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

-34.7 -34.7 -34.7 -34.4 -34.4 -34.4

droSim1

-36.6 -36.6 -36.6 -36.3 -36.3 -36.3

droSec1

-36.6 -36.6 -36.6 -36.3 -36.3 -36.3

droYak2

-38.5 -38.4 -38.4 -38.1 -38.1 -38.0

droEre2

-38.3 -38.1 -37.9 -37.7 -37.7 -37.7

droAna3

-34.4 -34.2 -34.2 -34.0 -34.0 -34.0

dp4

-43.3 -43.3 -42.9 -42.9 -42.9 -42.9

droPer1

-18.3 -17.9 -17.6

droWil1

-53.31 -53.1 -52.81 -52.8 -52.6 -52.45

droVir3

-12.8 -12.6 -12.5 -12.4 -12.3 -12.3

droMoj3

-12.1 -12.1 -12.0 -12.0 -11.8 -11.8

droGri2

-35.4 -35.3 -35.3 -35.3 -35.1 -35.1

Generated: 01/05/2013 at 05:25 PM