Secondary structure and small RNA-seq evidence for dme-mir-4980

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:3673811-3673963 +	CAAAAACGA--------AAGAGGGGAAGAGGCTGAGAGCGGGAAAGTGAGAAGTAGAGAGCGCAGATAGGGAGTGGG-AGCTTAT----------------------------A-----------------CCGTTATAAAGCCAACTTCCGTT--CT----GCGTTTCGTTCCAAC-C-----CCCCACCTCTCT-------TTCCC---TCTTTTGGCATTGCAAAA
droSim1	chr2R_random:948112-948272 +	CAAAAGCGGATGAGGTGAAGAGGGGAAGAGGCGGAGAGCGGGAAAGGGCGAAGAAGAGAGCGCAGACAGGGAGTGGG-AGCTTGT----------------------------A-----------------CCGTTATAAAGCCAACTTCCGTT--CT----GCGTTTCATTCCCCC-GCA---CCCCACCT--CT-------TTCCC---TCTTTTGGCATTGCAAAA
droSec1	super_1:1330268-1330428 +	CAAAAGCGGATGAGGTGAAGAGGGGAAGAGGCGGAGAGCGGGAAAGGGCGAAGAAGAGAGCGCAGACAGGGAGTGGG-AGCTTGT----------------------------A-----------------CCGTTATAAAGCCAACTTCCGTT--CT----GCGTTTCATTCCCCC-GCA---CCCGACCT--CT-------TTCCC---TCTTTTGGCATTGCAAAA
droYak2	chr2L:16346698-16346837 +	CAAAAGGGG--------AAGA--------CGCGGACAACGGGAAAGGGCAAACACGAGAGCGCAGGAAGGCAGTGGG-AGCTTGT----------------------------A-----------------CCGTTATAAAGTCAAATTCCGTT--CT----GTGTTTCTTTTCACC-------CCCCACCT--CT-------T--CC---TCTCTTGGCATTGCAAAA
droEre2	scaffold_4929:18933782-18933931 -	CCAGAGGGG--------AAGGAGGGAAGAGGCGGACAGCGGAAAAGGGCGAA-CAGTGAGCGCAGGAAGGGAGTGGG-AGCCTGT----------------------------A-----------------CCGTTATAAAGTCAATTTGCGTT--CC----GCGTTTCTTTCCACC-C-----CCCCACCT--CT-------TCATC---TCTTTTGGCATTGCAAAA
droAna3	scaffold_13266:10179298-10179443 +	AGCAGACGA----GGTGCAGGGGGAGAATAAAAATAACCAAAAAAAATAATAAGATAAAGTGAACTAAGAGAGTTGG-AATTT------------------------------------------------CCATATCAGCACCCATTTTCGAT--TT----ACATTCTCCTCCACCCT-----CCCCACCC--------------CACCTGCTG---CTGGTGCA--A
dp4	chrXL_group1e:1273472-1273542 -	AGAGAGAGA--------GAGAGAGAGAGAGAGAGAGAGAGGGAGAGGGAGAGGGAGAGGGTGATGGTTGGGTGTGGG-AG-----------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_4:2253896-2254021 +	CAAGAGAGA--------GAGAGAGAGAGAGAAAGAGAGCGAGAAAGATAGAAGCAGAGCGAGAGCGAAAGTGATAGA-TAT--------------------------------A-------------TAGTTTATACCAAACTTTTTTAATAAT--CC----ATGTTCTTTTCGATGTT-----T---------------------------------ATTTTC-----
droWil1	scaffold_181096:5834838-5834931 +	AGAGACAGA--------GAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAAGAGTGGTGAGTGGTGGAAGGGGGTGGG-GGCCAAT----------------------------A-----------------TTGTGCTAGTGCTGAAT---------------------------------------------------------------------------------
droVir3	scaffold_12963:19208738-19208883 +	TTAGTAAGA--------GAGAGAGAGAGAGAGAGGGAGAGCCAGCGAGTA--ATAGAGAGCAC---------ATGCG-AGCATAA----------------------------A-----------------CCGGTTTGAGCGC--TCTCCGCTGGCTATGCGCGCT----CCCAGG-C-CAGCGCTCACCT--GTGTACAAGTTCAC---TTTGTTGTTGTTG-----
droMoj3	scaffold_6496:13778911-13779004 +	CAACAGAGA--------CAGAGAGAGAGAGAGAGAGAGCGGGAGAGAGAGAAAGAGAGAGAGA-----GAGAGAGGGAGGCCATG----------------------------G-----------------CTGTAGCTGAGCTGCTT-----------------------------------------------------------------------------ACGT
droGri2	scaffold_15110:15752678-15752830 -	AGTGAGAGA--------GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA----------------GAGAGCTGGG-CACTTGTGTCTGGGGCTGTGCTCATGCAAAAATAAATGCGAACTGTGTGCAGATCGTAA---------------AT--TA----AAGTTTCTCTCGCTC-C-----CCCTATTT-------------CTC---TGTTC--CTGTT------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:3673811-3673963 +	CAAAAACG--------AAAGAGGGGAAGAGGCTGAGAGCGGGAAAGTGAGAAGTAGAGAGCGCAGATAGGGAGTGGGAGCTTATACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCGTTCCAACCCCC--CACCTCTCTTTCCCTCTTTTGGCATTGCAAAA
droSim1	chr2R_random:948112-948272 +	CAAAAGCGGATGAGGTGAAGAGGGGAAGAGGCGGAGAGCGGGAAAGGGCGAAGAAGAGAGCGCAGACAGGGAGTGGGAGCTTGTACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCATTCCCCCGCACCCC--ACCTCTTTCCCTCTTTTGGCATTGCAAAA
droSec1	super_1:1330268-1330428 +	CAAAAGCGGATGAGGTGAAGAGGGGAAGAGGCGGAGAGCGGGAAAGGGCGAAGAAGAGAGCGCAGACAGGGAGTGGGAGCTTGTACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCATTCCCCCGCACCCG--ACCTCTTTCCCTCTTTTGGCATTGCAAAA
droYak2	chr2L:16346698-16346837 +	CAAAA----------------GGGGAAGACGCGGACAACGGGAAAGGGCAAACACGAGAGCGCAGGAAGGCAGTGGGAGCTTGTACCGTTATAAAGTCAAATTCCGTTCTGTGTTTCTTTTCACC---CCCCA--CCTCTT--CCTCTCTTGGCATTGCAAAA
droEre2	scaffold_4929:18933782-18933931 -	CCAGAG--------GGGAAGGAGGGAAGAGGCGGACAGCGGAAAAGGGCGAAC-AGTGAGCGCAGGAAGGGAGTGGGAGCCTGTACCGTTATAAAGTCAATTTGCGTTCCGCGTTTCTTTCCACCC--CCCCA--CCTCTTCATCTCTTTTGGCATTGCAAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CAAAAGCGGATGAGGTGAAGAGGGGAAGAGGCGGAGAGCGGGAAAGGGCGAAGAAGAGAGCGCAGACAGGGAGTGGGAGCTTGTACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCATTCCCCCGCACCCCACCTCTTTCCCTCTTTTGGCATTGCAAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

AGAGAGAGA--------GAGAGAGAGAGAGAGAGAGAGAGGGAGAGGGAGAGGGAGAGGGTGATGGTTGGGTGTGGGAG----------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................GAGAGAGAGAGAGGGAGA....................................................................................................................	18	1	1.00	1	1	0
......................AGAGAGAGAGAGAGAGAGG........................................................................................................................	19	1	1.00	1	1	0
.........................GAGAGAGAGAGAGAGGGA......................................................................................................................	18	1	1.00	1	1	0
.......GA--------GAGAGAGAGAGAGAGA................................................................................................................................	18	7	0.71	5	5	0
........A--------GAGAGAGAGAGAGAGAGA..............................................................................................................................	19	7	0.29	2	2	0
AGAGAGAGA--------GAGAGAGAGAGAGAG.................................................................................................................................	24	5	0.20	1	0	1

Secondary Structure

dm3

-44.0	-44.0	-44.0	-44.0	-43.9	-43.9

droSim1

-49.6	-49.5	-49.2	-49.2	-49.2	-49.2

droSec1

-51.4	-51.0	-51.0	-51.0	-51.0	-51.0

droYak2

-27.1	-27.1	-27.1	-26.5	-26.5	-26.5

droEre2

-32.9	-32.7	-32.4	-32.4	-32.4	-32.4

droAna3

-8.1	-7.7	-7.5	-7.5	-7.4	-7.4

dp4

0.0

droPer1

-10.7	-10.6	-10.6	-10.3	-10.3	-10.3

droWil1

-8.4	-8.0	-8.0	-7.7	-7.6	-7.5

droVir3

-36.1	-35.9	-35.8	-35.6	-35.6	-35.5

droMoj3

-7.2	-7.1	-6.6	-6.5	-6.4	-6.3

droGri2

-41.0	-41.0	-41.0	-41.0	-40.7	-40.7

Generated: 01/05/2013 at 05:27 PM