Secondary structure and small RNA-seq evidence for dme-mir-4971

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:3463274-3463415 - GGAAG-GGCCAACTTCT---CGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droSim1 wop21h10.b1:281-423 + GGAAG-GGCCAATTTCT---CGGCTCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCAGTCACTGTTCGAGGAGATTATGTCGG--------GCTCGGATG
droSec1 super_129:25371-25512 - GGAAG-GGCCAACTTCT---CGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCAGTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droYak2 chrU:14964015-14964156 + GGAAG-GGCCAACTTCT---CGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCACTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droEre2 scaffold_4929:3498112-3498253 - GGAAG-GGCCAACTTCA---CGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCACTCGCTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droAna3 scaffold_12943:2497935-2498076 + GGCAG-AGCCAACTTCG---GAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CATAAAGAATCCTGCCGC-------TGGCGACAG--ACAGTCGGCCA--CTGACAACGC----------------------GCACTCGCTGTTCGAGGAAATAATGTCTG--------GCTCCGACG
dp4 chr4_group3:936699-936854 - GGAGT-GCTCGTCTACG---TGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGC-------TGGCGACAG--ATTGTCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCTGATG
droPer1 super_1:2415168-2415323 - GGAGT-GCTCGTCTACG---TGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGC-------TGGCGACAG--ATTGTCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCTGATG
droWil1 scaffold_189765:461-602 - GTAAC-GATAGACGGAG---ATACCTT--------CGAGGTGGTGGACGAGTTCGTCTACCTCGGATC------CTTGTTGATGGCTGACAA-------CAATG----------TTAGTCG--GGAAATACGA----------------------AGGCGCATTATCAGCGGAAGTCGTGCCTACTATTGGCTCCAGAAGA
droVir3 scaffold_12963:15952027-15952160 - ATTAGATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT---------------CAATGCTGCCGC-------TGGCGACAG----CCTCGGC-G--CTGACAAGGA----------------------GCATGCCATGTTTGAGTATTTCCTCAACG--------AAGATGACG
droMoj3 scaffold_6473:12510219-12510341 + GGTTT-G----------------------------------------TGTGTGTGTGTGTGGTGGAACTTC---AATGCGAACCT------CTTGCCACAATCGAGTGCAATTAACTGCCA--TGATATATGGCCAATCCCA-------------------TATGCAGACGGCGACCGAGTCGAA-------GTTCGGCTG
droGri2 scaffold_14853:4216060-4216150 - ------------------------------------------------------------------------------------TCGACCGC-------TGGCCACAA--ATGGCCGGACAGACAGACA-------GACAGACAGACAGACAGACAGACTCACTGACATAATTGATCATATC----------GCTTATACG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:3463274-3463415 - GGAAGGGCCAACTTCTCGGCCCTCGACACGGTGGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droSim1 wop21h10.b1:281-423 + GGAAGGGCCAATTTCTCGGCTCTCGACACGGTTGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATTATGTCGGGCTCGGATG
droSec1 super_129:25371-25512 - GGAAGGGCCAACTTCTCGGCCCTCGACACGGTTGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droYak2 chrU:14964015-14964156 + GGAAGGGCCAACTTCTCGGGCCTCGACACGGTGGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droEre2 scaffold_4929:3498112-3498253 - GGAAGGGCCAACTTCACGGGCCTCGACACGGTGGATGAGCTTGTCAGTGGTGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGAAGGGCCAATTTCTCGGCTCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATTATGTCGGGCTCGGATGSizeHit CountTotal NormTotalGSM343915
Embryo
.......................................TTGATGAGCTTGTCAGTGGCG................................................................................................2111.0011
dp4
GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..............................................................................................CAGATTGTCGGCCACTGAC...........................................1911.00110

Secondary Structure

dm3

dG=-44.8,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.9,  p-value=0.009901

droSim1

dG=-37.9,  p-value=0.009901 dG=-37.7,  p-value=0.009901 dG=-37.3,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.9,  p-value=0.009901

droSec1

dG=-37.9,  p-value=0.009901 dG=-37.7,  p-value=0.009901 dG=-37.3,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.9,  p-value=0.009901

droYak2

dG=-40.5,  p-value=0.009901 dG=-39.6,  p-value=0.009901 dG=-39.6,  p-value=0.009901

droEre2

dG=-39.2,  p-value=0.009901 dG=-38.3,  p-value=0.009901 dG=-38.3,  p-value=0.009901

droAna3

dG=-33.6,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.4,  p-value=0.009901 dG=-33.4,  p-value=0.009901 dG=-33.3,  p-value=0.009901 dG=-32.2,  p-value=0.009901

dp4

dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-32.8,  p-value=0.009901

droPer1

dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-33.1,  p-value=0.009901 dG=-32.8,  p-value=0.009901

droWil1

dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901 dG=-24.9,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-17.7,  p-value=0.009901

droVir3

dG=-37.6,  p-value=0.009901 dG=-37.3,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.8,  p-value=0.009901 dG=-36.8,  p-value=0.009901

droMoj3

dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-17.0,  p-value=0.009901

droGri2

dG=-12.6,  p-value=0.009901 dG=-12.6,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.5,  p-value=0.009901

Generated: 03/07/2013 at 06:18 PM