Secondary structure and small RNA-seq evidence for dme-mir-4941

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:16024273-16024406 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGATTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSim1	chr3L:15362441-15362574 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSec1	super_0:8124906-8125039 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAATATGGAGCGCACCG
droYak2	chr3L_random:1624866-1624999 -	CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droEre2	scaffold_4784:18269422-18269555 +	CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCTGCACTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droAna3	scaffold_13337:16593401-16593534 -	CACCCTCACGAACCCCCTGACCGGCGAGGAGATGCGCTTTCTGGAGCTGCTCACGTCCTTCGGCATGGACATCGAGACAGTGGCCACCGCCCTGGGCGTGGATATGCACACGCTGAACAACATGGAGCGGACGG
dp4	chrXR_group8:4268508-4268641 +	CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGACTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGG
droPer1	super_29:501948-502081 +	CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGGCTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGG
droWil1	scaffold_181024:787133-787266 +	CACATTAACCAATCCACTGACAGGTGAAGAGATGCGTTTCCTTGAGCTGCTCACCTCCTTCGGTTTGGATATTGAGGCAGTGGCAGCGGCGCTTGGCGTCGATATGCATACCCTCAACAATATGGAACGTACCG
droVir3	scaffold_13049:9209848-9209981 +	CACGCTAACAAATCCGCTGACCGGCGAGGAGATGCGCTTTCTCGAGCTGCTCACCTCCTTCGGCCTGGACATCGAGGCCGTCGCCGCCGCACTCGGCGTCGATATGCACACCCTGAACAACATGGAACGCACCG
droMoj3	scaffold_6680:6136665-6136798 -	CACGCTCACGAATCCGCTGACCGGCGAGGAGATGCGCTTCCTCGAACTGCTCACCTCCTTCGGTCTGGACATCGAAGCCGTGGCCGCAGCACTCGGCGTCGATATGCACACGCTGAACAACATGGAACGAACGG
droGri2	scaffold_15110:4981116-4981249 +	CACGCTCACGAATCCGCTAACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCTCATTCGGCTTGGACATTGAGGCGGTGGCAGCAGCGCTGGGTGTCGATATGCACACCCTGAATAACATGGAGCGAACGG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:16024273-16024406 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGATTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSim1	chr3L:15362441-15362574 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSec1	super_0:8124906-8125039 +	CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAATATGGAGCGCACCG
droYak2	chr3L_random:1624866-1624999 -	CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droEre2	scaffold_4784:18269422-18269555 +	CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCTGCACTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGACTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-44.0	-43.5	-43.2	-43.0	-43.0

droSim1

-39.3	-39.0	-38.8	-38.5	-38.5	-38.3

droSec1

-39.3	-39.0	-38.8	-38.5	-38.5	-38.3

droYak2

-41.2	-41.2	-40.7	-40.7	-40.4	-40.4

droEre2

-39.8	-39.8	-39.6	-39.6	-38.9	-38.9

droAna3

-34.1	-33.8	-33.7	-33.5	-33.4	-33.2

dp4

-36.5	-36.5	-36.5	-36.5	-35.9	-35.9

droPer1

-37.1	-37.1	-36.9	-36.9	-36.4	-36.4

droWil1

-31.6	-31.4	-31.3	-31.2	-31.1	-31.1

droVir3

-36.3	-36.3	-35.8	-35.4	-35.4	-35.4

droMoj3

-33.2	-33.1	-32.6	-32.6	-32.5	-32.4

droGri2

-35.6	-35.1	-35.1	-34.9	-34.8	-34.7

Generated: 01/05/2013 at 05:21 PM