Secondary structure and small RNA-seq evidence for dme-mir-284

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:8377222-8377351 -	ATAATCGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCTCAACAATG
droSim1	chr3R:13050845-13050974 +	ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droSec1	super_0:13609227-13609356 +	ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droYak2	chr3R:12662228-12662357 -	ATAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droEre2	scaffold_4770:13275536-13275665 +	TTAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droAna3	scaffold_12911:3307955-3308116 -	ACAAAAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGAACTGCTTCAGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGTACAGCA---GAAAGAGCCGTGAACCGTGTTCAATATGCCACGACAATG
dp4	chr2:2484958-2485100 -	ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droPer1	super_7:2652948-2653090 -	ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droWil1	scaffold_181130:2186197-2186330 -	GTGTGTGACAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTTAGGGGAAAGGCTTGAGCATTGCATACTAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCTCAACGTT--------------------------------CAACAGTG
droVir3	scaffold_12855:584465-584599 +	ATAAATGGAAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAAGGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGGACAACGTTGGAAAG------------TGTC------------------
droMoj3	scaffold_6540:12381805-12381927 -	TGTAT---TAATTGCGTTGCAGTTCCTGGAATAAAGTTGACTGTGTCGCCTGTAAGGGG-AAGGCTTTTGCATTGCTTACAAAGTCAGCAACTTGATTCCAGCAACTGCGGCCCAAGCT---------------------------------------CAACGTGG
droGri2	scaffold_14906:1700701-1700824 +	ATA--TGGAAATTGGGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAGAGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCTCAAACT---------------------------------------CAACGTTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:8377222-8377351 -	ATAATCGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCTCAACAATG
droSim1	chr3R:13050845-13050974 +	ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droSec1	super_0:13609227-13609356 +	ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGAT-----------------------------------ATTCCGCAACAATG
droYak2	chr3R:12662228-12662357 -	ATAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droEre2	scaffold_4770:13275536-13275665 +	TTAATGGGTGATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAT-----------------------------------ATTCCGCAACAATG
droAna3	scaffold_12911:3307955-3308116 -	ACAAAAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGC-AAGGCTTGAGAACTGCTTCAGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGTACAGCA---GAAAGAGCCGTGAACCGTGTTCAATATGCCACGACAATG
dp4	chr2:2484958-2485100 -	ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droPer1	super_7:2652948-2653090 -	ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGC-AAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCACAACGCTGAATGG------------TGCTCAAAATAC----------
droWil1	scaffold_181130:2186197-2186330 -	GTGTGTGACAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTTAGGGGAAAGGCTTGAGCATTGCATACTAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGCTCAACGTT--------------------------------CAACAGTG
droVir3	scaffold_12855:584465-584599 +	ATAAATGGAAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAAGGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAGGACAACGTTGGAAAG------------TGTC------------------
droMoj3	scaffold_6540:12381805-12381927 -	TGTAT---TAATTGCGTTGCAGTTCCTGGAATAAAGTTGACTGTGTCGCCTGTAAGGGG-AAGGCTTTTGCATTGCTTACAAAGTCAGCAACTTGATTCCAGCAACTGCGGCCCAAGCT---------------------------------------CAACGTGG
droGri2	scaffold_14906:1700701-1700824 +	ATA--TGGAAATTGGGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAGAGG-AAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCTCAAACT---------------------------------------CAACGTTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATAATGGGTAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGGCAAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGATATTCCGCAACAATG-----------------	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..................................................................................GTCAGCAACTTGATTCCAGCAA...........................................	22	1	75.00	75	75
..................................................................................GTCAGCAACTTGATTCCAGCA............................................	21	1	24.00	24	24
........................CCTGGAATTAAGTTGACTGTGTAGC..................................................................................................	25	1	23.00	23	23
........................CCTGGAATTAAGTTGACTGTGTAGCC.................................................................................................	26	1	18.00	18	18
........................CCTGGAATTAAGTTGACTGTGTAG...................................................................................................	24	1	3.00	3	3
.....GGGTAATTGCGTTGCAGTT...........................................................................................................................	19	1	2.00	2	2
.....................................................................................AGCAACTTGATTCCAGCAA...........................................	19	1	1.00	1	1
........................CCTGGAATTAAGTTGACTGTGTAGCCT................................................................................................	27	1	1.00	1	1
..........................................................................CTCCTGAAGTCAGCAACTTGATTCCA...............................................	26	1	1.00	1	1

dp4

ATCAGAGGCAATTGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGGCAAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAAG----CACAACGCTGAATGGTGCTCAAAATAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..................................................................................GTCAGCAACTTGATTCCAGCAA...........................................	22	1	1410.00	1410	244	1166
........................CCTGGAATTAAGTTGACTGTGTAGCC.................................................................................................	26	1	994.00	994	127	867
..................................................................................GTCAGCAACTTGATTCCAGCA............................................	21	1	981.00	981	53	928
........................CCTGGAATTAAGTTGACTGTGTAGC..................................................................................................	25	1	490.00	490	67	423
........................CCTGGAATTAAGTTGACTGTGTAG...................................................................................................	24	1	204.00	204	3	201
.....AGGCAATTGCGTTGCAGTT...........................................................................................................................	19	1	157.00	157	6	151
........................CCTGGAATTAAGTTGACTGTGT.....................................................................................................	22	1	93.00	93	1	92
........................CCTGGAATTAAGTTGACTGTG......................................................................................................	21	1	59.00	59	0	59
........................CCTGGAATTAAGTTGACTGTGTA....................................................................................................	23	1	50.00	50	1	49
..................................................................................GTCAGCAACTTGATTCCAGC.............................................	20	1	31.00	31	0	31
........................CCTGGAATTAAGTTGACTGTGTAGCCT................................................................................................	27	1	21.00	21	0	21
........................CCTGGAATTAAGTTGACTGT.......................................................................................................	20	1	8.00	8	0	8
.....................................................................................AGCAACTTGATTCCAGCAA...........................................	19	1	8.00	8	3	5
.....................................................................................AGCAACTTGATTCCAGCA............................................	18	1	7.00	7	1	6
..................................................................................GTCAGCAACTTGATTCCAG..............................................	19	1	4.00	4	0	4
........................CCTGGAATTAAGTTGACTG........................................................................................................	19	1	3.00	3	0	3
.........................CTGGAATTAAGTTGACTGTGTAGC..................................................................................................	24	1	3.00	3	1	2

Secondary Structure

dm3

-39.7	-39.7	-39.7	-39.5	-39.5	-38.8

droSim1

-40.9	-40.9	-40.0	-40.0	-39.9	-39.9

droSec1

-40.9	-40.9	-40.0	-40.0	-39.9	-39.9

droYak2

-42.9

droEre2

-42.9

droAna3

-41.5	-41.1	-41.1	-41.1	-40.7	-40.7

dp4

-42.4	-42.0	-42.0	-41.8	-41.7	-41.7

droPer1

-42.4	-42.0	-42.0	-41.8	-41.7	-41.7

droWil1

-40.8	-40.7	-40.4	-40.1	-40.1	-40.0

droVir3

-41.3	-41.3	-41.3	-41.3	-40.9	-40.9

droMoj3

-40.1	-40.1	-40.0	-39.7	-39.7	-39.5

droGri2

-42.2	-42.2	-42.2	-42.2	-41.7	-41.7

Generated: 01/05/2013 at 05:14 PM