Secondary structure and small RNA-seq evidence for dme-mir-210

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:18022237-18022366 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSim1	chrX_random:4635946-4636075 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSec1	super_8:332193-332322 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droYak2	chrX:16646312-16646441 +	CCATG-----------------------------------------------TCGCGAA-----CCGAAAGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCATA
droEre2	scaffold_4690:8350125-8350254 +	CCACG-----------------------------------------------TCGCGAA-----CCAAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCACA
droAna3	scaffold_13335:1603991-1604112 -	GC--G------------------------------------------------------------TTAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACCAATCAACTGACCA--C-------------------------------------------------CAG----------ATC
dp4	chrXL_group3a:1970441-1970623 -	ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAG------TT---TC
droPer1	super_11:2708510-2708698 +	ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACAAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGT-TTCATTCCA--
droWil1	scaffold_181096:12033222-12033334 +	CAATC-----------------------------------------------GCAAAAG-----CATAACGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCAGAAAACGACCAG--------------------------------------------------------------------------------
droVir3	scaffold_12928:1257190-1257317 -	T---A-----------------------------------------------TATTTAA-----ACGAGCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGAGAAACAGCGAAT-ATT----------------------------------------------------------TAACTATTTTTCC---
droMoj3	scaffold_6473:13732313-13732476 +	CCACATATACAGAGCATATATGTATATGCATATATCATACAAGTATATAGAATCCAGATCCATTGGGAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGATGCCAGAGAAGCAACA---------------------------------------------------------------------------------
droGri2	scaffold_15203:8453543-8453644 +	----------------------------------------------------------------------GGAGCTTATTGGAGCTGCTGGCCACTGCACAAGATTAGATTCAAAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGATA----ACAT-----C----------------------------------------------------------AAGCCAT---------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:18022237-18022366 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSim1	chrX_random:4635946-4636075 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSec1	super_8:332193-332322 +	CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droYak2	chrX:16646312-16646441 +	CCATG-----------------------------------------------TCGCGAA-----CCGAAAGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCATA
droEre2	scaffold_4690:8350125-8350254 +	CCACG-----------------------------------------------TCGCGAA-----CCAAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCACA
droAna3	scaffold_13335:1603991-1604112 -	GC--G------------------------------------------------------------TTAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACCAATCAACTGACCA--C-------------------------------------------------CAG----------ATC
dp4	chrXL_group3a:1970441-1970623 -	ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAG------TT---TC
droPer1	super_11:2708510-2708698 +	ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACAAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGT-TTCATTCCA--
droWil1	scaffold_181096:12033222-12033334 +	CAATC-----------------------------------------------GCAAAAG-----CATAACGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCAGAAAACGACCAG--------------------------------------------------------------------------------
droVir3	scaffold_12928:1257190-1257317 -	T---A-----------------------------------------------TATTTAA-----ACGAGCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGAGAAACAGCGAAT-ATT----------------------------------------------------------TAACTATTTTTCC---
droMoj3	scaffold_6473:13732313-13732476 +	CCACATATACAGAGCATATATGTATATGCATATATCATACAAGTATATAGAATCCAGATCCATTGGGAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGATGCCAGAGAAGCAACA---------------------------------------------------------------------------------
droGri2	scaffold_15203:8453543-8453644 +	----------------------------------------------------------------------GGAGCTTATTGGAGCTGCTGGCCACTGCACAAGATTAGATTCAAAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGATA----ACAT-----C----------------------------------------------------------AAGCCAT---------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCACGTCCGGA-----ACCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-------CCAGCCA-----------------------------------------TTGTTCCA---TC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................................CTTGTGCGTGTGACAGCGGCTAT............................................................................................	23	1	32.00	32	32
........................................................................TTGTGCGTGTGACAGCGGCTAT............................................................................................	22	1	29.00	29	29
........................................................................TTGTGCGTGTGACAGCGGCT..............................................................................................	20	1	11.00	11	11
.......................................................................CTTGTGCGTGTGACAGCGGCTA.............................................................................................	22	1	10.00	10	10
.......................................................................CTTGTGCGTGTGACAGCGGCT..............................................................................................	21	1	5.00	5	5
........................................................................TTGTGCGTGTGACAGCGGCTA.............................................................................................	21	1	4.00	4	4
...................................AGCTGCTGGCCACTGCACAAGA.................................................................................................................................	22	1	2.00	2	2
...................................AGCTGCTGGCCACTGCACAAGAT................................................................................................................................	23	1	2.00	2	2
...................................AGCTGCTGGCCACTGCACAAGATT...............................................................................................................................	24	1	1.00	1	1
........................................................................TTGTGCGTGTGACAGCGGC...............................................................................................	19	1	1.00	1	1
.......................................................................CTTGTGCGTGTGACAGCGGC...............................................................................................	20	1	1.00	1	1

dp4

ATATGT---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAAACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGTTTC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................................CTTGTGCGTGTGACAGCGGCTAT............................................................................................	23	1	53563.00	53563	23	53540
.......................................................................CTTGTGCGTGTGACAGCGGCT..............................................................................................	21	1	47134.00	47134	8	47126
........................................................................TTGTGCGTGTGACAGCGGCTAT............................................................................................	22	1	42465.00	42465	25	42440
........................................................................TTGTGCGTGTGACAGCGGCT..............................................................................................	20	1	22563.00	22563	8	22555
.......................................................................CTTGTGCGTGTGACAGCGGCTA.............................................................................................	22	1	18745.00	18745	6	18739
........................................................................TTGTGCGTGTGACAGCGGCTA.............................................................................................	21	1	18036.00	18036	7	18029
........................................................................TTGTGCGTGTGACAGCGGC...............................................................................................	19	1	15366.00	15366	0	15366
.......................................................................CTTGTGCGTGTGACAGCGGC...............................................................................................	20	1	4416.00	4416	5	4411
.......................................................................CTTGTGCGTGTGACAGCGG................................................................................................	19	1	2266.00	2266	0	2266
.......................................................................CTTGTGCGTGTGACAGCGGCTATT...........................................................................................	24	1	1867.00	1867	0	1867
........................................................................TTGTGCGTGTGACAGCGGCTATT...........................................................................................	23	1	1631.00	1631	0	1631
........................................................................TTGTGCGTGTGACAGCGG................................................................................................	18	1	1549.00	1549	0	1549
.......................................................................CTTGTGCGTGTGACAGCG.................................................................................................	18	1	153.00	153	0	153
.........................................................................TGTGCGTGTGACAGCGGCTAT............................................................................................	21	1	49.00	49	0	49
..........................................................................GTGCGTGTGACAGCGGCTAT............................................................................................	20	1	30.00	30	0	30
...................................AGCTGCTGGCCACTGCACAAGA.................................................................................................................................	22	1	29.00	29	2	27
...................................AGCTGCTGGCCACTGCACAAGAT................................................................................................................................	23	1	28.00	28	2	26
.........................................................................TGTGCGTGTGACAGCGGCT..............................................................................................	19	1	23.00	23	0	23
.........................................................................TGTGCGTGTGACAGCGGCTA.............................................................................................	20	1	20.00	20	0	20

Secondary Structure

dm3

-37.0	-36.9	-36.3	-36.2	-36.1

droSim1

-37.0	-36.9	-36.3	-36.2	-36.1

droSec1

-37.0	-36.9	-36.3	-36.2	-36.1

droYak2

-36.2	-36.1	-35.5

droEre2

-36.2	-36.1	-35.5

droAna3

-36.2	-36.1	-35.5

dp4

-49.0	-48.9	-48.3	-48.3	-48.2

droPer1

-49.0	-48.9	-48.3	-48.3	-48.2

droWil1

-36.2	-36.1	-35.5

droVir3

-35.9	-35.8

droMoj3

-36.5	-36.4

droGri2

-33.6	-33.2	-32.8

Generated: 01/05/2013 at 05:08 PM