Secondary structure and small RNA-seq evidence for dme-mir-4952

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:18306519-18306675 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSim1	chr3R:18115675-18115831 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSec1	super_0:18660821-18660977 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATATTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGATTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCAGTCTACGTGCCGCCCACCAAGCA
droYak2	chr3R:19151970-19152126 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGAGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droEre2	scaffold_4820:9770831-9770987 -	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droAna3	scaffold_12911:5347592-5347748 +	CTCCGGCGAGTGGCTATCCGGGTGCCCTGGACGATCTGATCTTCTCGGGAGCGGGATCCGGGTGCCGGGGCGATGACGAGGACGAGTGCACGCCACCCTTCGAGTCGGGCAGCGGGGACGACCTGATCACTCCGGTGTATGTACCGCCCACCAAGCA
dp4	chr2:13773155-13773311 -	CGCCGGCCAGCGGCTATCCCGGCACCATTGACGATCTGATCTTCTCCGGGGCCGGGTCCGGGTGCCGCGGCGACGACGAGGACGAGTGCACACCGCCCTTCGAGTCGGGCAGCGGCGATGACCTCATCACGCCCGTGTATGTGCCACCCACCAAGCA
droPer1	super_0:6673715-6673871 +	CGCCGGCCAGCGGCTATCCCGGCACCATTGACGATCTGATCTTCTCCGGGGCCGGGTCCGGGTGCCGCGGCGACGACGAGGACGAGTGCACACCGCCCTTCGAGTCGGGCAGCGGCGATGACCTCATCACGCCCGTGTATGTGCCACCCACCAAGCA
droWil1	scaffold_181089:2782020-2782176 +	CGCCGGCCAGTGGCTATCCTGGGGCCATAGATGATCTTATATTCTCCGGTGCCGGATCCGGTTGTCGCGGCGACGATGAAGACGAATGTACGCCGCCCTTCGAGTCGGGCAGTGGAGATGATCTAATCACACCTGTCTATGTGCCTCCGACAAAACA
droVir3	scaffold_12822:645540-645696 -	CGCCTGCGAGCGGCTATCCGGGCGCCATAGACGATCTGATCTTCTCCGGGGCCGGGTCCGGTTGTCGCGGCGACGACGAGGACGAATGCACGCCCCCCTTCGAGTCGGGCAGCGGGGATGACCTAATAACGCCCGTCTATGTGCCGCCCACCAAGCA
droMoj3	scaffold_6540:33300209-33300365 -	CGCCGGCTAGTGGCTATCCGGGCGCCATAGACGACCTGATCTTCTCCGGAGCCGGATCTGGGTGTCGCGGCGACGACGAGGATGAATGCACGCCGCCCTTCGAGTCGGGCAGTGGGGATGACCTGATCACACCCGTCTATGTGCCGCCCACCAAACA
droGri2	scaffold_15074:3142694-3142850 +	CGCCGGCGAGTGGTTATCCGGGTGCGATAGACGATCTGATCTTCTCCGGTGCGGGATCCGGGTGTCGCGGCGACGATGAGGACGAATGCACGCCGCCCTTCGAGTCGGGCAGCGGGGATGATCTAATTACGCCCGTCTATGTGCCACCCACCAAACA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:18306519-18306675 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSim1	chr3R:18115675-18115831 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSec1	super_0:18660821-18660977 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATATTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGATTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCAGTCTACGTGCCGCCCACCAAGCA
droYak2	chr3R:19151970-19152126 +	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGAGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droEre2	scaffold_4820:9770831-9770987 -	CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-47.0	-46.8

droSim1

-47.0	-46.8

droSec1

-45.0	-45.0	-44.8	-44.8	-44.1

droYak2

-45.4	-45.2

droEre2

-46.2	-46.0

droAna3

-46.4	-46.0	-45.9	-45.9	-45.6	-45.6

dp4

-49.3	-49.2	-49.1	-49.0	-48.5	-48.5

droPer1

-49.3	-49.2	-49.1	-49.0	-48.5	-48.5

droWil1

-43.5	-43.3	-42.8	-42.8	-42.8	-42.7

droVir3

-43.0	-42.9	-42.8	-42.3	-42.3	-42.2

droMoj3

-43.1	-42.9

droGri2

-45.6	-45.5	-45.0	-44.8	-44.8	-44.7

Generated: 01/05/2013 at 05:23 PM