Secondary structure and small RNA-seq evidence for dme-mir-275-as

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:7425780-7425907 -	ATGGT--GAA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TACAGTCGGGGGAACATCA
droSim1	chr2L:7217350-7217477 -	ATGGC--GGA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droSec1	super_3:2941240-2941367 -	ATGAC--GGA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droYak2	chr2L:5473766-5473897 +	ATATCGTGGA-------------------GTTGGAG--ATATATGTCTG-GCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTGTTCAGTCGGGGGAACATCA
droEre2	scaffold_4929:16344506-16344633 -	ATGGT--GGA-------------------GATGGAG--ATATATGTCTG-GCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droAna3	scaffold_12916:15333988-15334092 -	ATGGC--G---------------------------G--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT-----TGCA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG--GAGAGT-------------
dp4	chr4_group1:4175727-4175841 -	ACAC----------------------------AGAT--GTTCGTGTCTA-GCACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTGG-------
droPer1	super_5:1086448-1086562 +	ACAC----------------------------AGAT--GTTCGTGTCTA-GCACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTGG-------
droWil1	scaffold_180772:5257564-5257692 +	GTGTC--GTCGTTGTCGCCGTCGTCGTGCGA----TGAATCTTGGTCTA-AAACCACGCGCGCTACTTCAGGTACCTGACTGT---ATTGAATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC-----------------------
droVir3	scaffold_12963:15419953-15420066 +	AAGCT--TAA-------------------GA----T--GAATACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAACC-----AAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG--CGCAG--------------
droMoj3	scaffold_6500:18399385-18399491 +	GCAG-----A-----------------GCGT----T--GAATGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGAGATAATC-----GAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------
droGri2	scaffold_15126:5008401-5008495 -	ATG----------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAATC-----AAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC-----------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:7425780-7425907 -	ATGGT--GAA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TACAGTCGGGGGAACATCA
droSim1	chr2L:7217350-7217477 -	ATGGC--GGA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droSec1	super_3:2941240-2941367 -	ATGAC--GGA-------------------GATGGAG--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droYak2	chr2L:5473766-5473897 +	ATATCGTGGA-------------------GTTGGAG--ATATATGTCTG-GCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTGTTCAGTCGGGGGAACATCA
droEre2	scaffold_4929:16344506-16344633 -	ATGGT--GGA-------------------GATGGAG--ATATATGTCTG-GCACCACGCGCGCTACTTCAGGTACCTGACTGT---ATATAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT--TTCAGTCGGGGGAACATCA
droAna3	scaffold_12916:15333988-15334092 -	ATGGC--G---------------------------G--ATATATGTCTG-CCACCACGCGCGCTACTTCAGGTACCTGACTGT-----TGCA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG--GAGAGT-------------
dp4	chr4_group1:4175727-4175841 -	ACAC----------------------------AGAT--GTTCGTGTCTA-GCACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTGG-------
droPer1	super_5:1086448-1086562 +	ACAC----------------------------AGAT--GTTCGTGTCTA-GCACCACGCGCGCTACTTCAGGTACCTGACTGC---AGTGAA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT--TCAAGAAGGTGG-------
droWil1	scaffold_180772:5257564-5257692 +	GTGTC--GTCGTTGTCGCCGTCGTCGTGCGA----TGAATCTTGGTCTA-AAACCACGCGCGCTACTTCAGGTACCTGACTGT---ATTGAATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC-----------------------
droVir3	scaffold_12963:15419953-15420066 +	AAGCT--TAA-------------------GA----T--GAATACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAACC-----AAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG--CGCAG--------------
droMoj3	scaffold_6500:18399385-18399491 +	GCAG-----A-----------------GCGT----T--GAATGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGAGATAATC-----GAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC-----------------------
droGri2	scaffold_15126:5008401-5008495 -	ATG----------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGGGATAATC-----AAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC-----------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATGGCGGAGATGGAGATATATGTCTGCCACCACGCGCGCTACTTCAGGTACCTGACTGTATATAAAAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTTTTCAGTCGGGGGAACATCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

AC-------ACAGATGTTCGTGTCTAGCACCACGCGCGCTACTTCAGGTACCTGACTGCAGTGAAAAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTTTCAAGAAGGTGG-------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-34.4

droSim1

-34.4

droSec1

-33.1	-32.6	-32.6	-32.6	-32.5

droYak2

-31.8	-31.6

droEre2

-31.8

droAna3

-36.9	-36.1

dp4

-35.3	-34.7

droPer1

-35.3	-34.7

droWil1

-31.9	-31.6	-31.0

droVir3

-39.1

droMoj3

-30.2

droGri2

-37.7	-36.7

Generated: 01/05/2013 at 05:12 PM