Secondary structure and small RNA-seq evidence for dme-mir-184

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:9216892-9217021 -	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCACTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAACCAATACCCA--------TT
droSim1	chr2R:7673827-7673955 -	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCCCCA--------TT
droSec1	super_1:6740004-6740132 -	T--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCTCCA--------TT
droYak2	chr2R:7742247-7742374 +	C--TGGGCTG--------ACCCGAG-----------TGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCAT-TGAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCCCCA--------TT
droEre2	scaffold_4845:16598085-16598213 +	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCGTCAAGC-AATCCCCA--------GT
droAna3	scaffold_13266:16524568-16524693 -	CCCAGTGCCG--------G--CGAG------------TCCGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATAATGAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAGGT-TG--TCCA--------TC
dp4	chr3:696696-696816 +	----GGGTCG--------GCCCGGGGACTCCG----GGTCGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCA----------------------
droPer1	super_2:863138-863258 +	----GGGTCG--------GCCCGGGGACTCCG----GGTCGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCA----------------------
droWil1	scaffold_181009:2073162-2073280 -	A--CG----------------CGAAGAGTCAGTTAAAGCTGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCAACA----------------------
droVir3	scaffold_12875:243286-243412 +	T--TGGGCT-----------------------------TTGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAAGTCAACTAAC-TAAGTGCAGCAACTATTT
droMoj3	scaffold_6496:5255786-5255918 -	A--ATGGCCAATCTGCCGT--TGGG-----------CATTGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAAGTCAACTAA---ATACATG--------CG
droGri2	scaffold_15245:10719551-10719668 -	C--CAGCCTG--------CATATGG-----------TTTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGGATAACTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCAAA--------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:9216892-9217021 -	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCACTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAACCAATACCCA--------TT
droSim1	chr2R:7673827-7673955 -	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCCCCA--------TT
droSec1	super_1:6740004-6740132 -	T--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCTCCA--------TT
droYak2	chr2R:7742247-7742374 +	C--TGGGCTG--------ACCCGAG-----------TGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCAT-TGAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAGC-AATCCCCA--------TT
droEre2	scaffold_4845:16598085-16598213 +	C--TGGGCTG--------ACCCGAG-----------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCGTCAAGC-AATCCCCA--------GT
droAna3	scaffold_13266:16524568-16524693 -	CCCAGTGCCG--------G--CGAG------------TCCGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATAATGAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAGGT-TG--TCCA--------TC
dp4	chr3:696696-696816 +	----GGGTCG--------GCCCGGGGACTCCG----GGTCGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCA----------------------
droPer1	super_2:863138-863258 +	----GGGTCG--------GCCCGGGGACTCCG----GGTCGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCA----------------------
droWil1	scaffold_181009:2073162-2073280 -	A--CG----------------CGAAGAGTCAGTTAAAGCTGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCAACA----------------------
droVir3	scaffold_12875:243286-243412 +	T--TGGGCT-----------------------------TTGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAAGTCAACTAAC-TAAGTGCAGCAACTATTT
droMoj3	scaffold_6496:5255786-5255918 -	A--ATGGCCAATCTGCCGT--TGGG-----------CATTGGCCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAAGTCAACTAA---ATACATG--------CG
droGri2	scaffold_15245:10719551-10719668 -	C--CAGCCTG--------CATATGG-----------TTTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGGATAACTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCAAA--------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTGGGCTGACCCGAG-------GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATCAAG-CAATCCCCATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..................................................................................TGGACGGAGAACTGATAAGGGC.................................	22	1	134335.00	134335	134335
..................................................................................TGGACGGAGAACTGATAAGGG..................................	21	1	14525.00	14525	14525
..................................................................................TGGACGGAGAACTGATAAGG...................................	20	1	1613.00	1613	1613
..................................................................................TGGACGGAGAACTGATAAGGGCT................................	23	1	671.00	671	671
.................................................................................CTGGACGGAGAACTGATAAGGGC.................................	23	1	193.00	193	193
..................................................................................TGGACGGAGAACTGATAAG....................................	19	1	72.00	72	72
...........................................CCTTATCATTCTCTCGCCCCGT........................................................................	22	1	64.00	64	64
...................................................................................GGACGGAGAACTGATAAGGGC.................................	21	1	46.00	46	46
.................................................................................CTGGACGGAGAACTGATAAGGG..................................	22	1	25.00	25	25
....................................................................................GACGGAGAACTGATAAGGGC.................................	20	1	17.00	17	17
..................................................................................TGGACGGAGAACTGATAAGGGCTC...............................	24	1	6.00	6	6

dp4

--GGGTCGGCCCGGGGACTCCGGGTCGACCGGTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAACTCATCA--------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..................................................................................TGGACGGAGAACTGATAAGGGC.................................	22	1	143157.00	143157	64213	78944
..................................................................................TGGACGGAGAACTGATAAGGG..................................	21	1	87593.00	87593	7040	80553
..................................................................................TGGACGGAGAACTGATAAGG...................................	20	1	19820.00	19820	959	18861
..................................................................................TGGACGGAGAACTGATAAG....................................	19	1	4360.00	4360	41	4319
..................................................................................TGGACGGAGAACTGATAAGGGCT................................	23	1	2145.00	2145	332	1813
.................................................................................CTGGACGGAGAACTGATAAGGGC.................................	23	1	232.00	232	118	114
.................................................................................CTGGACGGAGAACTGATAAGGG..................................	22	1	148.00	148	13	135
..................................................................................TGGACGGAGAACTGATAA.....................................	18	1	121.00	121	6	115
...........................................CCTTATCATTCTCGCGCCCCGT........................................................................	22	1	88.00	88	65	23
...................................................................................GGACGGAGAACTGATAAGGGC.................................	21	1	73.00	73	27	46
.................................................................................CTGGACGGAGAACTGATAAGG...................................	21	1	54.00	54	3	51
...................................................................................GGACGGAGAACTGATAAGGG..................................	20	1	53.00	53	5	48
....................................................................................GACGGAGAACTGATAAGGGC.................................	20	1	28.00	28	9	19
...........................................CCTTATCATTCTCGCGCCCCG.........................................................................	21	1	21.00	21	18	3
....................................................................................GACGGAGAACTGATAAGGG..................................	19	1	20.00	20	1	19
...................................................................................GGACGGAGAACTGATAAGG...................................	19	1	16.00	16	0	16

Secondary Structure

dm3

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.5, p-value=0.009901

droSim1

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.5, p-value=0.009901

droSec1

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.5, p-value=0.009901

droYak2

dG=-27.3, p-value=0.009901	dG=-27.0, p-value=0.009901	dG=-26.6, p-value=0.009901

droEre2

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.5, p-value=0.009901

droAna3

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.2, p-value=0.009901

dp4

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901

droPer1

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901

droWil1

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.7, p-value=0.009901

droVir3

dG=-27.2, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.7, p-value=0.009901

droMoj3

dG=-27.8, p-value=0.009901	dG=-27.5, p-value=0.009901	dG=-27.0, p-value=0.009901

droGri2

dG=-29.8, p-value=0.009901	dG=-29.1, p-value=0.009901	dG=-29.1, p-value=0.009901

Generated: 03/07/2013 at 04:52 PM