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

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mature

star

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

-19.2	-19.2	-18.4

droSim1

-18.4	-17.8	-17.8

droSec1

-18.4	-17.8	-17.8

droYak2

-18.4	-17.8	-17.8

droEre2

-18.4	-17.8	-17.8

droAna3

-5.27	-4.7	-4.5

dp4

-9.9	-9.2	-9.1	-9.0

droPer1

-9.9	-9.2	-9.1	-9.0

droWil1

-10.8	-10.7	-9.9	-9.9	-9.8	-9.8

droVir3

-7.2	-7.1	-6.9	-6.6	-6.3	-6.3

droMoj3

-5.7	-5.6	-5.5	-5.3	-5.2	-4.9

droGri2

-7.7	-7.5	-7.0

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