Secondary structure and small RNA-seq evidence for dme-mir-4985

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:20181738-20181869 + ATAAAAAGTATGTCACT------------------T-GGGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGAATGGAAAATGTCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGTTTGGCCTACCCGTCTACCA-GCCAACC----AACCA
droSim1 chr2R:18643325-18643449 + ATAAAAAGTATGTCACT---------------TGGTG-GGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGCCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGATTG---------AAGGCC-C-GTGGCC----AACCA
droSec1 super_23:61187-61303 + ATAAAAAGTATGTCACT---------------TGGTG-GGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGTCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGATTG---------AAGGCC-C-GTG------------
droYak2 chr2R:20147877-20148015 + ATAAAAAGTATGTCACT------------------G-GGGG-GCGCTGCACT---------GGCACTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGCGAAATGTCGCCAAACGAAAAA----ATAAATCA----------------------------------------------------TAG------------------------------------------------------------------------TGTAACTCGTTTG---------AAGGCCACACCAACT----AGTAA
droEre2 scaffold_4845:21546843-21546980 + ATAAAAAGTATGTCACT---------------A----GGGGGCTTCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGTCGCCGCACAAAAAA--------AGTG----------------------------------------------------TAG------------------------------------------------------------------------TGTAAATCGTTTG---------AAGGCC-C-ATGGCCAACCAACCG
droAna3 scaffold_13266:14229911-14230049 - AAAAAAAGTATGTCACA---------------C--TG-GGG-GAACTGCACT---------GACATTGAAAAACTGAA------TTACATTGGACGGTGGATGGG-------------------------------------------TGGACTGATGGACTGATGGACTGACAGCCA-------------------------------------------------------CGATCATC--------ACTAGCGTCGCAGTTAAGTTATGTAA-------------------------------------ACCG
dp4 chr3:18492568-18492741 - GTAAAAAGTATGTCAGAGAAGAGAAGAGAACACAGTGGGCG-CTGCTGCACT---------GACATTGAAA-AGTGAA------TTGCATTGATCATGACGGGGGGTTGA-------CGCTG-------------------------------------------------ACTGCCACGAACCGCTCAGAACAATAGTGTAAATGTGGAATAATGCTCG--------------------------------------------------TAGAAC-CCATTC---------G----CA-GTCCATG----GGCTG
droPer1 super_45:328754-328870 - GTGAAATGTATTTGAAA---------------------------------CG---------AGTAACGGAA-ATTGCA------TTATTTCAATTACAAA-----------------------------------TCCAATGAGAGGGAGAGGG-------ACAGGGA----C---------------------------------------------AGGG-------------------------------------------ACCCAGCACAA-----------CCCTAGGAGCCA-GCCAGCC----AGCCA
droWil1 scaffold_180949:4063354-4063494 - ATTGAGGGCGTGATTTA------------------TG-CCC-GATCTACCCC---------ATCATTTAAT-GTTAAAGACAATGCTAATTGGCCATTAAAATAGGCCG-----------CA------------------------ACAGACAC-------AAATAGT----T---------------------------------------------TGGGACCTA------AAATCAAA-------------------------------------------GCCAACCGACCACCA-GCCAACC----AGCCA
droVir3 scaffold_12875:7276052-7276211 + GG----------------------------------------GCGCTGCATTTGCCAGGCCAGAGTTAAAA-AGTGAA------TTGAATTGGCCGCTTGATTGA-------------------------------------------CAG-CCGACGGGCTGA-------------------------------------ATATGTGCAGCAATGCCAACAAATCGATGCCAAAGTCAGTGTCAGTCCCACGTAATCGACAATCAGTTATTTAC-----------------------A-TACGAGC----CACAA
droMoj3 scaffold_6473:1699609-1699741 - ATAATCTATTAGTTATT---------------TAATA-TAT-GT------------------------------CAATCATTCAGCCACTCAATCATTAA-----------------------------------GTTAATCAACGAGTAACTC-------AATCAGT----C---------------------------------------------AGTCATTCAGTGCCTCAATCGTT----------------------------------------AAGTCTTCCAATAAGTCA-CTCAATC----AGTCA
droGri2 scaffold_15203:4626832-4626941 - GCCCATGCCA--------------------------------------------------------TAAAA-AGAGTT------TTGAACTAATCTTAAGCAGGCAGCGCAAATCGCTATAAATCAG-CTTTCTATTCTT--------------------------------------------------------TG------------------------------------------------------------------------TT---------TTGCCCCACTGTGCACCA-GCCAGCC----AGCCA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:20181738-20181869 + ATAAAAAGTATGTCACT------------------T-GGGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGAATGGAAAATGTCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGTTTGGCCTACCCGTCTACCA-GCCAACC----AACCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATAAAAAGTATGTCA---------------CTTGGTGG-GGGCGCTGCACTGGCATTGAAAAGTGAATTACATTGATCGTGACATGGGGATGGAAAATGCCGCCGAGCCATGTAAAT-------------------------------------------CGATTG-------------AAGGCCCGTGGCCAACCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GTAAAAAGTATGTCAGAGAAGAGAAGAGAACACAGTGGGCGCTGCTGCACTGACATTGAAAAGTGAATTGCATTGATCATGACGGGGGGTTG-------ACGCTGACTGCCACGAACCGCTCAGAACAATAGTGTAAATGTGGAATAATGCTCGTAGAACCCATTC-------------GCAGTCCATG---GGCTGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-23.2 -23.2 -23.1 -23.1 -23.0 -23.0

droSim1

-22.6 -22.4 -22.2 -21.9 -21.7 -21.6

droSec1

-20.2 -20.0 -19.8 -19.8 -19.7 -19.6

droYak2

-21.1 -20.9 -20.6 -20.5 -20.4 -20.4

droEre2

-18.4 -18.4 -18.0 -18.0 -17.9 -17.9

droAna3

-24.8 -24.7 -24.5 -24.4 -24.3 -24.2

dp4

-31.8 -31.8 -31.7 -31.7 -31.5 -31.5

droPer1

-13.5 -12.6

droWil1

-14.6 -14.3 -14.2 -14.0 -14.0 -13.8

droVir3

-33.9 -33.4 -33.4 -33.3 -33.3 -33.2

droMoj3

-3.4 -2.9 -2.9 -2.8 -2.7 -2.6

droGri2

-9.3 -9.1 -9.1 -8.9 -8.8 -8.7

Generated: 01/05/2013 at 05:28 PM