Secondary structure and small RNA-seq evidence for dme-mir-92a

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:21472213-21472337 +	TTTCAGCCGAA--------TATAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCTA-------------T----AAA
droSim1	chr3R:21300457-21300581 +	TTTCAGCCGAA--------TAAAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCAA-------------T----AAA
droSec1	super_13:258996-259120 +	TTTCAGCCGAA--------TAAAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCAA-------------T----CAA
droYak2	chr3R:25001360-25001484 -	TTTCGTTCGAA--------TATGAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATGCA-------------T----TTT
droEre2	scaffold_4820:6569995-6570123 -	TTTCGGCCGAA--------TATGAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTGAAATGAA-------------TTTTATAT
droAna3	scaffold_13340:3727762-3727906 +	TTTCCATCGAA--------TAT-AAT----------------------------------------------ACAAATTTCCCGTAGGACGGGAAGGTGTCAAGGTTTTGAATT-AAATT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTCAA-----ACACATCGATACATATTTTTAG---AAATATTTAAAATTTGG----ATA
dp4	chr2:23635253-23635419 -	CTTTA--------------------TATGCATATCCTGTAGGACAAGACTACAGTACTACTCGGAATACCATAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTAAATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTCAT-----ACACATCGAT-CGTACAACTAG---CAA-------------C----AAA
droPer1	super_3:6410293-6410459 -	CTTTA--------------------TATGCATATCCTGTAGGACAAGACTACAGTACTACTCGGAATACCATAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTCAT-----ACACATCGAT-CGTACAACTAG---CAA-------------C----AAA
droWil1	scaffold_181130:14578411-14578543 -	CTGTAGCCGGGTGAAACATT----ATCTGCAT----------------------------------------TCAAATTTCTCGTAGGACGGGAAGGTGTCAACGTTTTGCCTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTAAAAC----GACATC-----------CTAT---CA-------------------AAA
droVir3	scaffold_12855:6880771-6880902 +	CGACAATATGG--------CTTTATC----------------------------------------------ACAAACTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCTTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTGCCACAACAAACG------------ATTGAAAATAT------------GA----AAA
droMoj3	scaffold_6540:25734544-25734668 -	CTGCAAT--AC--------CCAAATC----------------------------------------------ATAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTACCTTTTGATTCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTATCTTAC----AACA------------ATCAGGTCCAA-------------T----AGA
droGri2	scaffold_14906:3023231-3023367 +	TTTTT---TAA--------TATATAT------ATTCT-TAA-AC-------------------GTGTACC--ATAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTGCAT----CTACA------------ACTGGT----T-------------T----AAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:21472213-21472337 +	TTTCAGCCGAA--------TATAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCTA-------------T----AAA
droSim1	chr3R:21300457-21300581 +	TTTCAGCCGAA--------TAAAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCAA-------------T----AAA
droSec1	super_13:258996-259120 +	TTTCAGCCGAA--------TAAAAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATCAA-------------T----CAA
droYak2	chr3R:25001360-25001484 -	TTTCGTTCGAA--------TATGAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTAAAATGCA-------------T----TTT
droEre2	scaffold_4820:6569995-6570123 -	TTTCGGCCGAA--------TATGAAT----------------------------------------------ATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAAT-----AAACA------------ACTGAAATGAA-------------TTTTATAT
droAna3	scaffold_13340:3727762-3727906 +	TTTCCATCGAA--------TAT-AAT----------------------------------------------ACAAATTTCCCGTAGGACGGGAAGGTGTCAAGGTTTTGAATT-AAATT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTCAA-----ACACATCGATACATATTTTTAG---AAATATTTAAAATTTGG----ATA
dp4	chr2:23635253-23635419 -	CTTTA--------------------TATGCATATCCTGTAGGACAAGACTACAGTACTACTCGGAATACCATAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTAAATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTCAT-----ACACATCGAT-CGTACAACTAG---CAA-------------C----AAA
droPer1	super_3:6410293-6410459 -	CTTTA--------------------TATGCATATCCTGTAGGACAAGACTACAGTACTACTCGGAATACCATAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTCAT-----ACACATCGAT-CGTACAACTAG---CAA-------------C----AAA
droWil1	scaffold_181130:14578411-14578543 -	CTGTAGCCGGGTGAAACATT----ATCTGCAT----------------------------------------TCAAATTTCTCGTAGGACGGGAAGGTGTCAACGTTTTGCCTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTAAAAC----GACATC-----------CTAT---CA-------------------AAA
droVir3	scaffold_12855:6880771-6880902 +	CGACAATATGG--------CTTTATC----------------------------------------------ACAAACTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCTTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTGCCACAACAAACG------------ATTGAAAATAT------------GA----AAA
droMoj3	scaffold_6540:25734544-25734668 -	CTGCAAT--AC--------CCAAATC----------------------------------------------ATAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTACCTTTTGATTCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTATCTTAC----AACA------------ATCAGGTCCAA-------------T----AGA
droGri2	scaffold_14906:3023231-3023367 +	TTTTT---TAA--------TATATAT------ATTCT-TAA-AC-------------------GTGTACC--ATAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTGCAT----CTACA------------ACTGGT----T-------------T----AAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTTCAGCCGAATAAAAATATGA--------------------------------------ATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAATAAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAATAAACAA-----------CTAAAATCAATAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................................................CATTGCACTTGTCCCGGCCTA..............................................	21	2	471.00	942	942
...........................................................................................................CATTGCACTTGTCCCGGCCT...............................................	20	2	167.00	334	334
...........................................................................................................CATTGCACTTGTCCCGGCC................................................	19	2	7.50	15	15
.....................................................................AGGACGGGAAGGTGTCAACGTTT..................................................................................	23	2	6.00	12	12
...........................................................................................................CATTGCACTTGTCCCGGC.................................................	18	2	1.00	2	2
.....................................................................AGGACGGGAAGGTGTCAAC......................................................................................	19	2	1.00	2	2
...........................................................................................................CATTGCACTTGTCCCGGCCTATG............................................	23	2	1.00	2	2
..........................................................................................................ACATTGCACTTGTCCCGGCCTAT.............................................	23	2	0.50	1	1

dp4

CTTTATATGCATATCCT---G-TAGGACAAGACTACAGTACTACTCGGAATACCATAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTAAATTTTGAACAAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTCATACACATCGATCGTACAACT---AGCAACAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................................................CATTGCACTTGTCCCGGCCTA..............................................	21	2	257.50	515	511	4
.....................................................................AGGACGGGAAGGTGTCAACGT....................................................................................	21	2	62.50	125	125	0
.....................................................................AGGACGGGAAGGTGTCAACG.....................................................................................	20	2	21.50	43	28	15
...........................................................................................................CATTGCACTTGTCCCGGCC................................................	19	2	20.50	41	40	1
.....................................................................AGGACGGGAAGGTGTCAAC......................................................................................	19	2	16.00	32	13	19
............................................................................................................ATTGCACTTGTCCCGGCCTAT.............................................	21	2	11.50	23	23	0
.....................................................................AGGACGGGAAGGTGTCAACGTTT..................................................................................	23	2	4.50	9	9	0
...........................................................................................................CATTGCACTTGTCCCGGC.................................................	18	2	1.50	3	3	0
.....................................................................AGGACGGGAAGGTGTCAA.......................................................................................	18	2	1.00	2	2	0
.............................................................................................................TTGCACTTGTCCCGGCCTAT.............................................	20	2	1.00	2	2	0
.................................................................................................................................GGGCGGCTTGTCATACAC...........................	18	2	0.50	1	1	0
................................................AATACCATAGAGATTGCCCGT.........................................................................................................	21	2	0.50	1	1	0
............................................................................................................ATTGCACTTGTCCCGGCCT...............................................	19	2	0.50	1	0	1
.......................................................................GACGGGAAGGTGTCAACGTT...................................................................................	20	2	0.50	1	1	0

Secondary Structure

dm3

dG=-31.5, p-value=0.009901

droSim1

dG=-31.5, p-value=0.009901

droSec1

dG=-31.5, p-value=0.009901

droYak2

dG=-31.5, p-value=0.009901	dG=-30.5, p-value=0.009901

droEre2

dG=-31.5, p-value=0.009901

droAna3

dG=-31.6, p-value=0.009901	dG=-31.0, p-value=0.009901	dG=-30.7, p-value=0.009901	dG=-30.7, p-value=0.009901	dG=-30.7, p-value=0.009901

dp4

dG=-30.7, p-value=0.009901	dG=-29.7, p-value=0.009901

droPer1

dG=-30.7, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-29.7, p-value=0.009901

droWil1

dG=-28.5, p-value=0.009901	dG=-27.6, p-value=0.009901	dG=-27.5, p-value=0.009901	dG=-27.5, p-value=0.009901

droVir3

dG=-21.1, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.4, p-value=0.009901	dG=-20.2, p-value=0.009901

droMoj3

dG=-21.1, p-value=0.009901	dG=-20.5, p-value=0.009901	dG=-20.2, p-value=0.009901

droGri2

dG=-21.1, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.5, p-value=0.009901

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