Secondary structure and small RNA-seq evidence for dme-mir-4961

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:1267640-1267803 + AGATATTACC--CAGAAGCGA-----------------------TATC------------------------CAATAGTAGCCAA-CTCTCTCG--CTCTC--T----------A----TGT--GTATGTATGTATCTTG---------------CTATCC---------------ATATA--TGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACG------ATATAACCCGAAACCACACTGG-CC-AGGAATA---------------------------------------------GCAAATCCA
droSim1 wjj76b12.b1:303-467 + AGATATTACC--CAGAAGCGA-----------------------TATC------------------------CAATAGTAGCCAA-CTCTCTCG--CTCTC--T----------A----TGT--GAATGTATGTATCTTG---------------CTATCC---------------ATATA--TGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACG------ATATAACCCGAAACCATACTGG-CC-AGGAATA---------------------------------------------GCAAATCCA
droSec1 super_10:1091085-1091248 + AGATATTACC--CAGAAGCAA-----------------------TATC------------------------CAATAGTAGCCAA-CTCTCTCG--CTCTC--T----------A----TGT--GAATGTATGTATCTTG---------------CTATCC---------------ATTTA--TGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACG------ATATAACCCGAAACCATACTGG-CC-AGGAATA---------------------------------------------GCAAATCCA
droYak2 chrX:1175521-1175702 + AGATATAACC--GAGAAGCAA-----------------------TACC------------------------CAATAGTAGCCAA-CTCTCTCGCTCTCTC--TGCGTCTCTCTA----TGT--GTATGTATGTATTTCG---------------CTATCC---------------ATATA--TGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACTATATCTATATAACCCGAAACCATACTGG-CC-AGGAATA---------------------------------------------GCAAATCCA
droEre2 scaffold_4644:1251466-1251631 + AGATATAACC--CAAAAGAAA-----------------------TACC------------------------GAATAGTAGCCAA-CTCTCTCG--CTCTCTCT----------A----TGT--GTATGTATGTATTTCG---------------TTATCC---------------ATATA--TGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACT------ATATAACCCAAAACCATACTGG-CC-AGGAATA---------------------------------------------GCAAGTCCA
droAna3 scaffold_13117:1856374-1856503 - --------------------------------------------------------------------------------------CTCTCTCT--CTCTC--TGTGTCTCTCTAAATGCAT--GTATGTATGTGTTGTA---------------TTATCC---------------GTATATATGTATATCCATGTTAGAGAGCCAGGACGGGTTGAGATT----------------GCCCAAGA----ACTGG-CCTAGGAATA---------------------------------------------GCAAAT-CA
dp4 chr2:10126391-10126530 + GAATAAT--CCATA-AACAAA-----------------------TATC------TA----------------T-GTAGTCA-CAT-CTATCTCT--CTCTC--T----------A----TAT--ATCTCTCTCTCTCTTT---------------CTTTAT---------------TTGTA--CATGTATTTATTTCATGGGTTTAGTTTTGC---AAATGGTATA------AAACATCTCCAAAATACATT-------------------------------------------------------------------
droPer1 super_2:4840479-4840636 - TAATATATTG--GAGTAGCAA-----------------------TATC------------------------TATTTGTATTCAG-ATTTGTAT--TTATT--T----------A----TGT--GTTTGTGGTGATACAG---------------ATATATA--------------GTATA--TATAGAAATATATTTTAAAATCA---TAGGTACATACAGTATA------TTGTATCCCTATCCAATGCATA-T-----GTGA---------------------------------------------ACGTACTTA
droWil1 scaffold_180700:3267577-3267741 + AAATATCATA--CCCA-AAAA-----------------------TATA------------------------TACTACTACACAACCTCTCTCT--CTCTC--T----------C----TAT--CTATCTATCTATCTTTGAACATAAAATGTACCTAT--ACTAAAACAAAAACTCTATA--TCTAAATCGTTGTGCT-TACCATTCATTTTCTACTACTATACT------ATATAGGGCGAAAC-------------------------------------------------------------------------
droVir3 scaffold_12855:2148540-2148695 + ATA----ACC--CAAAAGATA-----------------------CCTC------------------------AATTTGCATATAT-ATCTATGT--CTATA--T----------A----GAT--ATATACATACATATAT---------------ATATAC---------------ATATA--TATATATAAATATATGTGTGCGTGCATTA----TCGTCTTGTG------ACTAGGTCCAGAACTTTACAGG-TG-CGCAGTG---------------------------------------------TCGAAATCA
droMoj3 scaffold_6496:26031347-26031515 + TGATGCCACC--CAGC------------------------------CC------------------------CCACCGCCTCCTG-CTCCCTCC--CTCTC--TATGTTTATATG----TGT--ATATGTGTGT---------------------GTGTCT---------------GTGTG--TTTGTGTCCCTTC--------------------GATTGGCG------------------------TGCCTGAAT-GGCTGTGAAAACACAGCCAGTTGCAGCTGTATCCACAATCATTATCACAAAAGCAAACTAC
droGri2 scaffold_14853:6570585-6570746 + AAAAACAAAA--AACAAACGAAGTAACAGCCCAAGCCGACAATGGCTGAATATATATGTTATGTATTTGTATT-ATTGTC------------GT--GTATA--T----------A----TATCTATATATGTATATTACA---------------CTAT---------------------------------------------------------ATACTATATG-----TATATATATATAGACAATGTCTG-AT-GGCTATG---------------------------------------------CCAAAGCCA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:1267640-1267803 + AGATATTACCCAGAAGCGATATCCAATAGTAGCCAACTCTCTCGCT--CTCT----------A--TG--TGTATGTATGTATCTTGCTATCCAT--ATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCACACTGGCC-AGGAATAGCAAATCCA
droSim1 wjj76b12.b1:303-467 + AGATATTACCCAGAAGCGATATCCAATAGTAGCCAACTCTCTCGCT--CTCT----------A--TG--TGAATGTATGTATCTTGCTATCCAT--ATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA
droSec1 super_10:1091085-1091248 + AGATATTACCCAGAAGCAATATCCAATAGTAGCCAACTCTCTCGCT--CTCT----------A--TG--TGAATGTATGTATCTTGCTATCCAT--TTATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA
droYak2 chrX:1175521-1175702 + AGATATAACCGAGAAGCAATACCCAATAGTAGCCAACTCTCTCGCTCTCTCTGCGTCTCTCTA--TG--TGTATGTATGTATTTCGCTATCCAT--ATATGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACTATATCTATATAACCCGAAACCATACTGGCC-AGGAATAGCAAATCCA
droEre2 scaffold_4644:1251466-1251631 + AGATATAACCCAAAAGAAATACCGAATAGTAGCCAACTCTCTCGCTCTCTCT----------A--TG--TGTATGTATGTATTTCGTTATCCAT--ATATGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACTA------TATAACCCAAAACCATACTGGCC-AGGAATAGCAAGTCCA
droAna3 scaffold_13117:1856374-1856503 - ------------------------------------CTCTCTCTCT--CTCTGTGTCTCTCTAAATGCATGTATGTATGTGTTGTATTATCCGTATATATGTATATCCATGTTAGAGAGCCAGGACGGGTTGAGATT----------------GCCCAAGA----ACTGGCCTAGGAATAGCAAAT-CA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AGATATTACCCAGAAGCGATATCCA-ATAGTAGCCAACTCTCTCGCTCTCTATGTGAATGTATGTATCTTGCTATCCATATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGATATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCASizeHit CountTotal NormTotalGSM343915
Embryo
................................................................................TATGTATATCCATATCAGAGAGC..............................................................2312.0022
................................................................................TATGTATATCCATATCAGAGAG...............................................................2211.0011
dp4
GAATAATCCATA-AACAAATATCTATGTAGTCA-CATCTATCTCTCTCTCTATATATCTCTCTCTCTCTTTCTTTATTTGTACATGTATTTATTTCATGGGTTTAGTTTTGC---AAATGGTATAAAACATCTCCAAAATACATT--------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-22.8,  p-value=0.009901 dG=-22.0,  p-value=0.009901

droSim1

dG=-22.8,  p-value=0.009901 dG=-22.0,  p-value=0.009901

droSec1

dG=-21.9,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droYak2

dG=-21.2,  p-value=0.009901 dG=-20.8,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droEre2

dG=-20.7,  p-value=0.009901 dG=-20.4,  p-value=0.009901

droAna3

dG=-23.8,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.1,  p-value=0.009901

dp4

dG=-1.9,  p-value=0.009901

droPer1

dG=-11.9,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.8,  p-value=0.009901

droWil1

dG=0.0,  p-value=0.019802 dG=0.0,  p-value=0.009901 dG=0.2,  p-value=0.009901 dG=0.3,  p-value=0.009901 dG=0.4,  p-value=0.009901

droVir3

dG=-15.0,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.6,  p-value=0.009901 dG=-12.0,  p-value=0.009901

droMoj3

dG=-0.9,  p-value=0.009901 dG=-0.8,  p-value=0.009901 dG=-0.6,  p-value=0.009901 dG=-0.6,  p-value=0.009901 dG=-0.5,  p-value=0.009901

droGri2

dG=-7.5,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-6.9,  p-value=0.009901

Generated: 03/07/2013 at 06:10 PM