Secondary structure and small RNA-seq evidence for dme-mir-995

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:16561630-16561749 +	TTGACG---------------AATGTCA-------------------------TCCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------GTA----ATCCGTAGCACCACATGATTCGGCTTCGTGGTACA-----------------GGATATCATCGGT-TTTTGCTA
droSim1	chr3R:4901723-4901838 -	-----A---------------AATGTCG-------------------------TTCAC--------------------------CTGTACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------AAA----GTCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGATATCATCGGT-TTTTGCTA
droSec1	super_27:174263-174377 -	---------------------AATGTCG-------------------------TTCAC--------------------------CTGTACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------GAA----GTCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGATATCATCGGT-TTTTGCTA
droYak2	chr3R:5351033-5351167 +	TGGACGTTGCCATCCTGGATTAAACTCA-------------------------TTCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCT-----------AAA----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGACATCAGCAAT-TTTTGGTA
droEre2	scaffold_4770:5101897-5102016 -	CTGACG---------------AATGTCA-------------------------TTCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CTGTTTTC-----------AGG----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGACATCAGCGGT-TTTTGCTA
droAna3	scaffold_13340:13021664-13021782 -	TTGACA---------------AATGTCA-------------------------TTCGC--------------------------CTGTCCTACGCAGCCCGGATTCTGTGGGAGCTGCG----CCGTTCTT-----------TCT----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGGCATCATCC-T-GTTGGCTG
dp4	chr2:5900237-5900376 +	TTGACG---------------AATGTCA-------------------------AACACCTC-GCAGGCTCTGCAGCAGACCCTGCTGCACAACGCAGCCCGGATTCTGTGTGTGCTGCG----CTGTGTTC---------TTAAA----AGCCGTAGCACCACATGATTCGGCTGCGTGGTCAG-----------------CCACACCTTCAG--------TA
droPer1	super_19:1637056-1637197 +	TTGACG---------------AATGTCA-------------------------AACACCTC-GCAGGCTCTGCAGCAGACCCTGCTGCACAACGCAGCCCGGATTCTGTGTGTGCTGCG----CTGTGTTC---------TTAAA----AGCCGTAGCACCACATGATTCGGCTGCGTGGTCAG-----------------CCACACCTTCAGT-ATC-----
droWil1	scaffold_181108:2305175-2305323 -	TTGACG---------------AATGTCAAATTTTCTGACTCCTGCAACTCATGTAAGG--------------------------CTTCACCAAGCAGCCCGGATTCTGCGAGTGCTGCG----CTACAACA-----------AGAACTAAGACGTAGCACCACATGATTCGGCTTCATGGTGAA-----------------GTACATCGCAACG-TCATCGTG
droVir3	scaffold_13047:12148438-12148588 -	TTGACG---------------AATGTCA-------------------------AACGGCTTGGCCGGCTCAACA---------GCTGTACAACGAAGCCCGGATACTGTGTGTGTTGCG----CTGTTTA------------GAG----GTACGTAGCACCACATGATTCGGCTTCGTGGTGCACGCAACTGCAACAGA--GGGCGTCAACGGT-ATTTATTA
droMoj3	scaffold_6540:29636954-29637102 +	TTGACG---------------AATGTCA-------------------------AACAGCTTGGCTGGCTTGGTA---------GCTGAACTACGAAGCCCGGGTTTTGTGTGTGCCGCG----CTGTTTTG-------------A----GTACGTAGCACCACATGATTCGGCTTGGTAGTACAGGCTCATTCAACAAATTAGG---CATCAAT-TTTATAGA
droGri2	scaffold_14830:1051305-1051441 +	TTGACG---------------AATGTCA-------------------------AAT---------------------------GCTGTACAGTGAAGCCCGGATTCTGTGTGTGCTGCGTTTGCTGATTTGCCATACACATAAAT----ATACGTAGCACCACATGATTCGGCTTCGTGGTGCTAG---------------CAACTCCATCGCCAGTTAGATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:16561630-16561749 +	TTGACG---------------AATGTCA-------------------------TCCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------GTA----ATCCGTAGCACCACATGATTCGGCTTCGTGGTACA-----------------GGATATCATCGGT-TTTTGCTA
droSim1	chr3R:4901723-4901838 -	-----A---------------AATGTCG-------------------------TTCAC--------------------------CTGTACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------AAA----GTCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGATATCATCGGT-TTTTGCTA
droSec1	super_27:174263-174377 -	---------------------AATGTCG-------------------------TTCAC--------------------------CTGTACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCC-----------GAA----GTCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGATATCATCGGT-TTTTGCTA
droYak2	chr3R:5351033-5351167 +	TGGACGTTGCCATCCTGGATTAAACTCA-------------------------TTCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CCGTTTCT-----------AAA----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGACATCAGCAAT-TTTTGGTA
droEre2	scaffold_4770:5101897-5102016 -	CTGACG---------------AATGTCA-------------------------TTCAC--------------------------CTGCACCCCGCAGCCCGAATTATGTGGGAGCTGCG----CTGTTTTC-----------AGG----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGACATCAGCGGT-TTTTGCTA
droAna3	scaffold_13340:13021664-13021782 -	TTGACA---------------AATGTCA-------------------------TTCGC--------------------------CTGTCCTACGCAGCCCGGATTCTGTGGGAGCTGCG----CCGTTCTT-----------TCT----ATCCGTAGCACCACATGATTCGGCTTCGTGGTGCA-----------------GGGCATCATCC-T-GTTGGCTG
dp4	chr2:5900237-5900376 +	TTGACG---------------AATGTCA-------------------------AACACCTC-GCAGGCTCTGCAGCAGACCCTGCTGCACAACGCAGCCCGGATTCTGTGTGTGCTGCG----CTGTGTTC---------TTAAA----AGCCGTAGCACCACATGATTCGGCTGCGTGGTCAG-----------------CCACACCTTCAG--------TA
droPer1	super_19:1637056-1637197 +	TTGACG---------------AATGTCA-------------------------AACACCTC-GCAGGCTCTGCAGCAGACCCTGCTGCACAACGCAGCCCGGATTCTGTGTGTGCTGCG----CTGTGTTC---------TTAAA----AGCCGTAGCACCACATGATTCGGCTGCGTGGTCAG-----------------CCACACCTTCAGT-ATC-----
droWil1	scaffold_181108:2305175-2305323 -	TTGACG---------------AATGTCAAATTTTCTGACTCCTGCAACTCATGTAAGG--------------------------CTTCACCAAGCAGCCCGGATTCTGCGAGTGCTGCG----CTACAACA-----------AGAACTAAGACGTAGCACCACATGATTCGGCTTCATGGTGAA-----------------GTACATCGCAACG-TCATCGTG
droVir3	scaffold_13047:12148438-12148588 -	TTGACG---------------AATGTCA-------------------------AACGGCTTGGCCGGCTCAACA---------GCTGTACAACGAAGCCCGGATACTGTGTGTGTTGCG----CTGTTTA------------GAG----GTACGTAGCACCACATGATTCGGCTTCGTGGTGCACGCAACTGCAACAGA--GGGCGTCAACGGT-ATTTATTA
droMoj3	scaffold_6540:29636954-29637102 +	TTGACG---------------AATGTCA-------------------------AACAGCTTGGCTGGCTTGGTA---------GCTGAACTACGAAGCCCGGGTTTTGTGTGTGCCGCG----CTGTTTTG-------------A----GTACGTAGCACCACATGATTCGGCTTGGTAGTACAGGCTCATTCAACAAATTAGG---CATCAAT-TTTATAGA
droGri2	scaffold_14830:1051305-1051441 +	TTGACG---------------AATGTCA-------------------------AAT---------------------------GCTGTACAGTGAAGCCCGGATTCTGTGTGTGCTGCGTTTGCTGATTTGCCATACACATAAAT----ATACGTAGCACCACATGATTCGGCTTCGTGGTGCTAG---------------CAACTCCATCGCCAGTTAGATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

-----AAATGTCGTTCACC-------------------------TGTACCCCGCAGCCCGAATTATGTGGGAGCTGCGCCGTTTCC--AAAGTCCGTAGCACCACATGATTCGGCTTCGTGGTGCAGGATATCATCGGTTTTTGCTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................................................TAGCACCACATGATTCGGCTT..............................	21	1	1372.00	1372	1372
................................................................................................TAGCACCACATGATTCGGCT...............................	20	1	230.00	230	230
.......................................................GCCCGAATTATGTGGGAGCTGC......................................................................	22	1	49.00	49	49
.......................................................GCCCGAATTATGTGGGAGCTGCG.....................................................................	23	1	23.00	23	23
................................................................................................TAGCACCACATGATTCGGC................................	19	1	10.00	10	10
........................................................CCCGAATTATGTGGGAGCTGCG.....................................................................	22	1	7.00	7	7
........................................................CCCGAATTATGTGGGAGCTGC......................................................................	21	1	3.00	3	3
.....................................................................................C--AAAGTCCGTAGCACCACATGATTCG..................................	26	1	1.00	1	1
...............................................................................................GTAGCACCACATGATTCGGCT...............................	21	1	1.00	1	1
................................................................................................TAGCACCACATGATTCGGCTTC.............................	22	1	1.00	1	1
................................................................................................TAGCACCACATGATTCGG.................................	18	1	1.00	1	1

dp4

TTGACGAATGTCAAACACCTCGCAGGCTCTGCAGCAGACCCTGCTGCACAACGCAGCCCGGATTCTGTGTGTGCTGCGCTGTGTTCTTAAAAGCCGTAGCACCACATGATTCGGCTGCGTGGTCAGCCACACCTTCAGT-------A	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................................................TAGCACCACATGATTCGGCTG..............................	21	1	11806.00	11806	7803	4003
................................................................................................TAGCACCACATGATTCGGCT...............................	20	1	495.00	495	169	326
.......................................................GCCCGGATTCTGTGTGTGCTGCG.....................................................................	23	1	127.00	127	96	31
................................................................................................TAGCACCACATGATTCGGCTGC.............................	22	1	63.00	63	45	18
................................................................................................TAGCACCACATGATTCGGC................................	19	1	26.00	26	14	12
................................................................................................TAGCACCACATGATTCGG.................................	18	1	24.00	24	10	14
.......................................................GCCCGGATTCTGTGTGTGCTG.......................................................................	21	1	24.00	24	16	8
.......................................................GCCCGGATTCTGTGTGTGCTGC......................................................................	22	1	16.00	16	13	3
...................................................................................................CACCACATGATTCGGCTG..............................	18	1	11.00	11	4	7
.......................................................GCCCGGATTCTGTGTGTGCT........................................................................	20	1	9.00	9	5	4
.................................................................................................AGCACCACATGATTCGGCTG..............................	20	1	6.00	6	4	2
.......................................................GCCCGGATTCTGTGTGTGC.........................................................................	19	1	2.00	2	0	2
..................................................................................................GCACCACATGATTCGGCTG..............................	19	1	2.00	2	1	1

Secondary Structure

dm3

dG=-33.9, p-value=0.009901	dG=-33.9, p-value=0.009901	dG=-33.9, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901

droSim1

dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901

droSec1

dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901

droYak2

dG=-33.7, p-value=0.009901	dG=-33.7, p-value=0.009901	dG=-33.7, p-value=0.009901	dG=-33.2, p-value=0.009901	dG=-33.2, p-value=0.009901

droEre2

dG=-36.0, p-value=0.009901	dG=-36.0, p-value=0.009901	dG=-36.0, p-value=0.009901	dG=-35.3, p-value=0.009901

droAna3

dG=-28.5, p-value=0.009901	dG=-28.5, p-value=0.009901	dG=-28.5, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901

dp4

dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901

droPer1

dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-39.3, p-value=0.009901

droWil1

dG=-21.5, p-value=0.009901	dG=-21.5, p-value=0.009901	dG=-21.5, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901

droVir3

dG=-31.5, p-value=0.009901	dG=-31.5, p-value=0.009901	dG=-31.5, p-value=0.009901	dG=-30.8, p-value=0.009901	dG=-30.8, p-value=0.009901

droMoj3

dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901

droGri2

dG=-33.5, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-33.4, p-value=0.009901	dG=-33.4, p-value=0.009901

Generated: 03/07/2013 at 07:25 PM