Secondary structure and small RNA-seq evidence for dme-mir-966

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:6045612-6045728 - ATT------T---CGC-TCGGCTGTAACCTGATCCG-----------------CTGCT--GTGGGTTGTGGGCTGTG-------TGGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-AG-----------------------CGTGGGCA-CGGACCCACTGGTCGTCAACCGC
droSim1 chr2L:5834370-5834493 - ATT------T---CGT-TCGGCTGTAACCTGATCCG-----------------CTGCT--GTGGGCTGTGGGCTGTGGGCTGTAAGGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-AG-----------------------CGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droSec1 super_5:4116543-4116659 - ATT------T---CGT-TCGGCTGTAACCTGATCCG-----------------CTGCT--GCGGGTTGTGGGCTGTG-------AGGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-AG-----------------------CGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droYak2 chr2L:13146709-13146824 + ATT------C---CGC-TCGGCTGTAACCTGATCCG-----------------CTGCT--GTGGGATGTGGGATGTG--------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-AG-----------------------CGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droEre2 scaffold_4929:11075516-11075624 + ATT--CC-AT---CAT-TCGGCTGTAACCTGATCCC-----------------CTGCT--GTGG----------------------GCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-AG---------C----ACAG-----CGTGGGCA-CGGC-CCACTGGTCGTCAACCGC
droAna3 scaffold_12916:8156171-8156273 + CAT--CCGATC--TGA-TTGGCAGTAACCTGATCCG-----------------CGGTT--GTG-----------------------GTTGTGG-----TGGAGGTGC---TACTTGATAACCCAC-TG-----------------------CGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
dp4 chr4_group1:223208-223319 + GGA------T---CGG-GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCG--GTGG--------------------------AGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-AG-----------------------CGTAGGCA-CTGGT---ATGGTTGTGAACGGC
droPer1 super_1:219437-219548 + GGA------T---CGG-GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCT--GTGG--------------------------AGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-AG-----------------------CGTAGGCA-CTGGT---ATGGTTGTCAACGGC
droWil1 scaffold_180708:7887454-7887585 + GGATTGC-AATTGGTTGTGGGCTGTAACCTGATCTGGA----------------AGCT--ATAG-----------------------ATGTGATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAGGGTAGACAGCTTAGACAT-----CGTAGGCA-TTGGC---CTGGTTGTCAACGGC
droVir3 scaffold_12963:3941701-3941794 - ATT------G---GGCGTCTGCTGTAACTTGAAGCG-----------------CTGATCTG-------------------------------------------------TGGTTGATAACCCCC-TG---------C----CAAGGTGCTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC
droMoj3 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15252:1454932-1454939 + -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:6045612-6045728 - ATTTCGCTCGGCTGTAACCTGATCCGCTGCTGTGGGTTGTGGGCTGTG-------TGGCTGTGGTATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGACCCACTGGTCGTCAACCGC
droSim1 chr2L:5834370-5834493 - ATTTCGTTCGGCTGTAACCTGATCCGCTGCTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGTGGTATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGCCCCACTGGTCGTCAACCGC
droSec1 super_5:4116543-4116659 - ATTTCGTTCGGCTGTAACCTGATCCGCTGCTGCGGGTTGTGGGCTGTG-------AGGCTGTGGTATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGCCCCACTGGTCGTCAACCGC
droYak2 chr2L:13146709-13146824 + ATTCCGCTCGGCTGTAACCTGATCCGCTGCTGTGGGATGTGGGATGTG--------GGCTGTGGTATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGCCCCACTGGTCGTCAACCGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATTTCGTTCGGCTGTAACCTGATCCGCTGCTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGTGGT------ATAGGTGCCGCCAGTTGATAACCCCCAGCGTGGGCACGGCCCCACTGGTCGTCAACCGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGATCGGGTGGCTGTAACCTGATCTGG-------------GAGCGGT--GCAGCAGGGCTGCGGTGGAGTTGGAGGTGTCGGCTGTTGATAACCCCCAGCGTAGGCACTGG---TATGGTTGTGAACGGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-32.9,  p-value=0.009901

droSim1

dG=-27.7,  p-value=0.009901 dG=-27.7,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-26.5,  p-value=0.009901

droSec1

dG=-29.1,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-28.8,  p-value=0.009901

droYak2

dG=-24.1,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-23.8,  p-value=0.009901

droEre2

dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droAna3

dG=-16.2,  p-value=0.009901 dG=-15.4,  p-value=0.009901

dp4

dG=-22.9,  p-value=0.009901 dG=-22.9,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-15.0,  p-value=0.009901

droPer1

dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-14.7,  p-value=0.009901

droWil1

dG=-19.8,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-15.9,  p-value=0.009901

droVir3

dG=-5.3,  p-value=0.019802 dG=-4.9,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.5,  p-value=0.009901

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

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