Secondary structure and small RNA-seq evidence for dme-mir-315

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:18854056-18854169 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTG-TTTACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCCCTCAACGCTG-----
droSim1	chr3L:18159364-18159477 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATTG-TTTACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTCTCATCGCTG-----
droSec1	super_19:820227-820338 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATTG---TACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCCCTCATCGCTG-----
droYak2	chr3L:21787014-21787126 -	GAGTTCCG-C------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTACTA-TTTAAC---AGCTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTTACAACATTG-----
droEre2	scaffold_4784:18670595-18670707 +	GAGTTCCTAC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCT-ATTA-TCTAAC---AGCTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTTACAACGCTG-----
droAna3	scaffold_13337:18585473-18585582 -	GAGCTCCTAA------------ATGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATAA-ATTATT---AGCTGGCTTTCGAGCAATAATTGAAACCAAATAAGTGATCCTGACAAC---------
dp4	chrXR_group6:4103840-4103943 -	G---------------------CCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAA-TTAACC---AGTTGGCTTTCGAGCAATTATCAAAGCCAAATAAGTGATCCCAACAACATT------
droPer1	super_9:2393048-2393151 -	A---------------------CCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAA-TTAACC---AGTTGGCTTTCGAGCAATTATCAAAGCCAAATAAGTGATCCCAACAACATT------
droWil1	scaffold_180955:104826-104946 +	GGTTTGCTTATTTGCCCA---TCTGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTACTTTATC---AGTTGGCTTTCGAGCAATAATTGAAACCAAATAAGTGAGCCTGTCAACA--------
droVir3	scaffold_13049:18083575-18083698 -	CATTTCCTTCCTACCTCACAAAACGGACGCCTATATCATTTTGATTGTTGCTCAGAAAGCCCTG--CA-TTCAAT---ACTTGGCTTTCGAGTAATAATCGAAACCAAATAAGCGATCCTAACTACGTTT-----
droMoj3	scaffold_6680:23648550-23648660 -	----------------------ACGGACCCTTATATAATTTTGATTGTTGCTCAGAAAGCCCGTAA---TTTAACTTAACATGGCTTTCGAGTAATAATCGAAACCAAATAAGGCATCCAAACATCATTTTGTCA
droGri2	scaffold_15110:24135484-24135597 -	CAGCCAACTACT----------ATGGACGCTCATATAATTTTGATTGTTGCTCAGAAAGCCTTT--CA-CTTGAC---ACTTGGCTTTCGAGTAATAATCGAAACCAAATAAGCGATCCTAACTACAATT-----

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:18854056-18854169 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTG-TTTACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCCCTCAACGCTG-----
droSim1	chr3L:18159364-18159477 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATTG-TTTACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTCTCATCGCTG-----
droSec1	super_19:820227-820338 +	GAGTTCCTTC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATTG---TACC---AGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCCCTCATCGCTG-----
droYak2	chr3L:21787014-21787126 -	GAGTTCCG-C------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTACTA-TTTAAC---AGCTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTTACAACATTG-----
droEre2	scaffold_4784:18670595-18670707 +	GAGTTCCTAC------------ACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCT-ATTA-TCTAAC---AGCTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTTACAACGCTG-----
droAna3	scaffold_13337:18585473-18585582 -	GAGCTCCTAA------------ATGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATAA-ATTATT---AGCTGGCTTTCGAGCAATAATTGAAACCAAATAAGTGATCCTGACAAC---------
dp4	chrXR_group6:4103840-4103943 -	G---------------------CCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAA-TTAACC---AGTTGGCTTTCGAGCAATTATCAAAGCCAAATAAGTGATCCCAACAACATT------
droPer1	super_9:2393048-2393151 -	A---------------------CCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAA-TTAACC---AGTTGGCTTTCGAGCAATTATCAAAGCCAAATAAGTGATCCCAACAACATT------
droWil1	scaffold_180955:104826-104946 +	GGTTTGCTTATTTGCCCA---TCTGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTACTTTATC---AGTTGGCTTTCGAGCAATAATTGAAACCAAATAAGTGAGCCTGTCAACA--------
droVir3	scaffold_13049:18083575-18083698 -	CATTTCCTTCCTACCTCACAAAACGGACGCCTATATCATTTTGATTGTTGCTCAGAAAGCCCTG--CA-TTCAAT---ACTTGGCTTTCGAGTAATAATCGAAACCAAATAAGCGATCCTAACTACGTTT-----
droMoj3	scaffold_6680:23648550-23648660 -	----------------------ACGGACCCTTATATAATTTTGATTGTTGCTCAGAAAGCCCGTAA---TTTAACTTAACATGGCTTTCGAGTAATAATCGAAACCAAATAAGGCATCCAAACATCATTTTGTCA
droGri2	scaffold_15110:24135484-24135597 -	CAGCCAACTACT----------ATGGACGCTCATATAATTTTGATTGTTGCTCAGAAAGCCTTT--CA-CTTGAC---ACTTGGCTTTCGAGTAATAATCGAAACCAAATAAGCGATCCTAACTACAATT-----

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GAGTTCCTTCACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATTGTTTACCAGTTGGCTTTCGAGCAATAATTGAAACCAGATAAGTGATCCTCTCATCGCTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................TTTTGATTGTTGCTCAGAAAGCC.................................................................	23	1	8652.00	8652	8652
..........................TTTTGATTGTTGCTCAGAAAGC..................................................................	22	1	2182.00	2182	2182
..........................TTTTGATTGTTGCTCAGAAAG...................................................................	21	1	229.00	229	229
..........................TTTTGATTGTTGCTCAGAAA....................................................................	20	1	16.00	16	16
....................................................................CTTTCGAGCAATAATTGAAACC........................	22	1	13.00	13	13
...........................TTTGATTGTTGCTCAGAAAGCC.................................................................	22	1	11.00	11	11
..........................TTTTGATTGTTGCTCAGAAAGCCC................................................................	24	1	3.00	3	3
.................................................CTTATTGTTTACCAGTTGG..............................................	19	1	2.00	2	2
..........................TTTTGATTGTTGCTCAGA......................................................................	18	1	2.00	2	2
..........................TTTTGATTGTTGCTCAGAA.....................................................................	19	1	2.00	2	2
...........................TTTGATTGTTGCTCAGAAAG...................................................................	20	1	1.00	1	1
..............................GATTGTTGCTCAGAAAGCC.................................................................	19	1	1.00	1	1
...........................TTTGATTGTTGCTCAGAAAGC..................................................................	21	1	1.00	1	1
.........................ATTTTGATTGTTGCTCAGAAAGC..................................................................	23	1	1.00	1	1
............................TTGATTGTTGCTCAGAAAG...................................................................	19	1	1.00	1	1
..................................................TTATTGTTTACCAGTTGG..............................................	18	1	1.00	1	1

dp4

GC---------CGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAATTAACCAGTTGGCTTTCGAGCAATTATCAAAGCCAAATAAGTGATCCCAACAACATT-	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................TTTTGATTGTTGCTCAGAAAGCC.................................................................	23	1	8395.00	8395	6602	1793
..........................TTTTGATTGTTGCTCAGAAAGC..................................................................	22	1	2535.00	2535	1872	663
..........................TTTTGATTGTTGCTCAGAAAG...................................................................	21	1	600.00	600	203	397
..........................TTTTGATTGTTGCTCAGAAA....................................................................	20	1	60.00	60	12	48
....................................................................CTTTCGAGCAATTATCAAAGCC........................	22	1	40.00	40	32	8
..........................TTTTGATTGTTGCTCAGAA.....................................................................	19	1	26.00	26	1	25
.........................TTTTTGATTGTTGCTCAGAAAGC..................................................................	23	1	20.00	20	19	1
...........................TTTGATTGTTGCTCAGAAAGCC.................................................................	22	1	10.00	10	7	3
..........................TTTTGATTGTTGCTCAGAAAGCCC................................................................	24	1	9.00	9	5	4
..........................TTTTGATTGTTGCTCAGA......................................................................	18	1	9.00	9	1	8
....................................................................CTTTCGAGCAATTATCAAAGC.........................	21	1	4.00	4	2	2
.........................TTTTTGATTGTTGCTCAGAAAGCC.................................................................	24	1	4.00	4	4	0
............................TTGATTGTTGCTCAGAAAGC..................................................................	20	1	2.00	2	2	0
............................TTGATTGTTGCTCAGAAAGCC.................................................................	21	1	2.00	2	2	0
..............................GATTGTTGCTCAGAAAGCC.................................................................	19	1	2.00	2	2	0
...........................TTTGATTGTTGCTCAGAAAGC..................................................................	21	1	1.00	1	0	1
.........................TTTTTGATTGTTGCTCAGAAAG...................................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

dG=-27.7, p-value=0.009901	dG=-26.7, p-value=0.009901

droSim1

dG=-27.7, p-value=0.009901	dG=-26.7, p-value=0.009901

droSec1

dG=-27.0, p-value=0.009901	dG=-26.0, p-value=0.009901

droYak2

dG=-25.0, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901

droEre2

dG=-25.1, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.1, p-value=0.009901

droAna3

dG=-25.9, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.4, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-25.0, p-value=0.009901

dp4

dG=-23.8, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-22.9, p-value=0.009901

droPer1

dG=-23.8, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-22.9, p-value=0.009901

droWil1

dG=-25.3, p-value=0.009901	dG=-25.1, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.3, p-value=0.009901

droVir3

dG=-26.0, p-value=0.009901	dG=-25.0, p-value=0.009901

droMoj3

dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-25.3, p-value=0.009901

droGri2

dG=-27.3, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.3, p-value=0.009901

Generated: 03/07/2013 at 05:18 PM