Secondary structure and small RNA-seq evidence for dme-mir-4963

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:5684770-5684909 +	CACCCACTGCGAATTGCTGTAGGAAAT-------TTTTT-GGGGTACTTCTGGTTTCATAACGCAGAGAATCATC-----------AGCGTGAAGGAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGATTTTAA---CCAGG
droSim1	chrX:4425250-4425396 +	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTT-GGGGTACTTCTGGTTTCATACTGCAGAGAATCTTC-----------AGCGTGCAGTAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA---CCAGG
droSec1	super_4:1079282-1079434 -	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTT-GGGGTACTTCTGGTTTCATAACTCAGAGAATCTTCATGATTTCTTAATCA-----TAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA---CCAGG
droYak2	chrX:2788911-2789034 -	CACCCACTGCGAAATGCTATAGGACATGATGGAGCTTCTGGAGGTACTTCTGGTTTTATAATGCAGAGAATCGTA-----------ATCGTGAAGGAATGATTCTATGCGTACTGAAATCGGGAGTCCTGCAGAT---------------------------
droEre2	scaffold_4690:3033374-3033523 +	CACCCACTGCGAAATGCTATAGGAAACGATGGGGTTTCT-GGGGTACTTCTGGTTTTATAACGCACGGAATCTGA-----------ATCGTGAATGAATGATTCCTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGATTTGAAGTTTCGGA
droAna3	scaffold_13117:1117754-1117783 +	CACCCACTGCGACGTACTTTAGAGAGTTGT------------------------------------------------------------------------------------------------------------------------------------
dp4	chr3:13862643-13862665 +	CACCAGCTGTGGGCTGCTTTAGG-------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_4:1457976-1457998 -	CACCAACTGTGGGCTGCTTTAGG-------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7345062-7345085 -	AACCCACTGTGATGTCCTGTAAAA------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13324:2924689-2924720 +	CACGGCCTGTGGTGTGCTATAAATTTT------------------------------------------------------------------------------ATGTG----------------------------------------------------
droMoj3	scaffold_6496:13805954-13805976 -	CACCGACTGCGGCGTCCTCTGAG-------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15112:3786307-3786359 +	CACCAGCTGCGGCGTGCTATAAATTC--------TTTTC-GTTGTATTTCTGGGTGTTCAAC----------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:5684770-5684909 +	CACCCACTGCGAATTGCTGTAGGAAAT-------TTTTTGG-GGTACTTCTGGTTTCATAACGCAGAGAATCATC-----------AGCGTGAAGGAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGATTTTAA---CCAGG
droSim1	chrX:4425250-4425396 +	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATACTGCAGAGAATCTTC-----------AGCGTGCAGTAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA---CCAGG
droSec1	super_4:1079282-1079434 -	CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGG-GGTACTTCTGGTTTCATAACTCAGAGAATCTTCATGATTTCTTAATCA-----TAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAA---CCAGG
droYak2	chrX:2788911-2789034 -	CACCCACTGCGAAATGCTATAGGACATGATGGAGCTTCTGGAGGTACTTCTGGTTTTATAATGCAGAGAATCGTA-----------ATCGTGAAGGAATGATTCTATGCGTACTGAAATCGGGAGTCCTGCAGAT---------------------------
droEre2	scaffold_4690:3033374-3033523 +	CACCCACTGCGAAATGCTATAGGAAACGATGGGGTTTCTGG-GGTACTTCTGGTTTTATAACGCACGGAATCTGA-----------ATCGTGAATGAATGATTCCTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGATTTGAAGTTTCGGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGGGGTACTTCTGGTTTCATACTGCAGAGAATCTTCAGCGTGCAGTAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAACCAGG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

dG=-38.5, p-value=0.009901	dG=-38.4, p-value=0.009901	dG=-37.5, p-value=0.009901

droSim1

dG=-29.5, p-value=0.009901

droSec1

dG=-25.3, p-value=0.009901	dG=-24.4, p-value=0.009901

droYak2

dG=-27.7, p-value=0.009901	dG=-26.8, p-value=0.009901

droEre2

dG=-30.3, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.1, p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

dG=0.0, p-value=1.0

droMoj3

No secondary structure predictions returned

droGri2

dG=0.0, p-value=1.0

Generated: 03/07/2013 at 06:11 PM