Secondary structure and small RNA-seq evidence for dme-mir-1008

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:6773023-6773109 +	AAGTTCCTCATCTATGTAAATA-TCTAAA-------------------GTTGAACTTGGCCAATG-------------------------------GCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droSim1	chr2R:5362602-5362688 +	AAGTTCCTCATCTATGTAAATA-TCTAAA-------------------GTTGAACTTGGCCAACG-------------------------------GCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droSec1	super_1:4360092-4360178 +	AAGTTCCTCATCTATGTAAATA-TCTAAA-------------------GTTGAACTTGGCCAACG-------------------------------GCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droYak2	chr2R:2355901-2355987 -	AAGTTCCTGATATACGTAAATA-TCTAAA-------------------GTTGAACTTGGCCAACG-------------------------------GCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAATACTTC
droEre2	scaffold_4845:19001852-19001938 -	AAGTTCCTCATATACGTAAATA-TCTAAA-------------------GTTGAACTTGGCCAACG-------------------------------GCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droAna3	scaffold_13266:18269903-18269989 +	AAGTTTCTTATCTACGTAAGGA-ACTCAA-------------------TTTT------------------------------TACATTAAACCGAAGCAATTTAACACGTTTCTTATT-TCAGGAGAACGAGTACTTC
dp4	chr3:12187375-12187468 +	AAGTTTCTCATTTATGTAAGGG-ATCGGC-------------------G-AGAGTTTTTCCCACG-GA----ATA---TCATTATATT---------------ATATTGTTATGTGCCTGCAGGAAAACGAGTACTTT
droPer1	super_44:370822-370915 +	AAGTTTCTCATTTATGTAAGGG-ATCGGC-------------------G-AGAGTTTTTCCCACG-GA----ATA---TCATTATATT---------------ATATTGTTATGTGCCTGCAGGAAAACGAGTACTTT
droWil1	scaffold_180697:3635906-3636001 -	AAGTTTCTTATCTATGTAAGACAATCCAC-------------------G-AGGTGGTT------GGGAAGACAAATTTTGAATA-ATT---------------GGATTTTGATTTTTCTACAGGAAAACGAATATTTT
droVir3	scaffold_12875:11727599-11727677 +	AAATTTCTCATCTATGTAAGTG-ATGA---------------------------TGCGTCCATTGGGA----ATA---TCATTT------------------------AATTTGTGTTGGTAGGAAAACGAATATTTT
droMoj3	scaffold_6496:15129877-15129967 -	AAGTTTCTCATCTATGTAAGTA-GTAATA-------------------GGTGTTTGTAGACAT-----------AT--TCAG--------------TTAATTTTCGCATTTGTGTATTGGCAGGAAAACGAATATTTT
droGri2	scaffold_15245:6497403-6497490 -	AAATTTCTCATCTATGTAAGTG-ATGCAAATGAATAAATATTAATCATATTGCCTTTAATCAATG-------------------------------GT------------------CTTGCAGGAGAATGAGTATTTC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:6773023-6773109 +	AAGTTCCTCATCTATGTAAATATCTAAAGTTGAACTTGGCCAATGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droSim1	chr2R:5362602-5362688 +	AAGTTCCTCATCTATGTAAATATCTAAAGTTGAACTTGGCCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droSec1	super_1:4360092-4360178 +	AAGTTCCTCATCTATGTAAATATCTAAAGTTGAACTTGGCCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC
droYak2	chr2R:2355901-2355987 -	AAGTTCCTGATATACGTAAATATCTAAAGTTGAACTTGGCCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAATACTTC
droEre2	scaffold_4845:19001852-19001938 -	AAGTTCCTCATATACGTAAATATCTAAAGTTGAACTTGGCCAACGGCAAGTCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGTTCCTCATCTATGTAAATATCTAAAGTTGAACTTGGCCAACGGCAAG--------TCACAGCTTTTTGTGTTTACAGGAGAACGAGTACTTC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................................................TCACAGCTTTTTGTGTTTACAG...............	22	1	110.00	110	110
..........................................................TCACAGCTTTTTGTGTTTACA................	21	1	6.00	6	6
............................................................ACAGCTTTTTGTGTTTACAG...............	20	1	3.00	3	3
...............GTAAATATCTAAAGTTGAACT...........................................................	21	1	3.00	3	3

dp4

AAGTTTCTCATTTATGTAAGGGATCGGCG-AGAGTTTTTCCCACGGAATATCATTATATTATATTGTTATGTGCCTGCAGGAAAACGAGTACTTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-19.2, p-value=0.009901	dG=-19.2, p-value=0.009901	dG=-18.4, p-value=0.009901

droSim1

dG=-18.4, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droSec1

dG=-18.4, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droYak2

dG=-18.4, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droEre2

dG=-18.4, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droAna3

dG=-5.27, p-value=0.009901	dG=-4.7, p-value=0.009901	dG=-4.5, p-value=0.009901

dp4

dG=-9.9, p-value=0.009901	dG=-9.2, p-value=0.009901	dG=-9.1, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-8.1, p-value=0.009901

droPer1

dG=-9.9, p-value=0.009901	dG=-9.2, p-value=0.009901	dG=-9.1, p-value=0.009901	dG=-9.0, p-value=0.009901	dG=-8.1, p-value=0.009901

droWil1

dG=-10.8, p-value=0.009901	dG=-10.7, p-value=0.009901	dG=-9.9, p-value=0.009901	dG=-9.9, p-value=0.009901	dG=-9.8, p-value=0.009901	dG=-7.4, p-value=0.009901

droVir3

dG=-7.2, p-value=0.009901	dG=-7.1, p-value=0.009901	dG=-6.9, p-value=0.009901	dG=-6.6, p-value=0.009901	dG=-6.3, p-value=0.009901

droMoj3

dG=-5.7, p-value=0.009901	dG=-5.6, p-value=0.009901	dG=-5.5, p-value=0.009901	dG=-5.3, p-value=0.009901	dG=-5.2, p-value=0.009901

droGri2

dG=-7.7, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-7.0, p-value=0.009901

Generated: 03/07/2013 at 04:47 PM