Secondary structure and small RNA-seq evidence for dme-mir-3644

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:11018004-11018094 -	TTATTGCTGCAGGAGGTGAGTGATTAT----G-GTTTA----AGT-------AATACGAATTACATAAACTATATTTA-------ACCACTATTCTTAGATACAAAACACTGCT
droSim1	chr3R:10448012-10448102 +	TTACTGCTGCAGGAGGTGAGTGTTTAT----G-GTTTA----AAT-------TATACGATTTACATAAACTATATTTA-------ACCACTACTCTTAGATCCAAAACACCGCT
droSec1	super_0:10933739-10933828 +	TTACTGCTGCAGGAGGTGAGGTTTTAT----G-GT-TA----AGT-------TATACGATTTGCATAAACTATATTTA-------ACCACTACTCTTAGATCCAAAACACCGCT
droYak2	chr3R:15416636-15416724 +	TTACTGCTTCAGGAGGTAAGTTTTT------G-GTTCA----GGT-------TTCATGAATTACATAAACTATATTTA-------ACCACATTCCTTAGATCCAAAATACCGCT
droEre2	scaffold_4770:10539530-10539618 -	TTACTGCTTCAGGAGGTCAGTTTTT------G-GTTCG----ATT-------TCAACGATTTACATAAACTGTATTTA-------ACCATATTTCGTAGATCCAAAACACCGCT
droAna3	scaffold_13340:6107797-6107878 -	TTGTTGCTGCAGGAGGTGGGTAGTG---------------AA---C------TTTTCAAATTACTATACC--------TTCATGAATGTTCTTTTGTAGATTCAAAATACTGCG
dp4	chr2:21002920-21003004 -	CTGTTGCTGCAGGAGGTAGGCTACA------GAG------AA---C----ATTTAG---------TAAATAATAGTCGCTCATTC-TTTTCCCTAATAGATCCAAAACACTGCC
droPer1	super_3:3754054-3754138 -	CTGTTGCTGCAGGAGGTAGGCTACA------GAG------AA---C----TTTAAG---------TAAATAATAGTCGCTCATTC-TCTTCCCTAATAGATCCAAAACACTGCC
droWil1	scaffold_181130:7245340-7245433 +	TTGCTATTGCAAGAGGTCAGTTAGAAT----A-GCAAA----AGACACTCTTGGGATGGTTAATAATA----------TTCATAT-TTGGTTTTTGCAGATTCAAAATACTGCC
droVir3	scaffold_13047:7744104-7744193 -	CTGCTGCTTCAAGAGGTGAGCAACTGCTTTTG-GCTTA----TGT----------TCGATTTTCAATGAT--------CTCTCG-AATACTTTTTATAGATACAAAACACAGCG
droMoj3	scaffold_6540:3682572-3682661 -	TTGCTGCTGCAAGAGGTAAAATGTT------GAGCTCATAAAAGT----------TTCCTTT---TCAATTACA----TTCACAT-TCATTCGTTTTAGATACAAAATACGGCC
droGri2	scaffold_14830:3558248-3558343 -	CTGCTGCTGCAGGAGGTGAGTTGCACCAACTG-ACACA----G-----TGTTTCCATAATTTACATTTTCTCTTTAT--------ATCTTTGTTCTCAGATACAAAACACGGCT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:11018004-11018094 -	TTATTGCTGCAGGAGGTGAGTGATTATGGTTTAAGTAATACGAATTACATAAACTATATTTAACCACTATTCTTAGATACAAAACACTGCT
droSim1	chr3R:10448012-10448102 +	TTACTGCTGCAGGAGGTGAGTGTTTATGGTTTAAATTATACGATTTACATAAACTATATTTAACCACTACTCTTAGATCCAAAACACCGCT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTACTGCTGCAGGAGGTGAGTGTTTATGGTTTAAATTATACGATTTACA------------TAAACTATATTTAACCACTACTCT------TAGATCCAAAACACCGCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CTGTTGCTGCAGGAGGTAGGC------------------------TACAGAGAACATTTAGTAAATAATAGTCGCTCATTCTTTTCCCTAATAGATCCAAAACACTGCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-14.7	-14.1	-13.9

droSim1

-8.3	-8.3	-8.2	-7.9	-7.4

droSec1

-9.1	-8.7	-8.7	-8.5	-8.2	-8.2

droYak2

-6.2	-5.9	-5.8	-5.7	-5.3	-5.3

droEre2

-7.6	-7.0

droAna3

-4.8	-4.3	-4.0	-4.0	-3.9	-3.8

dp4

-3.7	-3.4	-2.9	-2.8	-2.8	-2.7

droPer1

-6.3	-6.0	-5.4	-5.3	-5.3

droWil1

-8.7	-8.1	-7.8	-7.8	-7.8	-7.8

droVir3

-7.4	-7.3	-7.2	-7.1	-7.1	-7.0

droMoj3

-3.0	-2.8	-2.7	-2.44	-2.4	-2.3

droGri2

-6.7	-6.4	-6.2	-5.9

Generated: 01/05/2013 at 05:19 PM