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

-37.0 -36.7

droSim1

-37.0 -36.9 -36.7 -36.4

droSec1

-33.5 -33.4 -33.2

droYak2

-31.8 -31.7 -31.6 -31.5 -31.4 -31.3

droEre2

-29.3 -29.2 -29.2 -29.1 -29.1 -29.0

droAna3

-35.4 -35.2 -35.2 -35.1 -35.0 -34.9

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-29.2 -28.8 -28.5 -28.4 -28.2 -28.2

droVir3

-29.4 -28.9 -28.9 -28.7 -28.4

droMoj3

-28.2 -28.2 -27.7 -27.7 -27.5 -27.5

droGri2

-30.8 -30.3 -30.0 -29.9

Generated: 01/05/2013 at 05:34 PM