Secondary structure and small RNA-seq evidence for dme-mir-1016

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:10120620-10120707 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSim1 chr2R:8883298-8883385 - CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSec1 super_1:7628246-7628333 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATAT------TCCAAT----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droYak2 chr2R:10057668-10057755 - CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droEre2 scaffold_4845:15723071-15723158 + CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAA------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droAna3 scaffold_13266:5804278-5804360 + CTCTAAACTTTTTCAGTGAGTACTTGTAATATA-AATCCATAAA--------TCAAA----------ACT-----------------CACTT-TTTCCA-AC-TTAGTCGCCGTGGTGTGAT
dp4 chr3:17369366-17369470 - CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCAT
droPer1 super_31:422912-423016 + TTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATTGTCTGAAACTAATGTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGGCGCGGCGTCAT
droWil1 scaffold_180700:1839743-1839828 + TTCCAAATTGTTCCAGTAAGTTAAAA-----TGATCTAAAATCAT------TTCAAA----------T-T----------GATT---CAATAATCTCTTCCA-TTAGTCGACGCGGTGTCAT
droVir3 scaffold_12875:17586457-17586541 + TTCCAAACTATTTCAGTAAGTAGCA------GGTGCTGAGTGCAT------G----A----TTGTCTCTA----TATCTT--------GATT-----ATCTTTGCAGTCGACGCGGGGTTAT
droMoj3 scaffold_6496:11208550-11208642 + TTCCAAGCTGTTTCAGTAAGTAGAGCACGCATTTCCAGTACCCAACTA----------------TTCGTTACTATATCTG--------TACA-----ATTTTTGTAGTCGACGCGGGGTTAT
droGri2 scaffold_15245:14096515-14096602 - TTCCAAACTGTTTCAGTAAGTGGTAACACA-ACTACTATGTTTGT------GC-AAC----------ATT----------TAATGGACAG-T-----ATCTTTGCAGTCGACGGGGAGTTAT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:10120620-10120707 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droSim1 chr2R:8883298-8883385 - CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droSec1 super_1:7628246-7628333 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATATTCCAATGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droYak2 chr2R:10057668-10057755 - CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droEre2 scaffold_4845:15723071-15723158 + CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAATCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTCCAAGCTTTTCCAGTAAGTACAGAGATG---------------ATGTAATGCG----TAAATTCCAAAGTTCACCTCTCTCCATACT-TAGTCGTCGAGGGGTTATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCC---CTTCACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-20.9 -20.4

droSim1

-9.8 -9.2 -8.9

droSec1

-16.5 -15.5 -15.5

droYak2

-19.3 -18.4

droEre2

-19.3 -18.9 -18.4

droAna3

-6.1 -5.4

dp4

-9.5 -9.1 -8.74 -8.5

droPer1

-10.2 -10.1 -9.7 -9.6 -9.6 -9.5

droWil1

-3.5 -3.0 -2.8 -2.8 -2.7 -2.7

droVir3

-9.5 -9.1 -8.9 -8.8 -8.6

droMoj3

-1.7 -1.6 -1.6 -1.6 -1.5 -1.4

droGri2

-8.2 -8.0 -8.0 -7.8 -7.8 -7.8

Generated: 01/05/2013 at 05:06 PM