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

Legend:maturestarmismatch

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
CACCCACTGCGAATTGCTATAGGAAATGATGGAGTTTTTGGGGTACTTCTGGTTTCATACTGCAGAGAATCTTCAGCGTGCAGTAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGATTTTAACCAGGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CACCAGCTGTGGGCTGCTTTAGG----------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-48.8 -48.7 -48.4 -48.3 -48.2 -48.1

droSim1

-44.8 -44.4 -44.2 -44.1 -43.8

droSec1

-40.6 -40.2 -40.0 -39.9 -39.7 -39.6

droYak2

-41.6 -41.3 -40.7 -40.7

droEre2

-50.4 -50.3 -50.2 -49.8 -49.7 -49.6

droAna3

-0.3 0.0 0.5

dp4

0.0

droPer1

0.0

droWil1

0.0

droVir3

0.0

droMoj3

0.0

droGri2

-1.1 -0.2

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