Secondary structure and small RNA-seq evidence for dme-mir-4977

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:3294222-3294357 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGAACGGCCG-TACAATACCCAAG
droSim1	chrU:460991-461115 -	TTTT----------------TAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAACACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droSec1	super_1:944262-944397 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droYak2	chr2L:15977521-15977656 -	TTTTCGTTTAC-----TTGTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ATCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TAAAATACCCAAG
droEre2	scaffold_4929:19300554-19300689 +	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTTT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AACAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droAna3	scaffold_13266:3498798-3498932 -	ACCC-CTTTAT-----TTTTATTTTCACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGGCGTGCAAAACCCT------------------------------------------------------------------------TTG--AGAAGTTT-TGC-ATCGTTCGAAATTAGGGGCAGCACCTCGAACA--GTACACGGCCG-TAAAATTCCTAAA
dp4	chr3:1570003-1570137 -	TTTTTGGTT---------TTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACACTT---------------------------------TTTTC---------------------------GCGTCTCTGTGG-AAAAGTTT-TGC-ATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droPer1	super_2:1744183-1744317 -	TTTTTGGTT---------TTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACACTT---------------------------------TTTTC---------------------------GCGTCTCTGTGG-AAAAGTTT-TGC-ATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droWil1	Unknown	TTTTTTTTTTT-----TGTTTTACCTTTTTGT--TGAGGAAA---------------------------CATTTCAAAAAATTCTCCGTTTAAGTGCAAGAAACG-------------------------------------------------TGCTCTGCCTACG--CCAAA-----A----------------GTAATACGGCCGTAAACATTCCAAAA
droVir3	scaffold_12875:10810504-10810650 -	TTTTGATTTACTTTAATTTCGTTTGCATCGAT--T-AAAACGTGT-TTG----TTTG---CGTGCAATCACT--------------------------------TTTTCCACCGTGTC----------------CCGGC--GTGTGCGA-GAAAGTCT-TGC-AACGTACAA-------AACAACACGTTGA----TAAGCACGGCCGCAAAAATTCCCAAA
droMoj3	scaffold_6496:16132312-16132448 +	TTTT--------------------GCATCGAT--T-AAAACGTGT-TTG----TTTGCG-TTTGCAACAACT--------------------------------TTTTCCACCGTGTCCCCCA-----------CCGGCGTGTGTGCGA-AAAAGTCTTTGC-AACGTTCCAAA-------CAACACGTCGA----TAAGTACGGCCGCAAAAATTCCTAAA
droGri2	scaffold_15245:3916304-3916452 -	TTTTCGTTTG---------------CATCGATTGT-GAAACGTGT-TTG----TTTGTAGCGTGCAACACACT-------------------------------TTTT-CAC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTGA-AAAAGTCTGTGC-AACGTTCAGA------AACAACACGTCGAA----CTCTACGGCCGCAAAAATTCCCAAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:3294222-3294357 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATAC--TCTG----------------------------------------TGGCAGAAGTCT-TGCACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGAACGGCCG-TACAATACCCAAG
droSim1	chrU:460991-461115 -	TTTT----------------TAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATAC--TCTG----------------------------------------TGGCAGAAGTCT-TGCACCGTTCCAAAAGAG-AGCAACACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droSec1	super_1:944262-944397 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATAC--TCTG----------------------------------------TGGCAGAAGTCT-TGCACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droYak2	chr2L:15977521-15977656 -	TTTTCGTTTAC-----TTGTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATAC--TCTG----------------------------------------TGGCAGAAGTCT-TGCATCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TAAAATACCCAAG
droEre2	scaffold_4929:19300554-19300689 +	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATAC--TTTG----------------------------------------TGGCAGAAGTCT-TGCACCGTTCCAAAAGAG-AACAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droAna3	scaffold_13266:3498798-3498932 -	ACC-CCTTTAT-----TTTTATTTTCACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGGCGTGCAAAAC--CCTT----------------------------------------TG--AGAAGTTT-TGCATCGTTCGAAATTAGGGGCAGCACCTCGAACA--GTACACGGCCG-TAAAATTCCTAAA
dp4	chr3:1570003-1570137 -	TTTTTGGT---------TTTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTTT-TGCATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droPer1	super_2:1744183-1744317 -	TTTTTGGT---------TTTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTTT-TGCATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droVir3	scaffold_12875:10810504-10810650 -	TTTTGATTTACTTTAATTTCGTTTGCATCGAT--T-AAAACGTGT-TTG----TTTG---CGTGCAATCA-CTTTT-TCCACCGTGTC----------------CCGGC--GTGTGCGA-GAAAGTCT-TGCAACGTACAA-------AACAACACGTTGA----TAAGCACGGCCGCAAAAATTCCCAAA
droMoj3	scaffold_6496:16132312-16132448 +	TTTT--------------------GCATCGAT--T-AAAACGTGT-TTG----TTTGCG-TTTGCAACAA-CTTTT-TCCACCGTGTCCCCCAC-----------CGGCGTGTGTGCGA-AAAAGTCTTTGCAACGTTCCAAA-------CAACACGTCGA----TAAGTACGGCCGCAAAAATTCCTAAA
droGri2	scaffold_15245:3916304-3916452 -	TTTTCGTTTG---------------CATCGATTGT-GAAACGTGT-TTG----TTTGTAGCGTGCAACACACTTTT-TC-AC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTGA-AAAAGTCTGTGCAACGTTCAGA------AACAACACGTCGAAC----TCTACGGCCGCAAAAATTCCCAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTTT-----------TAACCCTCCGCTCGAGAACGTGGTTTCTT--TTGCGACGTGCAATAC------------TCTGTGGCAGAAGTCTTGCACCGTTCCAAAAG-AGAGCAACACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................................................TCTTGCACCGTTCCAAAAG-AGAG.........................................	23	1	1.00	1	1
........................................................................................CTTGCACCGTTCCAAAAG-AGAG.........................................	22	1	1.00	1	1

dp4

TTTTTGGTTTTGT------------TTTGAGAACGTGCCTTCTTTTTTTTGGCGTGCAACACTTTTTTCGCGTCTCTGTGG-AAAAGTTTTGCATCGTTTCAAAAAAAAAGATACACGT----CGACACATACGGCCGCTAAGATTCCAAAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-38.1	-38.1	-38.1	-38.1	-37.5	-37.5

droSim1

-37.9	-37.9	-37.9	-37.9	-37.4	-37.4

droSec1

-38.1	-38.1	-38.1	-38.1	-37.6	-37.6

droYak2

-38.1	-38.1	-37.6	-37.6

droEre2

-36.5	-36.5	-36.4	-36.4	-36.4	-36.4

droAna3

-36.3	-36.3	-36.0	-36.0	-35.7	-35.7

dp4

-29.5	-29.5	-29.5	-29.5	-29.5	-29.5

droPer1

-29.5	-29.5	-29.5	-29.5	-29.5	-29.5

droWil1

-9.7	-9.5	-9.4	-9.2	-9.0	-9.0

droVir3

-35.2	-35.2	-35.2	-35.2	-35.2	-35.2

droMoj3

-36.8	-36.8	-36.8	-36.8	-36.8	-36.8

droGri2

-37.1	-37.1	-37.1	-37.1	-37.1	-37.1

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