Secondary structure and small RNA-seq evidence for dme-mir-4962

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:3671399-3671553 + TGTGTTTGGTTGTTTTTCCTTTCTTTTC------------TCTCCGTCTCTCTCTTTC------------CCTCTCTCTGTT-TACATTGAGCTG-------TTTTGTCCGTGCAC----------GTGCTA---G---------------------ACGATGTAGAGAGTGAGG--GAGA---------------GAGCG---------------------AATAGAATAACAGCTCATTGTGCTGAG-CGCCCAGCC-T
droSim1 chrX:2692027-2692181 + TATGTTTGGTTGTTTTTCCTTTCTTTTC------------TCTCCGTCTCTCTCTTTC------------CCTCTCTCTGTT-TACATTGAGCTG-------TTTTGTCCGTGCAC----------GTGCTA---G---------------------ACGATGTAGAGAGTGAGG--GAGA---------------GAGCG---------------------AATACAATAACAGCTCATTGTGCTGAG-CGCCCAGCC-T
droSec1 super_13710:747-901 + TATGTTTGGTTGTTTTTCCTTTCTTTTC------------TTTCCGTCTCTCTCTTTC------------CCTCTCTCTGTT-TACATTGAGCTG-------TTTTGTCCGTGCAC----------GTGCTA---G---------------------ACGATGTAGAGAGTGAGG--GAGA---------------GAGCG---------------------AATACAATAACAGCTCATTGTGCTGAG-CGTCCAGCC-T
droYak2 chrX:4740636-4740793 - TGTGCTTGGTTGTTTTTCCTTTCTTTTC------------TCTCCGCCTCTCTCTTTC------------CCTCTCTCTGTT-TACATTAAGCGG-------TTTTGCCCGTGCAC----------GTGCTA---G---------------------ACGATATAGAAAGAGAGAGGGAGA---------------GAGCG--------------AA------TAACAATAACAGCTCGTTTTGCTGAG-CGCCCAGCC-T
droEre2 scaffold_4690:1061104-1061256 + TGTGTTTGGTTGTTTTTCCTTTCTTTTC------------TCTCCGTCT--CTCATTC------------CCTCTCTCTGTT-TACATTAAGCGG-------TTTTGCCTCTGCAC----------GTGCTA---G---------------------ACGGTATAGAGAGAGAGG--GAGA---------------GAGCG---------------------ATTACAATAACAGCTCATTGTGCTGAG-CGCCCAGCC-T
droAna3 scaffold_13337:5571517-5571673 - TGTGTTTTTGTTTTTGTTGTCTCTGTTT------------TCTTCGCCTTTTTTTTC-------------TC-ATTTTTG-------TGGAGCTTTGCATGCCCGGCTGCAGGAGT----------GTTAGT---GAGTGGTTTGACTTGTTTTGCGGCAGCAGGCAGCACACGC--GCTG---------------CTGT-------------------------------------CGCCGTCGCCGC-TGTCTAGC---
dp4 Unknown_group_658:20580-20732 - TACATTTTTCCACTTGCCCACACTTTTCGCTGCGCT----GCTCTCTCGCTCTCTCTCTCTCTCATGCTCTC-------ACT-CTCAGAAAGCTG-------TGCAAT------------------GCACCATGCG---------------------ACGACTGAAAGCATGAGA--GTGA---------------G--CC--------------AG---CTTTCAGTGTGGCAGTTTTTTTCGTTG--------------
droPer1 super_23:1560592-1560751 - GTTTCTCTGCCTCTCCCTCTC-------------------------TCCCTCTCTCTCTCTCTCGCTGTCTTCCTCTTTCTC-AACTATGTGTGG-------CCATGTGTGTGTGT----------GTGTGT---G---------------------TGTGGGTTGTATCTGTGT--GTGA---------------GAGCG-------------AAGCG---CAGACAATTAGT-TTTATTATGCTTTGTTGCCGAGCTTC
droWil1 scaffold_181096:11652056-11652210 + TCTGTTTGTGAGGGTCCCTCTCTTTTAC------------TCTCTGTCGCTCTCTCTC------------TCTCTCGCGCTG-CACAAAAAAATTAG-----TCATACC-AAAAACAAAATACAGATTGCAA---A---------------------GCAATAGAGAGAGAGAGG--GAGA---------------GAGAG---------------------AGA------GTAAGTGAGTGTG-AGAG-CGCCCA-----
droVir3 scaffold_12855:8711965-8712121 + TCTCTTTCTTTATTTCTCTGCTT--TTCTCTGTCTCTCTTTATCTGTATCTCTCTCTC------------TTTCTCTCTATTTTCTATTGCTCTG-------TTATGTC-AAACATTTGCTGCATACTTTCA---G---------------------GCGATATTAAAAGCGTGC--AAGA---------------TTTTC---------------------ATTTGTATAACTGCGTATT--------------------
droMoj3 scaffold_6496:4311996-4312145 - TGTCTCTC--TATTTCTCTCTCTCTCTC------------TCTCTCTCTCTCTCTCTC------------TCTCTCTCTGCC-TGCCTTCA---C-------TTTTATACAAA---------------AATA---A---------------------TGGCCATCAAAATTAATA--AAAACGTAATCAGAGCGAATGACTACAGAGGAAAACGAAAAG--------TATAAAAG-------------------------C
droGri2 scaffold_15203:9842081-9842230 + TCCCTTCTCTCTCTC-------------------------TCTCTCTCGCTCTCTCTC------------TC------TCTC-TCTAT----TTG-------TCTCTTCCGCATA-----------GCGCAA---G---------------------TCGACGTCGGGGCTGACG--GGCA---------------GCGTTTCACAGGAGAATCGGGTGACTATCACCCTGATTGC-TGTTGTGCTG-C-TGTTCATCG-T

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:3671399-3671553 + TGTGTTTGGTTGTTTTTCCTTTCTTTTCTCTCCGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTTTGTCCGTGCACGTGCTAGACGATGTAGA--GAGTGAGGGAGAGAGCGAATA-GAATAACAGCTCATTGTGCTGAGCGCCCAGCCT
droSim1 chrX:2692027-2692181 + TATGTTTGGTTGTTTTTCCTTTCTTTTCTCTCCGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTTTGTCCGTGCACGTGCTAGACGATGTAGA--GAGTGAGGGAGAGAGCGAATA-CAATAACAGCTCATTGTGCTGAGCGCCCAGCCT
droSec1 super_13710:747-901 + TATGTTTGGTTGTTTTTCCTTTCTTTTCTTTCCGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTTTGTCCGTGCACGTGCTAGACGATGTAGA--GAGTGAGGGAGAGAGCGAATA-CAATAACAGCTCATTGTGCTGAGCGTCCAGCCT
droYak2 chrX:4740636-4740793 - TGTGCTTGGTTGTTTTTCCTTTCTTTTCTCTCCGCCTCTCTCTTTCCCTCTCTCTGTTTACATTAAGCGGTTTTGCCCGTGCACGTGCTAGACGATATAGAAAGAGAGAGGGAGAGAGCGAATAACAATAACAGCTCGTTTTGCTGAGCGCCCAGCCT
droEre2 scaffold_4690:1061104-1061256 + TGTGTTTGGTTGTTTTTCCTTTCTTTTCTCTCCGTCT--CTCATTCCCTCTCTCTGTTTACATTAAGCGGTTTTGCCTCTGCACGTGCTAGACGGTATAGA--GAGAGAGGGAGAGAGCGATTA-CAATAACAGCTCATTGTGCTGAGCGCCCAGCCT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TATGTTTGGTTGTTTTTCCTTTCTTTTCTCTCCGTCTCTCTCTTTCCCTCTCTCT-------------GTTTACATTGAGCTGTTTTGTCCGTGCACGTGCTAGACGA---TGTAGAGAGTGAGGGAGAG--AGCGAATACAATAACAGCTCATTGTGCTGAGCGCCCAGCCTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TACATTTTTCCACTTGCCCACACTTTTCGCTGCGCTGCTCTCTCGCTCTCTCTCTCTCTCATGCTCTCACTCTCAGAAAGCTGTGCAAT--------GCACCATGCGACGACTGAAAGCATGAGAGTGAGCCAGCTTTCAGTGTGGCAGTTTTTTTCGTTG------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.2,  p-value=0.009901 dG=-33.2,  p-value=0.009901

droSim1

dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.2,  p-value=0.009901 dG=-33.2,  p-value=0.009901

droSec1

dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.2,  p-value=0.009901 dG=-33.2,  p-value=0.009901

droYak2

dG=-37.2,  p-value=0.009901 dG=-36.5,  p-value=0.009901

droEre2

dG=-33.1,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.5,  p-value=0.009901

droAna3

dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-27.9,  p-value=0.009901

dp4

dG=-29.0,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.0,  p-value=0.009901

droPer1

dG=-14.3,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droWil1

dG=-31.11,  p-value=0.009901 dG=-30.9,  p-value=0.009901 dG=-30.6,  p-value=0.009901 dG=-30.31,  p-value=0.009901 dG=-30.25,  p-value=0.009901

droVir3

dG=-10.8,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-9.9,  p-value=0.009901

droMoj3

dG=-7.6,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.27,  p-value=0.019802

droGri2

dG=-13.4,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.0,  p-value=0.009901 dG=-12.7,  p-value=0.009901 dG=-12.7,  p-value=0.009901

Generated: 03/07/2013 at 06:12 PM