Secondary structure and small RNA-seq evidence for dme-mir-4943

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16528359-16528506 -	ATTTTAAACAACTA-TTTCGG-------ATCGTTTG---------------AATGACCAATTTTGT-------------CTTTTATTTTCTCT--G--------------T-G-----TTTT-----CAGTTAATG-AAAGAT-AG-TGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droSim1	chr2L_random:601476-601603 -	ATTT------------------------ATTT-TTG---------------AATGACCAATTTTGT-------------CTT---TCTTCTCT--G--------------T-C-----GTTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droSec1	super_7:174891-175018 -	ATTT------------------------ATTT-TTG---------------AATGACCAATTTTGT-------------CTT---TCTTCTCT--T--------------T-C-----TTTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droYak2	chr2R:4574442-4574584 +	ATTTTATAAAACTA-TGGGGG-------ATAC-TTA---------------GATAATTAATTTTGT-------------CAT---TGTTCTTT--G--------------T-C------TTT-----CAGTTAATG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droEre2	scaffold_4845:19592406-19592554 -	ATTTTATGCAACTA-TTGTGT-----GTATCT-TTA---------------AATGACTAATTTTGT-------------CAT---TCTTCTCT--G------TTT-----T-T-----TTTT-----CAGTTAATG-AATAGT-AG-CAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG
droAna3	scaffold_12916:16031637-16031788 +	ATGTT------------------------TAA-ATG---------------ATTAAAAAATTATGTTCAACTAATTATTAA-------TTTAT--A------TTTT-ATTGTCTTCCCATTA-----CAGTTAATGAAAAAGT-AATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCCC---------AAGAAGACCATGTTGATTG
dp4	chr4_group3:8251613-8251715 -	TT-----------------------------------------------------------------------------------TGTTCCTTTTC--------------T-C-----TTTA-----CAGTTATTTGCCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAA---------CAGAAGACGATGTTGATTG
droPer1	super_1:9700572-9700674 -	TT-----------------------------------------------------------------------------------TGTTCCTTTTC--------------T-C-----TTCA-----CAGTTATTTGCCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAA---------CAGAAGACGATGTTGATTG
droWil1	scaffold_180772:4810613-4810759 -	AAGTTTACCAATTAATAGCAA-------ATTG-TTGGTATTTCCATTTTAAAATTGCTAACATTTA---------CCTTAA-------TTTCT--C------TTCT-TTTC-T-----TTTT-----CAAT---------TCC-AG-CTTACGTTGCTATAAATGAGAAAGGATCAA------------GATCAA---------ACGAAAAGGATGTTGATTG
droVir3	scaffold_13052:1601321-1601473 -	ATATTGCGCAACCA-TTCTGGTCCGAATTTCA-TTG---------------AGTCAGTCATTTTGG----GTAACTCTT------------GA--GTTTATTTCTTAATTGTC------TTTCGCTGAAATTGTGCAATAAAT-AA-CA---ATTT---------------TACCATCAGCATTAGCCAGCACAC---------ACACGCACGCTATCGGTTT
droMoj3	scaffold_6500:21042727-21042874 -	AATTA------------------------TAA-TTG---------------AACACTTGA-TGCGATTGCCAAATTTTTGAT---TTTTGGTTCTA--------------T-T-----TTTA-----GAGTTACAG-CTAAAT-GA-AA---ACTATACCAATTATAAAATCAAAAGGGCTACACAAGAACATTTATGATTTCAAAGAAAAGTGTTTCATTTG
droGri2	scaffold_14822:853797-853916 -	GCATG-----------------------------------------------ATGACTTGTGGTCT-------------CTA---TTCTATAT--G--------------C-T-----GGTT-----GAGTTTGTG-AATGGTCAG-TTGCCGTGGCGAAAGATAAAAGACAAG--GAACAGGTTGGATTGACCA---------AAGAGAAATATGATCATAG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16528359-16528506 -	ATTTTAAACAACTA-TTTCGG-------ATCGTTTG---------------AATGACCAATTTTGT-------------CTTTTATTTTCTCT--G--------------T-G-----TTTT-----CAGTTAATG-AAAGAT-AG-TGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCC---------AAGAAGACGATGTTGATTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATTT---------ATT--------TTTGAATGACCAATTTTGTCTT---TCTTCTCTGTCGTTTCAGTTAAT-GAAAAGTAGTAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TTT--------------------------------------GTTCC---TTTTCTCT----TTACAGTTATTTGCCAAGCAG-AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAACAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................................................................................GAGACACAGTCGACAGAC......................	18	1	1.00	1	1	0

Secondary Structure

dm3

-25.3	-25.2	-25.2	-25.1	-24.8	-24.8

droSim1

-19.6	-19.4	-18.9	-18.8	-18.8	-18.8

droSec1

-22.2	-21.7	-21.4	-21.3	-21.3	-21.2

droYak2

-22.4	-22.3	-21.9	-21.8	-21.8	-21.8

droEre2

-22.4	-21.9	-21.9	-21.6	-21.5	-21.4

droAna3

-8.9	-8.6	-8.5	-8.4	-8.4	-8.2

dp4

-14.5	-14.4	-14.3	-14.2	-14.1	-14.1

droPer1

-14.5	-14.4	-14.3	-14.2	-13.8	-13.8

droWil1

-19.0	-19.0	-19.0	-18.9	-18.9	-18.9

droVir3

-19.8	-19.4	-19.1	-19.1	-18.8

droMoj3

-18.4	-18.4

droGri2

-20.3	-19.9	-19.4	-19.3

Generated: 01/05/2013 at 05:21 PM