Secondary structure and small RNA-seq evidence for dme-mir-978

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19455254-19455375 + AAGTACAATA---TCTTGGT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGC-------AA-TCGAAAATCGTGTCCAGTGCCGTAAATTGCAGTTGTGTGAA--CGCAAACGGCAGCAG--------------------CGAAGG
droSim1 chrX_random:5079001-5079113 + AAGTA------------GAT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGT-------GG-TCGAGAATCGTGTCCAGTGCCGTATATTGCAGTTGTGTGGA--CGCAAACGGCAGCAG--------------------CGAAGG
droSec1 super_8:1737859-1737971 + AAGTA------------GAT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGT-------AG-TCGAGAATCGTGTCCAGTCCCGTAAATTGCAGTTGTGTGGA--CGCAAACGGCAGCAG--------------------CGAAGG
droYak2 chrX:11883747-11883862 - AAGTGCATCC------AGGT--------GGGCGGCACAGCCAGCACTCTACGCCGCTGGCTTACGTTGT-------AC-TCGGAAATCGTGTCCAGTGCCGTTGATTGCAGTTGTGTGGA--CGCAAAGGGCAGCG-----------------------GAGA
droEre2 scaffold_4690:9691187-9691301 + AAGTGCATCC-------AGT--------GGGCGGCACAACCAGCATTCTACGCCGCTGGCTTACGTTGT-------AC-TCGAAAATCGTGTCCAGTGCCGTTGATTGCAATTGTGTGGA--CGCAAAGGGCAGCG-----------------------GAGG
droAna3 scaffold_13417:2460507-2460635 - GAGTGCGGACAGGGCAAGCT--------CGGCGGCACAGACAGCATTCGACGCTGCTGGCTTACGTGGT-------GG-TTGATATCCGTGTCCAGTGACGTTGATTGCAGTTGTGTAGA--CGCGAATTACAGCGACCG------A----------TAGTTG
dp4 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 super_14:1991206-1991216 - AACAAC--------------------------------------------------------------------------------------------------------------------------------------------------------AACTA
droWil1 scaffold_181096:7961115-7961220 + -------------------T--------TGGCAACACAGGCAGCATTCGACGACGCTGGCTTACGTTAAAAAC---AA-ACGATATCCGTGTCCAGTGACGTTGATTGCAGTTGTGTA------CAATGATTAGCGG--------------------CGATTT
droVir3 scaffold_13042:902659-902773 - ACA-----------------------------GGCACA-GCCGTACTCTACGCTTTTGGGA-ACGAG--CTCTTTGAC----GCACTCGGTTCCATTGCCGTTGAGTAGAGCTGTCCTGA--TGCATATCTCAACG---T------ATTGATTCAAACAAGAA
droMoj3 scaffold_6328:2897048-2897148 - CG------------------------------GGTACA-GCCGTACTCTACGCTTTTGGGA-ACGAG--CAATCATACAAAGCCACTCGGTTCCATAGCCGTTGAGTAGAGCTGCCCCCGTTTGCACATCACAAC----------------------------
droGri2 scaffold_15081:2040911-2041055 - AAGTACGGCA---GTTCGATAACCAACAC--AGGTCCA-GCCGTATTCAGCGCTTTTGGAA-GTAAG--GAACATGAT----TCTCCTAGTTTCAATGCCGCTGAGTAAAGCTGTCCCAA--TGCAAATCGCAACG---TAACTGAATCGAATCAATCAATAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19455254-19455375 + AAGTACAAT---ATCTTGGT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGC-------AA-TCGAAAATCGTGTCCAGTGCCGTAAATTGCAGTTGTGTGAA--CGCAAACGGCAGCAG--------------------CGAAGG
droSim1 chrX_random:5079001-5079113 + AAGTA------------GAT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGT-------GG-TCGAGAATCGTGTCCAGTGCCGTATATTGCAGTTGTGTGGA--CGCAAACGGCAGCAG--------------------CGAAGG
droSec1 super_8:1737859-1737971 + AAGTA------------GAT--------TGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGT-------AG-TCGAGAATCGTGTCCAGTCCCGTAAATTGCAGTTGTGTGGA--CGCAAACGGCAGCAG--------------------CGAAGG
droYak2 chrX:11883747-11883862 - AAGTGCATC------CAGGT--------GGGCGGCACAGCCAGCACTCTACGCCGCTGGCTTACGTTGT-------AC-TCGGAAATCGTGTCCAGTGCCGTTGATTGCAGTTGTGTGGA--CGCAAAGGGCAGCG-----------------------GAGA
droEre2 scaffold_4690:9691187-9691301 + AAGTGCATC-------CAGT--------GGGCGGCACAACCAGCATTCTACGCCGCTGGCTTACGTTGT-------AC-TCGAAAATCGTGTCCAGTGCCGTTGATTGCAATTGTGTGGA--CGCAAAGGGCAGCG-----------------------GAGG
droAna3 scaffold_13417:2460507-2460635 - GAGTGCGGACAGGGCAAGCT--------CGGCGGCACAGACAGCATTCGACGCTGCTGGCTTACGTGGT-------GG-TTGATATCCGTGTCCAGTGACGTTGATTGCAGTTGTGTAGA--CGCGAATTACAGCGACCG------A----------TAGTTG
droWil1 scaffold_181096:7961115-7961220 + -------------------T--------TGGCAACACAGGCAGCATTCGACGACGCTGGCTTACGTTAAAAAC---AA-ACGATATCCGTGTCCAGTGACGTTGATTGCAGTTGTGTA------CAATGATTAGCGG--------------------CGATTT
droVir3 scaffold_13042:902659-902773 - ACA-----------------------------GGCACA-GCCGTACTCTACGCTTTTGGGA-ACGAG--CTCTTTGAC----GCACTCGGTTCCATTGCCGTTGAGTAGAGCTGTCCTGA--TGCATATCTCAACG---T------ATTGATTCAAACAAGAA
droMoj3 scaffold_6328:2897048-2897148 - CG------------------------------GGTACA-GCCGTACTCTACGCTTTTGGGA-ACGAG--CAATCATACAAAGCCACTCGGTTCCATAGCCGTTGAGTAGAGCTGCCCCCGTTTGCACATCACAAC----------------------------
droGri2 scaffold_15081:2040911-2041055 - AAGTACGGC---AGTTCGATAACCAACAC--AGGTCCA-GCCGTATTCAGCGCTTTTGGAA-GTAAG--GAACATGAT----TCTCCTAGTTTCAATGCCGCTGAGTAAAGCTGTCCCAA--TGCAAATCGCAACG---TAACTGAATCGAATCAATCAATAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAGTA---------GATTGGCGGCACAATCTGCAATCTACGCCACTGGCTTACGTTGTGGTCGAGAATCGTGTCCAGTGCCGTATATTGCAGTTGTGTGGACGCAAACGGCAGCAGCGAAGGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
--------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-27.7,  p-value=0.009901 dG=-27.4,  p-value=0.009901

droSim1

dG=-27.7,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.1,  p-value=0.009901

droSec1

dG=-24.2,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droYak2

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-21.6,  p-value=0.009901

droEre2

dG=-20.2,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901

droAna3

dG=-27.5,  p-value=0.009901 dG=-27.1,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-24.3,  p-value=0.009901 dG=-24.0,  p-value=0.009901 dG=-23.6,  p-value=0.009901

droVir3

dG=-25.9,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.2,  p-value=0.009901 dG=-24.9,  p-value=0.009901

droMoj3

dG=-26.3,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.5,  p-value=0.009901

droGri2

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

Generated: 03/07/2013 at 07:18 PM