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

-35.0 -34.9 -34.9 -34.8 -34.3 -34.2

droSim1

-35.0 -34.9 -34.9 -34.8 -34.3 -34.2

droSec1

-32.2 -32.1 -32.1 -32.0 -31.7 -31.6

droYak2

-33.0 -32.9 -32.3 -32.3 -32.2 -32.1

droEre2

-30.9 -30.6 -30.3 -30.3 -30.2 -30.2

droAna3

-30.6 -30.2 -30.1 -30.0 -29.9 -29.6

dp4

-20.9 -20.8 -20.7 -20.7 -20.7 -20.6

droPer1

-10.5 -10.5 -10.2 -10.0 -9.9 -9.9

droWil1

No secondary structure predictions returned

droVir3

-8.8 -8.5 -8.3 -7.9

droMoj3

0.0 0.2

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:28 PM