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 + AGATATTACCCAGAAGCGATATCCAATAGTAGCCAACTCTCTCGCTC------------TCTATGTGTATGTATGTATCTTGCTATCCATATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCACACTGGCCAGGAATAGCAAATCCA
droSim1 wjj76b12.b1:303-467 + AGATATTACCCAGAAGCGATATCCAATAGTAGCCAACTCTCTCGCTC------------TCTATGTGAATGTATGTATCTTGCTATCCATATATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCA
droSec1 super_10:1091085-1091248 + AGATATTACCCAGAAGCAATATCCAATAGTAGCCAACTCTCTCGCTC------------TCTATGTGAATGTATGTATCTTGCTATCCATTTATGTATATCCATATCAGAGAGCCAGGATTGGTTGAGACCATACGA------TATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCA
droYak2 chrX:1175521-1175702 + AGATATAACCGAGAAGCAATACCCAATAGTAGCCAACTCTCTCGCTCTCTCTGCGTCTCTCTATGTGTATGTATGTATTTCGCTATCCATATATGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACTATATCTATATAACCCGAAACCATACTGGCCAGGAATAGCAAATCCA
droEre2 scaffold_4644:1251466-1251631 + AGATATAACCCAAAAGAAATACCGAATAGTAGCCAACTCTCTCGCTCTC----------TCTATGTGTATGTATGTATTTCGTTATCCATATATGTATATCCATGTCAGAGAGCCAGGATCGGTTGAGACCATACTA------TATAACCCAAAACCATACTGGCCAGGAATAGCAAGTCCA

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

-33.3 -32.9 -32.7 -32.6 -32.5 -32.4

droSim1

-33.3 -32.9 -32.7 -32.6 -32.5 -32.4

droSec1

-32.4 -32.0 -31.8 -31.7 -31.5 -31.4

droYak2

-30.2 -30.0 -29.9 -29.8 -29.6 -29.5

droEre2

-29.0 -28.7 -28.6 -28.6 -28.3 -28.3

droAna3

-34.4 -34.4 -33.5 -33.5 -33.4 -33.4

dp4

-12.1 -11.3 -11.2

droPer1

-24.4 -24.4 -24.1 -24.1 -23.7 -23.7

droWil1

-5.6 -5.6 -5.3 -5.2 -5.2 -5.1

droVir3

-29.3 -29.2 -29.1 -29.0 -29.0 -28.9

droMoj3

-5.5 -5.2 -5.2 -5.0 -5.0 -5.0

droGri2

-34.9 -34.7 -34.4 -34.2 -34.1 -34.0

Generated: 01/05/2013 at 05:25 PM