Secondary structure and small RNA-seq evidence for dme-mir-994

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:6233844-6233964 + C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAGC-----CTAGATCC
droSim1 chr3R:15159284-15159404 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCC
droSec1 super_0:15709450-15709570 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--ATTTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCC
droYak2 chr3R:10262359-10262479 + C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGTTCC
droEre2 scaffold_4770:15384035-15384155 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--AATTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGTTCC
droAna3 scaffold_13340:867356-867469 - -----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCTCG-AAGTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATTT
dp4 chr2:7233487-7233613 - T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATACA--AATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCG
droPer1 super_0:1094175-1094302 - T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATAAC-AAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCG
droWil1 scaffold_181108:495-611 + C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTCAAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTA-----
droVir3 scaffold_13047:1194160-1194276 + C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTAG--AAGCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CT------
droMoj3 scaffold_6540:5225156-5225284 + AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTC--AACCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CT------
droGri2 scaffold_14906:5077444-5077577 - G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTCC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:6233844-6233964 + C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAGC-----CTAGATCC
droSim1 chr3R:15159284-15159404 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCC
droSec1 super_0:15709450-15709570 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--ATTTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCC
droYak2 chr3R:10262359-10262479 + C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAG--AATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGTTCC
droEre2 scaffold_4770:15384035-15384155 - C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATG--AATTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGTTCC
droAna3 scaffold_13340:867356-867469 - -----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCTCG-AAGTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATTT
dp4 chr2:7233487-7233613 - T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATACA--AATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCG
droPer1 super_0:1094175-1094302 - T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATAAC-AAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTAGATCG
droWil1 scaffold_181108:495-611 + C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTCAAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CTA-----
droVir3 scaffold_13047:1194160-1194276 + C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTAG--AAGCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CT------
droMoj3 scaffold_6540:5225156-5225284 + AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTC--AACCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGC-----CT------
droGri2 scaffold_14906:5077444-5077577 - G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTCC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CG------CGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGAATTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGCCTAGATCCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATACAAATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGCCTAGATCGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..............................................................................CACAGTTGCTGTTTCTTTTAGAT..........................2311.00110
.................................TAAGGAAATAGTAGCCGTGA..........................................................................2011.00101

Secondary Structure

dm3

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901

droSim1

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.4,  p-value=0.009901

droSec1

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901

droYak2

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901

droEre2

dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-27.9,  p-value=0.009901

droAna3

dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.3,  p-value=0.009901

dp4

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901

droPer1

dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901

droWil1

dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.1,  p-value=0.009901

droVir3

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.3,  p-value=0.009901

droMoj3

dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.5,  p-value=0.009901

droGri2

dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901

Generated: 03/07/2013 at 07:23 PM