Secondary structure and small RNA-seq evidence for dme-mir-285

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:11939178-11939306 - AC-----TTGCC---CT---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAGAACCCACTCA---------ATTTAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSim1 chr3L:11307954-11308082 - AC-----TTGCC---CA---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSec1 super_0:4127812-4127940 - AC-----TTGCC---CA---------------TCCACTTCAAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droYak2 chr3L:11984774-11984902 - TC-----TTGCC---CT---------------ACCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGACAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droEre2 scaffold_4784:11929878-11930011 - TCAGGAGCTGCA---CT---------------CCCACTTCGAGTCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAAGCCCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGGA------------GTGTC
droAna3 scaffold_13337:6191341-6191461 - GC---------C---AG---------------GATAATTCGAATCAAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGGAGATCCGATCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAACCACTCAACAGA-----------------
dp4 chrXR_group6:1929779-1929903 - TC-----TTACA---AT---------------TACAGTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGCTAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droPer1 gnl|ti|738578230:636-763 + TC-----TTACA---AT-------------T-TACAGTGGGAATCGAAGAACCTGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGATAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droWil1 scaffold_180949:5768880-5769006 + AC-----A------------------------AATTGTTCGAATTAAAGAAC-TGAGATCGATTGGTGCATAGATAAT----ATGCGAATTCTATCATTTGATTTCATTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATTAGAACCAATCAACAAG-----------------
droVir3 scaffold_13049:21101427-21101556 + AT-----GCAC----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGCCCAAAA--AGTAATTCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTCGAACCGATCAGCGGC------------GCATC
droMoj3 scaffold_6680:15475365-15475526 + AC-----ACACCCAGCAGACATCAAACACCACACCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATAACGCCCAAAAAG--TCATTTT----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTGGAACCGATCAACGGTGTATGGGAACAAGTGTC
droGri2 scaffold_15110:22570097-22570226 - AT-----GTAG----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGTCCAAGAA---TAATTTA----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTGTATTGGAACCGATCAGCGGC------------GCATT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:11939178-11939306 - AC-----TTGCC---CT---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAGAACCCACTCA---------ATTTAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSim1 chr3L:11307954-11308082 - AC-----TTGCC---CA---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSec1 super_0:4127812-4127940 - AC-----TTGCC---CA---------------TCCACTTCAAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droYak2 chr3L:11984774-11984902 - TC-----TTGCC---CT---------------ACCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGACAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droEre2 scaffold_4784:11929878-11930011 - TCAGGAGCTGCA---CT---------------CCCACTTCGAGTCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAAGCCCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGGA------------GTGTC
droAna3 scaffold_13337:6191341-6191461 - GC---------C---AG---------------GATAATTCGAATCAAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGGAGATCCGATCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAACCACTCAACAGA-----------------
dp4 chrXR_group6:1929779-1929903 - TC-----TTACA---AT---------------TACAGTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGCTAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droPer1 gnl|ti|738578230:636-763 + TC-----TTACA---AT-------------T-TACAGTGGGAATCGAAGAACCTGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGATAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droWil1 scaffold_180949:5768880-5769006 + AC-----A------------------------AATTGTTCGAATTAAAGAAC-TGAGATCGATTGGTGCATAGATAAT----ATGCGAATTCTATCATTTGATTTCATTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATTAGAACCAATCAACAAG-----------------
droVir3 scaffold_13049:21101427-21101556 + AT-----GCAC----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGCCCAAAA--AGTAATTCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTCGAACCGATCAGCGGC------------GCATC
droMoj3 scaffold_6680:15475365-15475526 + AC-----ACACCCAGCAGACATCAAACACCACACCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATAACGCCCAAAAAG--TCATTTT----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTGGAACCGATCAACGGTGTATGGGAACAAGTGTC
droGri2 scaffold_15110:22570097-22570226 - AT-----GTAG----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGTCCAAGAA---TAATTTA----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTGTATTGGAACCGATCAGCGGC------------GCATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ACTTGCCCAGCCACTTCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAGGAAAACCCACTCAATTC-AACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAAGTGTCSizeHit CountTotal NormTotalGSM343915
Embryo
...............................................................................TAGCACCATTCGAAATCAGTGC.............................2214.0044
...............................................................................TAGCACCATTCGAAATCAGTG..............................2113.0033
...............................................................................TAGCACCATTCGAAATCAGTGCT............................2312.0022
...........................ACTGAGATCGATTGGTGCATAGA................................................................................2312.0022
...............................................................................TAGCACCATTCGAAATCAGT...............................2011.0011
dp4
TCTTACAATTACAGTTCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAAGAGGACTCGCTAATTTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----SizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
...............................................................................TAGCACCATTCGAAATCAGTGCT............................23124878.0024878324875
...............................................................................TAGCACCATTCGAAATCAGTGC.............................22112336.0012336112335
...............................................................................TAGCACCATTCGAAATCAGTG..............................2111854.00185401854
...............................................................................TAGCACCATTCGAAATCAGT...............................2011064.00106401064
...........................ACTGAGATCGATTGGTGCATAGA................................................................................231426.004262424
...............................................................................TAGCACCATTCGAAATCAG................................19194.0094094
...........................ACTGAGATCGATTGGTGCATAG.................................................................................22173.0073073
..........................AACTGAGATCGATTGGTGCATAGA................................................................................24155.0055055
...............................................................................TAGCACCATTCGAAATCAGTGCTT...........................24144.0044044
..........................AACTGAGATCGATTGGTGCATAG.................................................................................23144.0044044
..............................................................................CTAGCACCATTCGAAATCAGTGCT............................24134.0034034
................................................................................AGCACCATTCGAAATCAGTGCT............................22133.0033033
..........................AACTGAGATCGATTGGTGCAT...................................................................................21133.0033033
..............................................................................CTAGCACCATTCGAAATCAGTGC.............................23128.0028028
...........................ACTGAGATCGATTGGTGCAT...................................................................................20122.0022022
...........................ACTGAGATCGATTGGTGCATA..................................................................................21117.0017017
................................................................................AGCACCATTCGAAATCAGTGC.............................21117.0017017
.................................................................................GCACCATTCGAAATCAGTGCT............................21113.0013013
..........................AACTGAGATCGATTGGTGCATA..................................................................................2219.00909
..........................AACTGAGATCGATTGGTGCA....................................................................................2016.00606
............................CTGAGATCGATTGGTGCATAGA................................................................................2216.00606
.................................................................................GCACCATTCGAAATCAGTGC.............................2016.00606
..............................................................................CTAGCACCATTCGAAATCAGTG..............................2215.00505
..................................................TATCAAGAGGACTCGCTAATT...........................................................2114.00404
.............................TGAGATCGATTGGTGCATAGA................................................................................2114.00404
..................................................TATCAAGAGGACTCGCTAATTTTC........................................................2413.00303

Secondary Structure

dm3

-33.4 -33.3 -32.5 -32.5 -32.5 -32.5

droSim1

-30.6 -30.1 -30.0 -29.7 -29.7 -29.7

droSec1

-29.6 -29.3 -29.1 -29.0 -28.8 -28.7

droYak2

-30.0 -29.5 -29.1 -29.1 -29.1 -29.1

droEre2

-30.8 -30.6 -30.4 -30.2 -29.9 -29.9

droAna3

-33.4 -32.5 -32.5 -32.5 -32.5

dp4

-32.7 -31.9 -31.8 -31.8 -31.8 -31.8

droPer1

-29.4 -29.0 -28.5 -28.5

droWil1

-33.5 -33.2 -32.6 -32.6 -32.6 -32.6

droVir3

-27.6 -27.3 -26.7 -26.7

droMoj3

-29.3 -29.1 -29.0 -28.6 -28.4 -28.4

droGri2

-28.5 -27.9 -27.9 -27.8 -27.8 -27.6

Generated: 01/05/2013 at 05:14 PM