Secondary structure and small RNA-seq evidence for dme-mir-9c

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16697909-16698030 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------------------------------------------TGATAT----
droSim1	zdv96e12.b1:15-131 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droSec1	super_7:344892-345054 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCCA-AAACAGCCACAAATACAGGAATGATTAATGATAT----
droYak2	chr2R:4405017-4405183 -	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAACCAA-AAACAGCCACAAATACAGGAATGATTAAAAATATCTTT
droEre2	scaffold_4845:19767520-19767683 +	AT----------------------------TGC-ACCT---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCAAAAAACAGCCACAAATACAGGAATGATTTCTAATAT----
droAna3	scaffold_12916:15865465-15865583 -	CA----------------------------CGC-ACTCCCTTTCA--------------TTA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
dp4	chr4_group3:8443145-8443295 +	CT-CTCCCATTCGCTGTCTGTCGACTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droPer1	super_1:9894267-9894417 +	CT-CTCCCATTCGCTGTCTGCCGCCTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droWil1	scaffold_181061:30518-30658 -	CCTCCCCTCTTCACCATC-------------------T---TTTCCTCTCCCTCCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droVir3	scaffold_12963:12863840-12863951 -	CA----------------------------CAC-ACAA---TTT---------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT---ACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droMoj3	scaffold_6500:7201331-7201445 +	AT----------------------------TGCCACTC---TT----------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-C--ACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCG-------------------------------------------------
droGri2	scaffold_14978:830199-830317 +	AT----------------------------TGC-AATT---TCTT--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCT---ATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCT----------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16697909-16698030 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------------------------------------------TGATAT----
droSim1	zdv96e12.b1:15-131 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droSec1	super_7:344892-345054 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCCA-AAACAGCCACAAATACAGGAATGATTAATGATAT----
droYak2	chr2R:4405017-4405183 -	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAACCAA-AAACAGCCACAAATACAGGAATGATTAAAAATATCTTT
droEre2	scaffold_4845:19767520-19767683 +	AT----------------------------TGC-ACCT---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCAAAAAACAGCCACAAATACAGGAATGATTTCTAATAT----
droAna3	scaffold_12916:15865465-15865583 -	CA----------------------------CGC-ACTCCCTTTCA--------------TTA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
dp4	chr4_group3:8443145-8443295 +	CT-CTCCCATTCGCTGTCTGTCGACTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droPer1	super_1:9894267-9894417 +	CT-CTCCCATTCGCTGTCTGCCGCCTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droWil1	scaffold_181061:30518-30658 -	CCTCCCCTCTTCACCATC-------------------T---TTTCCTCTCCCTCCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droVir3	scaffold_12963:12863840-12863951 -	CA----------------------------CAC-ACAA---TTT---------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT---ACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droMoj3	scaffold_6500:7201331-7201445 +	AT----------------------------TGCCACTC---TT----------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-C--ACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCG-------------------------------------------------
droGri2	scaffold_14978:830199-830317 +	AT----------------------------TGC-AATT---TCTT--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCT---ATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCT----------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CT---------------------------TGCACTATTTA--------TCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................................................TCTTTGGTATTCTAGCTGTAG..........................................................................	21	1	7156.00	7156	7156
..............................................................TCTTTGGTATTCTAGCTGTAGA.........................................................................	22	1	4089.00	4089	4089
..............................................................TCTTTGGTATTCTAGCTGTAGAT........................................................................	23	1	29.00	29	29
................................................................TTTGGTATTCTAGCTGTAGATT.......................................................................	22	1	20.00	20	20
................................................................TTTGGTATTCTAGCTGTAGA.........................................................................	20	1	18.00	18	18
..............................................................TCTTTGGTATTCTAGCTGTA...........................................................................	20	1	18.00	18	18
................................................................TTTGGTATTCTAGCTGTAG..........................................................................	19	1	14.00	14	14
..............................................................................................................TAAAGCTTTTATACCAAAGCT..........................	21	1	9.00	9	9
...............................................................CTTTGGTATTCTAGCTGTAG..........................................................................	20	1	5.00	5	5
...............................................................CTTTGGTATTCTAGCTGTAGA.........................................................................	21	1	4.00	4	4
..............................................................................................................TAAAGCTTTTATACCAAAGCTC.........................	22	1	4.00	4	4
.................................................................TTGGTATTCTAGCTGTAGA.........................................................................	19	1	3.00	3	3
..............................................................TCTTTGGTATTCTAGCTGTAGATT.......................................................................	24	1	3.00	3	3
.................................................................TTGGTATTCTAGCTGTAG..........................................................................	18	1	3.00	3	3

dp4

CTCTCCCATTCGCTGTCTGTCGACTTCCATGCACTTTTTGTTCTCCTTTAATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................................TCTTTGGTATTCTAGCTGTAG..........................................................................	21	1	7678.00	7678	6709	969
..............................................................TCTTTGGTATTCTAGCTGTAGA.........................................................................	22	1	3324.00	3324	2969	355
..............................................................TCTTTGGTATTCTAGCTGTA...........................................................................	20	1	76.00	76	47	29
..............................................................TCTTTGGTATTCTAGCTGTAGAT........................................................................	23	1	71.00	71	63	8
..............................................................TCTTTGGTATTCTAGCTGT............................................................................	19	1	26.00	26	8	18
..............................................................................................................TAAAGCTTTTATACCAAAGCT..........................	21	1	16.00	16	11	5
................................................................TTTGGTATTCTAGCTGTAGA.........................................................................	20	1	12.00	12	12	0
................................................................TTTGGTATTCTAGCTGTAG..........................................................................	19	1	10.00	10	9	1
................................................................TTTGGTATTCTAGCTGTAGATT.......................................................................	22	1	8.00	8	6	2
..............................................................TCTTTGGTATTCTAGCTGTAGATT.......................................................................	24	1	7.00	7	5	2
...............................................................CTTTGGTATTCTAGCTGTAG..........................................................................	20	1	7.00	7	6	1
...............................................................CTTTGGTATTCTAGCTGTAGA.........................................................................	21	1	6.00	6	6	0
....................................................................................TTGTTTTTTGCACATTGTATATCATC...............................................	26	1	5.00	5	5	0
..............................................................................................................TAAAGCTTTTATACCAAAGCTC.........................	22	1	4.00	4	4	0
...............................................................CTTTGGTATTCTAGCTGTAGAT........................................................................	22	1	4.00	4	4	0
................................................................TTTGGTATTCTAGCTGTAGAT........................................................................	21	1	4.00	4	4	0
.................................................................TTGGTATTCTAGCTGTAGA.........................................................................	19	1	3.00	3	3	0

Secondary Structure

dm3

-26.0	-25.9	-25.7	-25.6	-25.6	-25.5

droSim1

-26.0	-25.9	-25.7	-25.6	-25.6	-25.5

droSec1

-26.0	-25.9	-25.7	-25.6	-25.6	-25.5

droYak2

-26.3	-26.2	-26.0	-25.9	-25.9	-25.8

droEre2

-26.3	-26.2	-26.0	-25.9	-25.9	-25.8

droAna3

-26.0	-25.9	-25.7	-25.6	-25.6	-25.5

dp4

-27.0	-26.7	-26.6	-26.5	-26.3	-26.2

droPer1

-27.0	-26.7	-26.6	-26.5	-26.3	-26.2

droWil1

-26.4	-26.0	-25.9	-25.7	-25.6	-25.5

droVir3

-26.2	-25.9	-25.8	-25.8	-25.6	-25.5

droMoj3

-25.6	-25.4	-25.3	-25.3	-25.1	-25.1

droGri2

-25.6	-25.3	-24.9	-24.9	-24.6	-24.6

Generated: 01/05/2013 at 05:37 PM