Secondary structure and small RNA-seq evidence for dme-mir-4983

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:15524903-15525041 + AA--CACATCTGCCCGCTGG-CTGGCTG------T---------CTTGACCCACTTGCT---CG---TTTGCA------TT-TCT--GAAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTGA-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC
droSim1 chr2R:14228631-14228769 + AA--CACATCTGCCCGCTGG-CTGGCTG------T---------CTTGACCCACTTGCT---CG---TTTGCA------TT-TCT--GAAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTGA-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC
droSec1 super_1:13039564-13039702 + AA--CACATCTGCCCGCTGG-CTGGCTG------T---------CTTGACCCACTTGCT---TG---TTTGCA------TT-TCT--GAAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTGA-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC
droYak2 chr2R:13649050-13649195 - AA--CACATCTGCCCGCTGG-CTGGCTG------T---------CTTGACCCACTTGCT---CG---TTTGCATTTGTATTTTCT--GAAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTGA-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC
droEre2 scaffold_4845:9723500-9723642 + AA--CACATCTGCCCGCTGG-CTGGCTGGCTG--T---------CTTGACCCACTTGCT---CG---CTTGCA------TT-GCT--GAAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCCTTTGA-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC
droAna3 scaffold_13266:9754397-9754555 - AAAACACAAACGCCCGCTGG-----CTG------T---------CTTGACCCACTTGCT---TG---TTTGCA------TT-TCTCGCAAAAATATTCATATGCAAGACCAAAATCAGAATCAGAAATTCTTTTGG-GCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTCTATATGTACATCTAGTAC
dp4 chr3:12652733-12652881 + AA--CACGTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCT---TTTGAA------TT-TTA--GAAATATGT---------------AAATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTTATACTAAA----------------
droPer1 super_2:8929657-8929759 - AA--CACTTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCT---TTTGAA------TT-TTA--GAAATATGT---------------AAATCAAATTCTGAAACATTT------------------------------------------------------------------
droWil1 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12875:4153222-4153295 - AA--CACTTTTGAGTGCCAG-CTTTCTG------A---------GCATATC-AAACGCT---CGACATTTGTC------TT-TTT--GAGGGGGGT--TCTCGCAC-----A--------------------------------------------------------------------------------------
droMoj3 scaffold_6496:20896701-20896727 + AA--CACTTTTGACTGCTGC-CAGCCTG------C---------C---------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:15524903-15525041 + AACACATCTGCCCGCTGGCTGGCTGTCTTGACCCACTTGCTCGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAGCAAGTGTGTCATGAAATTGCCATTCGTTTCTGCTCTATATAC
droSim1 chr2R:14228631-14228769 + AACACATCTGCCCGCTGGCTGGCTGTCTTGACCCACTTGCTCGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAGCAAGTGTGTCATGAAATTGCCATTCGTTTCTGCTCTATATAC
droSec1 super_1:13039564-13039702 + AACACATCTGCCCGCTGGCTGGCTGTCTTGACCCACTTGCTTGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAGCAAGTGTGTCATGAAATTGCCATTCGTTTCTGCTCTATATAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AACACATCTGCCCGCTGG---------CTGGCTGT-------CTTGACCCACTTGCT---CGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAG-CAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATATACSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AACACGTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCTTTTGAATTTTAGAAATATGTA--------AATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTTATACTAAA---SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-26.0,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901 dG=-25.2,  p-value=0.009901

droSim1

dG=-26.0,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901 dG=-25.2,  p-value=0.009901

droSec1

dG=-23.2,  p-value=0.009901 dG=-23.1,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.6,  p-value=0.009901

droYak2

dG=-24.0,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-23.3,  p-value=0.009901 dG=-23.1,  p-value=0.009901 dG=-22.0,  p-value=0.009901

droEre2

dG=-21.6,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droAna3

dG=-22.7,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-17.8,  p-value=0.009901

dp4

dG=-12.0,  p-value=0.009901 dG=-11.8,  p-value=0.009901 dG=-11.7,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.2,  p-value=0.009901

droPer1

dG=-5.6,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-4.6,  p-value=0.009901 dG=-3.8,  p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

dG=-6.3,  p-value=0.009901 dG=-5.4,  p-value=0.009901

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 06:48 PM