTCTGAGTATTCCTGATTGC-ATAGCTTTGGCCTTT------GATTGCTATACGGTCTGGGACACTTTTAACGTGGTATCAA-ATCTG---------ATTCA----------------ACCGAAGG
droEre2 scaffold_4929:5729522-5729643 + CAAC---G-----CA------------CCGCCCGC---------------------G---TTTTTTGTGCCAGATTCAGAGTATTCCAGATTGC-ATAGCTTTGGGCTTT------GATTGCTATACGGTCTGGGACACTTTAAACGTGGCATCAA--TCCT---------ATTCA----------------ACTGATGG
droAna3 scaffold_12916:11084824-11084972 + TATC---G-----GCCAATAGGCCAATTAACCCGGACC---A------ATCAATATG---AGTTTTGTGCCAGATTCTGAGTATTCCTGATTGC-ATAGCTCTGTGTTGT------GACTGCTATACGGTCTGGGACACTTCTAACATGGCATCAA-ATCTG---------TGTCAAC--------------GGCAGCAG
dp4 chr4_group4:3182464-3182586 - TGTG---G-----GT------------GTGCGTGT---------------------GTGCGGGTGTGTGCTATATTCTGAGTATTGCCTCCTGTTGTAGTTGTGGAATATTGAAATATCAACTATACGGTTCGGAATCCTCTAAATATGGCAGCC--------------------A----------------CTAAAGAC
droPer1 super_10:2201395-2201525 - TATACACGTAAATGT------------GTGTGGGT---------------------GTGCGGGTGTGTTCTATATTCTGAGTATTGCCTCCTGTTGTAGTTGTGGAATATTGAAATATCAACTATACGGTTCGGAATCCTCTAAATATGGCAGCC--------------------A----------------CTAAAGAC
droWil1 scaffold_180708:8626131-8626297 - TAAG---A-----AT------------TAACTTTGAATTGGAAACGATATTGAAA-T---GAATTTATGCTAAATTCTGAGTATTCCTGATTGC-ATAGTGTGTATTTGA------TACTACTATACGGTCGGGGAAACTTTTAACATGGCCCAAA--TGATAAATGACAGTGACAATGAAAAAGAAAATACCAAAACAG
droMoj3 scaffold_6500:14018206-14018306 + TAA-----------------------------------------------------------------GTCATGCTTTGAGTATTCCTTATTGC-ATAGTTTAC--ATAT------AATTACTATACAGTCTGGAGCACTTAAAGTTGGGCATAGACAACCG---------AACAA----------------CTTAGGAG
droGri2 scaffold_15252:3146997-3147109 + TGTT---G-----AT------------TGGCCTTG---------------------G-------TTATGCTAAATTCCAAGTATTCCTTATTGC-ATAGTTTATAAT--T------GAATACTATACAATCTGGCGTTCTTAGAATTTGTCATAAG-AC-------------TTCA----------------CATAACAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CATCGTCACGCCCACG---GGTTTTGTACCACATTCAGAGTATTCCA---------GGTTGCATAGCTTTGTGCTACTATTGCTGTACGATCTGGGACACTTTTAACATGGTATCAAATCTGATTCCCCCAAACGSizeHit CountTotal NormTotalGSM343915
Embryo
......................................AGTATTCCA---------GGTTGCATAGCTT..................................................................2211.0011
....................................AGAGTATTCCA---------GGTTGCATAGC....................................................................2211.0011
dp4
TGTGGGTGTGCGTGTGTGCGGGTGTGTGCTATATTCTGAGTATTGCCTCCTGTTGTAGTTGTGGAATATTGAAATATCA--ACTATACGGTTCGGAATCCTCTAAATATGGCAGC----------CACTAAAGACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
....................................TGAGTATTGCCTCCTGTTGTAG.............................................................................22156.0056056
....................................TGAGTATTGCCTCCTGTTGTAGT............................................................................23120.0020020
....................................TGAGTATTGCCTCCTGTTGTA..............................................................................21110.0010010
....................................TGAGTATTGCCTCCTGTTG................................................................................1919.00909
....................................TGAGTATTGCCTCCTGTTGTAGTT...........................................................................2415.00505
....................................TGAGTATTGCCTCCTGTTGT...............................................................................2013.00303
...................................................................................TATACGGTTCGGAATCCTCTAA..............................2213.00303

Secondary Structure

dm3

dG=-22.3,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droSim1

dG=-22.9,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901

droSec1

dG=-22.8,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.8,  p-value=0.009901

droYak2

dG=-17.1,  p-value=0.009901 dG=-16.2,  p-value=0.009901

droEre2

dG=-22.3,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droAna3

dG=-18.1,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.3,  p-value=0.009901

dp4

dG=-14.3,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.5,  p-value=0.009901

droPer1

dG=-14.3,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.5,  p-value=0.009901

droWil1

dG=-22.6,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

dG=-20.4,  p-value=0.009901

droGri2

dG=-12.4,  p-value=0.009901 dG=-12.3,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.8,  p-value=0.009901 dG=-11.7,  p-value=0.009901

Generated: 03/07/2013 at 07:08 PM