Secondary structure and small RNA-seq evidence for dme-mir-33

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:19791046-19791174 +	CTG-----AGTGCCACCAGACTCT--------TCCT-CTGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACATA-CAAC------------GCCG---AATG------
droSim1	chr3L:19083102-19083230 +	CTG-----AGTGCCACCAGACTCC--------TCCT-CCGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACACA-CAAC------------GCCG---AATG------
droSec1	super_29:452742-452870 +	CTG-----AGTGCCACCAGACTCT--------TCCT-CCGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACACA-CAAC------------GCCG---AATG------
droYak2	chr3L:20771315-20771443 -	CTG-----AGTGCCACCAGACTCT--------TACT-CCAGAGATGTCACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCG---AGTG------
droEre2	scaffold_4784:19550563-19550691 +	CTG-----AGTGCCACCAGACTCT--------CACT-CCAGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCG---AGTG------
droAna3	scaffold_13337:19456783-19456919 -	CCG-----AATACCAGCAGACACTATACACCCGCCC-TCGGAGATGTCACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCACTT---GC-TCCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCA---ACTT------
dp4	chrXR_group6:5913809-5913939 +	AAA-----AACCAAACCAAACACT-----------C-CCGGAGATGACACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CATCTT---GATTTCAGGCAATACAACTGCAATGCAAGCTCTGTGCATTTCATAAATCAAC------------GCCGTCCAATG------
droPer1	super_47:413986-414116 +	AAA-----AACCAAACCAAACACT-----------C-CCGGAGATGACACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CATCTT---GATTTCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCATAAATCAAC------------GCCGTCCAATG------
droWil1	scaffold_180698:8572488-8572628 +	CGG-----AACCTAAACAAAT------------------TGAAGTTACACGAAGGTGCATTGTAGTCGCATTGTCTGTGCTCCAAAAAAAAAAAACCCCCAGTT-T-CTATTCAGGCAATACAACTGCAGTGCAAGCTTCGTGTGACTTATAAG-CAAC------------GGCA---AATA------
droVir3	scaffold_13049:22941104-22941227 -	CCA-----AAATC----CGACA-----------TCT-CTGGAGCTGTTACGGAGGTGCATTGTAGTCGCATTGTCTGTC-------------------TCAAAT-TTGC-CCGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACACG-CAAC------------GTCG---GAAG------
droMoj3	scaffold_6680:17552824-17552948 -	CAG-----CATTCCGACA---------------TCT-TTGGAGCTGTGACGGAGGTGCATTGTAGTCGCATTGTCTGTA-------------------TCCTTTATTCT-CTGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACTCG-CAAC------------GTCG---GACA------
droGri2	scaffold_15110:18214439-18214590 -	CTCTGCACAGTTAGGGCAGACA-----------TCTCCAGGAGCTGTCACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CAAAAA-TTGC-ATGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACTAG-CAACAACTCTTTGATCGCTG---ATCGATCTGA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:19791046-19791174 +	CTG-----AGTGCCACCAGACTCT--------TCCT-CTGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACATA-CAAC------------GCCG---AATG------
droSim1	chr3L:19083102-19083230 +	CTG-----AGTGCCACCAGACTCC--------TCCT-CCGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACACA-CAAC------------GCCG---AATG------
droSec1	super_29:452742-452870 +	CTG-----AGTGCCACCAGACTCT--------TCCT-CCGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACACA-CAAC------------GCCG---AATG------
droYak2	chr3L:20771315-20771443 -	CTG-----AGTGCCACCAGACTCT--------TACT-CCAGAGATGTCACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCG---AGTG------
droEre2	scaffold_4784:19550563-19550691 +	CTG-----AGTGCCACCAGACTCT--------CACT-CCAGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCAATT---GC-TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCG---AGTG------
droAna3	scaffold_13337:19456783-19456919 -	CCG-----AATACCAGCAGACACTATACACCCGCCC-TCGGAGATGTCACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CCACTT---GC-TCCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCACAAA-CAAC------------GCCA---ACTT------
dp4	chrXR_group6:5913809-5913939 +	AAA-----AACCAAACCAAACACT-----------C-CCGGAGATGACACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CATCTT---GATTTCAGGCAATACAACTGCAATGCAAGCTCTGTGCATTTCATAAATCAAC------------GCCGTCCAATG------
droPer1	super_47:413986-414116 +	AAA-----AACCAAACCAAACACT-----------C-CCGGAGATGACACGCAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CATCTT---GATTTCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCATAAATCAAC------------GCCGTCCAATG------
droWil1	scaffold_180698:8572488-8572628 +	CGG-----AACCTAAACAAAT------------------TGAAGTTACACGAAGGTGCATTGTAGTCGCATTGTCTGTGCTCCAAAAAAAAAAAACCCCCAGTT-T-CTATTCAGGCAATACAACTGCAGTGCAAGCTTCGTGTGACTTATAAG-CAAC------------GGCA---AATA------
droVir3	scaffold_13049:22941104-22941227 -	CCA-----AAATC----CGACA-----------TCT-CTGGAGCTGTTACGGAGGTGCATTGTAGTCGCATTGTCTGTC-------------------TCAAAT-TTGC-CCGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACACG-CAAC------------GTCG---GAAG------
droMoj3	scaffold_6680:17552824-17552948 -	CAG-----CATTCCGACA---------------TCT-TTGGAGCTGTGACGGAGGTGCATTGTAGTCGCATTGTCTGTA-------------------TCCTTTATTCT-CTGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACTCG-CAAC------------GTCG---GACA------
droGri2	scaffold_15110:18214439-18214590 -	CTCTGCACAGTTAGGGCAGACA-----------TCTCCAGGAGCTGTCACGAAGGTGCATTGTAGTCGCATTGTCTGTC-------------------CAAAAA-TTGC-ATGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCACTAG-CAACAACTCTTTGATCGCTG---ATCGATCTGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTGAGTGCCACCAGACTCCTCCTCCGGAGATGACACGAAGGTGCATTGTAGTCGCATTGTCTGTCCCAATTGCT-TCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCACACA-CAACGCCG---AATG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
........................................GTGCATTGTAGTCGCATTGTC.........................................................................	21	1	952.00	952	952
........................................GTGCATTGTAGTCGCATTGT..........................................................................	20	1	157.00	157	157
.............................................................TGTCCCAATTGCT-TCAGG......................................................	18	1	38.00	38	38
........................................GTGCATTGTAGTCGCATTGTCT........................................................................	22	1	35.00	35	35
................................................................................CAATACAACTTCAGTGCAAGCT................................	22	1	29.00	29	29
........................................GTGCATTGTAGTCGCATTGTCTG.......................................................................	23	1	23.00	23	23
........................................GTGCATTGTAGTCGCATTG...........................................................................	19	1	20.00	20	20
................................................................................CAATACAACTTCAGTGCAAGC.................................	21	1	6.00	6	6
................................................................................CAATACAACTTCAGTGCAAG..................................	20	1	6.00	6	6
..............................................................................GGCAATACAACTTCAGTGCAAGC.................................	23	1	2.00	2	2
........................................GTGCATTGTAGTCGCATTGTCTGT......................................................................	24	1	1.00	1	1
...............................................................................GCAATACAACTTCAGTGCAAG..................................	21	1	1.00	1	1
..........................................GCATTGTAGTCGCATTGTC.........................................................................	19	1	1.00	1	1

dp4

AAAAACCAAACCAAACACTCC---CGGAGATGACACGCAGGTGCATTGTAGTCGCATTGTCTGTCCATCTTGATTTCAGGCAATACAACTGCAATGCAAGCTCTGTGCATTTCATAAATCAACGCCGTCCAATG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
........................................GTGCATTGTAGTCGCATTGTC.........................................................................	21	1	8637.00	8637	698	7939
........................................GTGCATTGTAGTCGCATTGT..........................................................................	20	1	2221.00	2221	148	2073
................................................................................CAATACAACTGCAATGCAAGCT................................	22	1	275.00	275	42	233
........................................GTGCATTGTAGTCGCATTG...........................................................................	19	1	236.00	236	39	197
........................................GTGCATTGTAGTCGCATTGTCT........................................................................	22	1	181.00	181	26	155
.............................................................TGTCCATCTTGATTTCAGG......................................................	19	1	70.00	70	66	4
........................................GTGCATTGTAGTCGCATT............................................................................	18	1	39.00	39	0	39
........................................GTGCATTGTAGTCGCATTGTCTG.......................................................................	23	1	15.00	15	1	14
................................................................................CAATACAACTGCAATGCAAGC.................................	21	1	14.00	14	5	9
................................................................................CAATACAACTGCAATGCAAG..................................	20	1	9.00	9	4	5
................................................................................CAATACAACTGCAATGCAA...................................	19	1	6.00	6	0	6
.......................................GGTGCATTGTAGTCGCATTGTC.........................................................................	22	1	3.00	3	1	2
.................................................................................AATACAACTGCAATGCAAGCT................................	21	1	2.00	2	0	2
..........................................GCATTGTAGTCGCATTGTC.........................................................................	19	1	2.00	2	0	2
.........................................TGCATTGTAGTCGCATTGTC.........................................................................	20	1	2.00	2	0	2

Secondary Structure

dm3

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901

droSim1

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901

droSec1

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901

droYak2

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901

droEre2

dG=-19.5, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.9, p-value=0.009901

droAna3

dG=-28.1, p-value=0.009901	dG=-27.4, p-value=0.009901

dp4

dG=-28.6, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

droPer1

dG=-28.6, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

droWil1

dG=-29.3, p-value=0.009901	dG=-28.4, p-value=0.009901

droVir3

dG=-29.0, p-value=0.009901	dG=-28.6, p-value=0.009901	dG=-28.5, p-value=0.009901	dG=-28.2, p-value=0.009901	dG=-28.1, p-value=0.009901

droMoj3

dG=-29.9, p-value=0.009901	dG=-29.4, p-value=0.009901

droGri2

dG=-22.5, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-21.9, p-value=0.009901

Generated: 03/07/2013 at 05:22 PM