Secondary structure and small RNA-seq evidence for dme-mir-4959

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:19063148-19063296 -	TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1	chrX:14724057-14724205 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1	super_8:1352288-1352436 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2	chrX:17654811-17654959 -	TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2	scaffold_4690:9326382-9326530 -	TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC
droAna3	scaffold_12903:667658-667806 +	TCCTGATGGCCCTGATGTCCGGCCTGAATTTGGTCTGTCGCGTGGCGATGATTATCAGCAAGACCCTAAGAGAGCAGATGATCCGGAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTCCAGAGGGCGCTGAGGGATCTGACGATCGGG
dp4	chrXL_group1e:10756223-10756371 -	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGG
droPer1	super_14:190427-190575 -	TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTTCGCGACCTCACCATCGGG
droWil1	scaffold_181096:8247011-8247159 -	TGCTGATGGCCATCATGTCGGGCCTCAATCTACTCTGTCGCCTGGCCATGATGCTGAGCAAGAGTGTGCGTGAGCAAATGATTCGCAGTCAATTGCGTTTTATGCCCAAACGGCATATCCAACGAGCTCTCAGGGATCTAACCATTGGC
droVir3	scaffold_12726:998444-998592 -	TGCTGATGGCCTTCATGTCCGGCCTGAACCTGCTCTGCCGTCTGGCCATGATGCTCAGCCGGACGCTGCGTGAGCTGATGATACGCAGCCAATTGCGCTTCATGACCAAGCAGCATGTACAGCGCGTTTTCCGGGATCTAACCATCGGT
droMoj3	scaffold_6473:9166585-9166733 +	TGCTGATGGCCTTCATGTCCGGCCTGAATCTGCTCTGTCGCCTGGCCATGATGCTCAGCCGGACGCTGCGCGAGCTGATGATACGCAGCCAATTGCGCTATATGACCAAACAGCATGTGCAGCACGTCTTCAGGGATCTGACCATCGGC
droGri2	scaffold_14853:5433396-5433544 -	TCCTCATGGCGATCATCGCTGGCCTAAATCTGCTCTGTCGCCTAACCATGATGGTCAGCCGGACGCTGCGCGAACTGATGATTCGCAGCCAGTTGCGATTCATGACCAAAGAGCATGTGCAGCGCATCTTTAGCCATTTAACCATCGGC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:19063148-19063296 -	TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1	chrX:14724057-14724205 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1	super_8:1352288-1352436 -	TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2	chrX:17654811-17654959 -	TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2	scaffold_4690:9326382-9326530 -	TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-42.2	-42.0	-42.0	-41.8	-41.5	-41.4

droSim1

-43.6	-43.5	-43.4	-43.3	-43.3	-43.2

droSec1

-44.0	-43.9	-43.8	-43.8	-43.7	-43.7

droYak2

-43.5	-43.4	-43.2	-43.1	-42.8	-42.5

droEre2

-44.1	-43.7	-43.3	-43.3	-43.1	-43.1

droAna3

-31.0	-30.9	-30.8	-30.8	-30.8	-30.7

dp4

-32.0	-31.8	-31.3	-31.3	-31.3	-31.2

droPer1

-32.0	-31.8	-31.3	-31.3	-31.3	-31.2

droWil1

-33.3	-33.2	-32.9	-32.8	-32.7	-32.6

droVir3

-41.8	-41.8	-41.7	-41.7	-41.5	-41.5

droMoj3

-41.3	-41.3	-41.3	-41.3	-41.1	-41.1

droGri2

-33.8	-33.8	-33.7	-33.7	-33.6	-33.6

Generated: 01/05/2013 at 05:24 PM