Secondary structure and small RNA-seq evidence for dme-mir-13b-2

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:8985248-8985347 +	TCTA---CCTCT------------------GCT------------------GTCTATTAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GACAG-CCAGCCT
droSim1	chrX_random:2632466-2632565 +	TCTG---CCTCT------------------GCT------------------GTCTATCAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAG-CCAGCCT
droSec1	super_34:345603-345702 +	CCTG---CCTCT------------------GCT------------------GTCTATCAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAG-CCAGCCT
droYak2	chrX:12330556-12330651 -	CTTA---CCCCT------------------GCT------------------GTCTAGTAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGCTG-GCCAGT-----CT
droEre2	scaffold_4690:6132295-6132393 -	TTTAAACCCCCT------------------GCT------------------GTCTATTAGCGCGTCAAAGTGACTGTGAACTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAGC-C----C
droAna3	scaffold_13047:797460-797571 +	TGTCCCGCTTCT------------------GCTT----CATTAC--CT---GTTTCCCAGCGCGTCGAAATGACTGTGACTTATGCGT----ATTTGA-TGTCATATCACAGCCATTTTGACGAGTTTGGTG-GACAGT-GAAAGT
dp4	chrXL_group1e:7000785-7000885 -	GCTA---CTGCT------------------GCT------------------GCACATTTACGCGTCAAAATGACTGTGAGCTATGTGT----TTTTGA-TCTCATATCACAGCCATTTTGACGAGTTTGATG-TGCAGTCCCACTC
droPer1	super_13:1553253-1553353 +	GCTA---CTGCT------------------GCT------------------GCACATTTACGCGTCAAAATGACTGTGAGCTATGTGT----TTTTGA-TCTCATATCACAGCCATTTTGACGAGTTTGATG-TGCAGTCCCACTC
droWil1	scaffold_180777:2053037-2053171 +	TCCC---CCAATGTACCTACCCCTGCAACTGCTGTGCTT---ACAACTGATGTCCATGGTCGCGTCAAAATGACTGTGAGCTATGTTAACCGGTCAGAAATTCATATCACAGCCATTTTGACGAGTTCGATG-GGCAT-AC---GA
droVir3	scaffold_12970:9304312-9304422 +	TCTC---TCGCT------------------GCT---------GCCAATGCTCCATATTGGCGCGTCAAAATGACTGTGAGCTATGTTGTTGCATTTGCCATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGC-CA----
droMoj3	scaffold_6473:13342549-13342650 -	TCCT---CTAAT------------------GCT------------------CCATATTTGCGCGTCAAATTGACTGTGAGCTATGTTT----ATGAGATTATCATATCACAGCCATTTTGACGAGTTTGATGTGGCAG-CCACCAA
droGri2	scaffold_15203:306998-307104 +	TCG-------TT------------------GCT---------ATCAGTGCTCCATATTGGCGCGTCAAATTGACTGTGAGCTATGTTGTTGCAGTTGTAATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGC-CA----

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:8985248-8985347 +	TCTA---CCTCT------------------GCT------------------GTCTATTAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GACAG-CCAGCCT
droSim1	chrX_random:2632466-2632565 +	TCTG---CCTCT------------------GCT------------------GTCTATCAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAG-CCAGCCT
droSec1	super_34:345603-345702 +	CCTG---CCTCT------------------GCT------------------GTCTATCAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAG-CCAGCCT
droYak2	chrX:12330556-12330651 -	CTTA---CCCCT------------------GCT------------------GTCTAGTAACGCGTCAAAATGACTGTGAGCTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGCTG-GCCAGT-----CT
droEre2	scaffold_4690:6132295-6132393 -	TTTAAACCCCCT------------------GCT------------------GTCTATTAGCGCGTCAAAGTGACTGTGAACTATGTGG----ATTTGA-CTTCATATCACAGCCATTTTGACGAGTTTGTTG-GGCAGC-C----C
droAna3	scaffold_13047:797460-797571 +	TGTCCCGCTTCT------------------GCTT----CATTAC--CT---GTTTCCCAGCGCGTCGAAATGACTGTGACTTATGCGT----ATTTGA-TGTCATATCACAGCCATTTTGACGAGTTTGGTG-GACAGT-GAAAGT
dp4	chrXL_group1e:7000785-7000885 -	GCTA---CTGCT------------------GCT------------------GCACATTTACGCGTCAAAATGACTGTGAGCTATGTGT----TTTTGA-TCTCATATCACAGCCATTTTGACGAGTTTGATG-TGCAGTCCCACTC
droPer1	super_13:1553253-1553353 +	GCTA---CTGCT------------------GCT------------------GCACATTTACGCGTCAAAATGACTGTGAGCTATGTGT----TTTTGA-TCTCATATCACAGCCATTTTGACGAGTTTGATG-TGCAGTCCCACTC
droWil1	scaffold_180777:2053037-2053171 +	TCCC---CCAATGTACCTACCCCTGCAACTGCTGTGCTT---ACAACTGATGTCCATGGTCGCGTCAAAATGACTGTGAGCTATGTTAACCGGTCAGAAATTCATATCACAGCCATTTTGACGAGTTCGATG-GGCAT-AC---GA
droVir3	scaffold_12970:9304312-9304422 +	TCTC---TCGCT------------------GCT---------GCCAATGCTCCATATTGGCGCGTCAAAATGACTGTGAGCTATGTTGTTGCATTTGCCATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGC-CA----
droMoj3	scaffold_6473:13342549-13342650 -	TCCT---CTAAT------------------GCT------------------CCATATTTGCGCGTCAAATTGACTGTGAGCTATGTTT----ATGAGATTATCATATCACAGCCATTTTGACGAGTTTGATGTGGCAG-CCACCAA
droGri2	scaffold_15203:306998-307104 +	TCG-------TT------------------GCT---------ATCAGTGCTCCATATTGGCGCGTCAAATTGACTGTGAGCTATGTTGTTGCAGTTGTAATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGC-CA----

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TCTGCCTCTGCTGTCTATCAACGCGTCAAAATGACTGTGAGCTATGTGGATTTGACTTCATATCACAGCCATTTTGACGAGTTTGTTGGGCAG-CCAGCCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................TATCACAGCCATTTTGACGAGT...................	22	3	13886.00	41658	41658
............................................................TATCACAGCCATTTTGACGAGTT..................	23	3	4715.67	14147	14147
............................................................TATCACAGCCATTTTGACGAGTTT.................	24	3	72.33	217	217
................................................................ACAGCCATTTTGACGAGTT..................	19	3	33.33	100	100
......................GCGTCAAAATGACTGTGAGCTATG.......................................................	24	2	19.50	39	39
..............................................................TCACAGCCATTTTGACGAGT...................	20	3	5.33	16	16
...........................................................ATATCACAGCCATTTTGACGAGT...................	23	3	2.00	6	6
...............................................................CACAGCCATTTTGACGAGT...................	19	3	2.00	6	6
...GCCTCTGCTGTCTATCAAC...............................................................................	19	2	1.50	3	3
......................GCGTCAAAATGACTGTGAGCTATGT......................................................	25	2	0.50	1	1

dp4

GCTACTGCTGCTGCACATTTACGCGTCAAAATGACTGTGAGCTATGTGTTTTTGATCTCATATCACAGCCATTTTGACGAGTTTGATGTGCAGTCCCACTC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................TATCACAGCCATTTTGACGAGT...................	22	3	7602.00	22806	0	22806
............................................................TATCACAGCCATTTTGACGAGTT..................	23	3	4953.33	14860	14860	0
............................................................TATCACAGCCATTTTGACGAG....................	21	3	1349.00	4047	3114	933
......................GCGTCAAAATGACTGTGAGCTATG.......................................................	24	2	18.50	37	37	0
.............................................................ATCACAGCCATTTTGACGAGT...................	21	3	17.00	51	31	20
...........................................................ATATCACAGCCATTTTGACGAG....................	22	3	11.33	34	31	3
............................................................TATCACAGCCATTTTGACG......................	19	3	7.33	22	22	0
..............................................................TCACAGCCATTTTGACGAGTT..................	21	3	5.00	15	15	0
................................................................ACAGCCATTTTGACGAGTTT.................	20	3	4.33	13	5	8
...........................................................ATATCACAGCCATTTTGACGAGT...................	23	3	2.67	8	8	0
...............................................................CACAGCCATTTTGACGAGTT..................	20	3	2.33	7	0	7
...................TACGCGTCAAAATGACTGTG..............................................................	20	2	2.00	4	0	4
......................GCGTCAAAATGACTGTGAGCT..........................................................	21	2	1.50	3	1	2
............................................................TATCACAGCCATTTTGACGAGTTTG................	25	3	1.00	3	0	3
.............................................................ATCACAGCCATTTTGACGAG....................	20	3	1.00	3	3	0
.................................................................CAGCCATTTTGACGAGTT..................	18	3	1.00	3	3	0

Secondary Structure

dm3

dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.7, p-value=0.009901

droSim1

dG=-26.6, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.8, p-value=0.009901

droSec1

dG=-26.6, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.8, p-value=0.009901

droYak2

dG=-26.7, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901

droEre2

dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droAna3

dG=-29.0, p-value=0.009901	dG=-29.0, p-value=0.009901

dp4

dG=-23.6, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.0, p-value=0.009901

droPer1

dG=-23.6, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.0, p-value=0.009901

droWil1

dG=-23.5, p-value=0.009901

droVir3

dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droMoj3

dG=-21.6, p-value=0.009901

droGri2

dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

Generated: 03/07/2013 at 04:51 PM