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

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mature

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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

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

Secondary Structure

dm3

-34.2

droSim1

-34.2

droSec1

-33.5

droYak2

-31.5	-31.0	-30.6

droEre2

-31.6	-30.9	-30.8

droAna3

-31.6	-31.5	-31.1	-31.0	-30.7	-30.7

dp4

-29.7	-29.1	-28.9	-28.8

droPer1

-29.7	-29.1	-28.9	-28.8

droWil1

-31.0	-30.8	-30.7

droVir3

-29.0

droMoj3

-31.9	-31.7	-31.6	-31.1	-31.1

droGri2

-30.6	-30.4	-29.7	-29.6

Generated: 01/05/2013 at 05:17 PM