Secondary structure and small RNA-seq evidence for dme-mir-2493

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:10956461-10956596 - TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCATGTGCATGG----AGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATGG
droSim1 chr3R:10501806-10501941 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATAG
droSec1 super_0:10986595-10986730 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACACA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATTTGTGCGAGGCGTTGGCGTTCTGACC----AGCA------GAAGAGGAAGATAG
droYak2 chr3R:15471091-15471226 + TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACACACACAGG--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCGTGT------------GTATGTGTGCGAGGCGTTGGCGTTCTGACC----AGAA------GAAGAGGAAGATAA
droEre2 scaffold_4770:10485021-10485154 - TATAA------------TGTGTGTG------------TGC-GCTATTATTAAAACCCCC----------------------------------------AAC----------GCTCACACAC--ACAGA--GCCGTGTGCATGG----GGCA-----AAAA-----A-------------CTATGGCCATGT------------GTATGTGTGCGAGGCGTTGGCGTTCTGACC----AGAA------GAAGAGGAAGATAA
droAna3 scaffold_13340:6023187-6023339 - TATAA------------TGTGTGTGTGTGTG--TGTTTGT-GCTATTATTAAAACCCCC----------------------------------------CTC----------GCAAGCACCC-CCCACT--GCCAC-TGCATAG----AGCAAAAAAAAAAAAAAAA-------------CTATAGTGGTGT------------GTG-GCAGGCGAGGCGTTGGCGTTTTGACC----AAAA------GCTGAAGAAGAGGA
dp4 chr2:20937547-20937682 - TATAA------------CGTGTGTGTGAGTG------TGT-GCTATTATTAAACTCCCT---------CCCTAA---------------------------------------CAC----G--CACACA--ACTATGT-TATG----------------TA-----A-------------GTGTGTGTGTGT------------GTGTGTGTGTGAGGCGTTGGCGTTTTGACC----AGAAGCTGAAGAAGAGGAAGAATA
droPer1 super_3:3688114-3688249 - TATAA------------CGTGTGTGTGAGTG------TGT-GCTATTATTAAACTCCCT---------CCCTAA---------------------------------------CAC----G--CATACA--ACTATGT-TGTG----------------TA-----A-------------GTGTGTGTGTGT------------GTGTGTGTGTGAGGCGTTGGCGTTTTGACC----AGAAGCTGAAGAAGAGGAAGAATA
droWil1 scaffold_181130:7306738-7306938 + CAAATGGTATGCGTCTATGTGTATGTGTGTGCCTGTGTGTGGCTATTATTAAAAATCCACACCTCCTACCCCAACCCCCCGTTACATATACACACAACCAATACATCCATACGCCCACACATACACATA--CATGAAAAGAAAA----GGA------AAAAAAAGAA-------------CT------------------------------ATGAGGCGTTGGCGTTCGTTCCGGGCACTA------CAAGAAGAAGAAGA
droVir3 scaffold_13047:7645546-7645687 - CATAT------------TGTACGTG------------TGT-GCTATTATTAAAATGCCA----------------------------------------CAC----------GCACGCACAC--ATAGAGACGGGGGGACACGGACACGGCA-----AAAAGAAAAACTATTCTC--------AGAGTGTGT------------GTGCGCCTACGAGGCGTTGGCGTTTTGGCT----AGAA------GAAGC--------A
droMoj3 scaffold_6540:3604660-3604829 - TATAT------------TGTATGTG------------TGT-GCTATTATTAAAATACCA----------------------------------------CAT----------GCACGCACACACAGAGA--GGCAGAGACACGGACACAGCA-----AAAAGAAAAACTATTTACAGTTGCTGCGACTGTGTGTATATACATATATGCGCCTACGAGGCGTTGGCGTTTCAGCA----AGCG------AGAGAGTGAGAGAG
droGri2 scaffold_15245:14649244-14649349 + AACAA----------------------------------------------------GC----------------------------------------AAC----------ACACACACACACACACA--CACACACGCA-------GACA-----AAGA-----A-------------ACACACACTCAC------------ATACATC-TTGATGTGTTCATATTTATGCCA---AGTC------AAACTCAAAAGCTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:10956461-10956596 - TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCATGTGCATGGAGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATGG
droSim1 chr3R:10501806-10501941 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATAG
droSec1 super_0:10986595-10986730 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGCAGAAGAGGAAGATAG
droYak2 chr3R:15471091-15471226 + TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACACACACAGGGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAAGAAGAGGAAGATAA
droEre2 scaffold_4770:10485021-10485154 - TATAATGTGTGTGTGCGCTATTATTAAAACCCCCAACGCTCACACA--CACAGAGCCGTGTGCATGGGGCAAAAAACTATGGCCATGTGTATGTGTGCGAGGCGTTGGCGTTCTGACCAGAAGAAGAGGAAGATAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TATAATGTGTGT------GTGCGCTATTATTAAAACCCCCAACGCTCACACACACACACAGCCGTGTGCATGGGGCAAAAAACTATGGCCGTGTGTATTTGTGCGAGGCGTTGGCGTTCTGACCAGC------AGAAGAGGAAGATAGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATAACGTGTGTGTGAGTGTGTGCTATTATTAAACTCCCT----CCCTAACACGCACACAACTATGT-TATG-------TAAGTGTGTGTGTGTGTGTGTGTGTGAGGCGTTGGCGTTTTGACCAGAAGCTGAAGAAGAGGAAGAATASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..................................................................................GTGTGTGTGTGTGTGTGTGTGTG...........................................2361.00606
...................................................................................TGTGTGTGTGTGTGTGTGT..............................................19150.13202

Secondary Structure

dm3

-37.6 -37.6 -36.7 -36.7

droSim1

-37.1 -37.1 -36.2 -36.2

droSec1

-37.1 -37.1 -36.2 -36.2

droYak2

-42.6 -42.4 -42.2 -41.8 -41.8 -41.7

droEre2

-33.7 -33.6 -33.5 -33.4 -33.3 -33.2

droAna3

-28.3 -28.2 -28.2 -28.1 -28.1 -28.0

dp4

-24.5 -24.2 -24.1 -24.0 -23.8 -23.7

droPer1

-22.2 -22.1 -21.8 -21.8 -21.8 -21.8

droWil1

-12.37 -12.27 -12.0 -11.87 -11.8 -11.7

droVir3

-34.7 -34.6 -34.5 -34.5 -34.4 -34.4

droMoj3

-29.57 -28.97 -28.77 -28.77 -28.67

droGri2

-6.4 -6.2 -5.6 -5.5 -5.5 -5.4

Generated: 01/05/2013 at 05:10 PM