Secondary structure and small RNA-seq evidence for dme-mir-975

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19452771-19452891 + ATCCAA--------------TTGGCAATATTGAATTTTTGATTTTAAACACTTCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGGTACAGATGTGGGAGTCGTTTGCACTCAGAGATTTCACAGAATTCGAGGATC-GA
droSim1 chrX:15018379-15018489 + -------------------------AATATTGAGTTTTTGATTTTAAACACTGCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGATACAGTTGTAGGAGTCGTTTGCAGTCAGAGATTTCACAGACTGCGAGGATC-GA
droSec1 super_8:1735110-1735229 + A-AAA--------------TTAATTAATATTGAGTTTTTGATTTTAAACACTCCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGATACAGTTGTAGGAGTCGTTTGCAGTCAGAGATTTCACAGACTGCGAGGATC-GC
droYak2 chrX:11885955-11886071 - ATCCA------------------GCAATATTGAATTCTTGACTTTAAACACTGCCTACATACTGTATGTGT-TTTG----------------------------CACCCGATACAGATGTGGGGGTCGTTTGCAATCAGAGATTCCGCAGGCTACGAGGATC-GG
droEre2 scaffold_4690:9688756-9688876 + -TCCA--------------ACCATCAACATTGAATTCTTGACTTTAAACACTTCCTACATCCTGTATGTGT-TTTG----------------------------CGCCCTATACAGATGTGGGGGTCGTTTGCACTCAGGGATTCCACAGGCTGCAAGGATC-GG
droAna3 scaffold_13417:2467701-2467813 - GTCCAAG------------CCAGTCGACAATGAATATTTGATTTTAAACACTACCTACATCCAGTATGTTACTTGA----------------------------CTCCCAATACGGATGTGGAGGGCGTTTACACTCAGAGATTCTGGAG-----------C-CA
dp4 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7956608-7956722 + GTTTTGTAGATGTGTTGGAATC-ACGACATTCAACTGTTATGTTTACATATGTCTAACATTCTGT-----------------TATAGTATAACAGTGTGTCTTGCG----------------------TTCCTACTCAACAC-TCAACAT-TCGC--------AA
droVir3 scaffold_13042:906902-907003 - ----------------------------------TCTTTGATTTTAGATACTCCCTATATCCAGTATGTGT-GCCACTT-ATTGAAATACA-----------------------AGATGTATGGGGTGTCTGCAATCACAAACCACGTAG-CCGCAA---TCAGC
droMoj3 scaffold_6328:2901122-2901224 - ----------------------------------TCTTTGATTGTAGATACTCCCTATATCCCGTATGTGC-GATACTTTGATAAAATACA-----------------------AGATGTATGGGGTGTCTGCAATCACAAACCACATAG-CCGCAA---TCAAA
droGri2 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19452771-19452891 + ATCCAA--------------TTGGCAATATTGAATTTTTGATTTTAAACACTTCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGGTACAGATGTGGGAGTCGTTTGCACTCAGAGATTTCACAGAATTCGAGGATC-GA
droSim1 chrX:15018379-15018489 + -------------------------AATATTGAGTTTTTGATTTTAAACACTGCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGATACAGTTGTAGGAGTCGTTTGCAGTCAGAGATTTCACAGACTGCGAGGATC-GA
droSec1 super_8:1735110-1735229 + A-AAA--------------TTAATTAATATTGAGTTTTTGATTTTAAACACTCCCTACATCCTGTATGTGT-TTTG----------------------------CATCCGATACAGTTGTAGGAGTCGTTTGCAGTCAGAGATTTCACAGACTGCGAGGATC-GC
droYak2 chrX:11885955-11886071 - ATCCA------------------GCAATATTGAATTCTTGACTTTAAACACTGCCTACATACTGTATGTGT-TTTG----------------------------CACCCGATACAGATGTGGGGGTCGTTTGCAATCAGAGATTCCGCAGGCTACGAGGATC-GG
droEre2 scaffold_4690:9688756-9688876 + -TCCA--------------ACCATCAACATTGAATTCTTGACTTTAAACACTTCCTACATCCTGTATGTGT-TTTG----------------------------CGCCCTATACAGATGTGGGGGTCGTTTGCACTCAGGGATTCCACAGGCTGCAAGGATC-GG
droAna3 scaffold_13417:2467701-2467813 - GTCCAAG------------CCAGTCGACAATGAATATTTGATTTTAAACACTACCTACATCCAGTATGTTACTTGA----------------------------CTCCCAATACGGATGTGGAGGGCGTTTACACTCAGAGATTCTGGAG-----------C-CA
droWil1 scaffold_181096:7956608-7956722 + GTTTTGTAGATGTGTTGGAATC-ACGACATTCAACTGTTATGTTTACATATGTCTAACATTCTGT-----------------TATAGTATAACAGTGTGTCTTGCG----------------------TTCCTACTCAACAC-TCAACAT-TCGC--------AA
droVir3 scaffold_13042:906902-907003 - ----------------------------------TCTTTGATTTTAGATACTCCCTATATCCAGTATGTGT-GCCACTT-ATTGAAATACA-----------------------AGATGTATGGGGTGTCTGCAATCACAAACCACGTAG-CCGCAA---TCAGC
droMoj3 scaffold_6328:2901122-2901224 - ----------------------------------TCTTTGATTGTAGATACTCCCTATATCCCGTATGTGC-GATACTTTGATAAAATACA-----------------------AGATGTATGGGGTGTCTGCAATCACAAACCACATAG-CCGCAA---TCAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
A-----------ATATTGAGTTTTTGATTTTAAACACTGCCTACATCCTGTATGTGTTTTGCATCCGATACAGTTGTAGGAGTCGTTTGCAGTCAGAGATTTCACAGACTGCGAGGATCGASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droSim1

dG=-23.3,  p-value=0.009901

droSec1

dG=-23.3,  p-value=0.009901 dG=-23.3,  p-value=0.009901 dG=-23.3,  p-value=0.009901

droYak2

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droEre2

dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901

droAna3

dG=-17.8,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.9,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-11.0,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-10.1,  p-value=0.009901

droVir3

dG=-25.4,  p-value=0.009901 dG=-24.5,  p-value=0.009901

droMoj3

dG=-32.1,  p-value=0.009901 dG=-31.6,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:17 PM