Secondary structure and small RNA-seq evidence for dme-mir-4939

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:18872718-18872857 - ATGCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGATCTCTACCAATTTTCCTTGCACTCT------TTGTCCTTTCCAAAAGTGACACGGGT----GCAGGTGAAGATTCG---GAAGAGGACGACGAAAACGACT---GCAAC-CGGACGACTCTTGGT
droSim1 chr2R:17459524-17459663 - ATCCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGAT----GCAGGTGAAGATTCG---GAGGAGGACGACAGCGAAGACT---GCAAC-AGGACGACTCTTGGT
droSec1 super_9:2164747-2164886 - ATCCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGAT----GCAGGTGAAGATTCA---GAGGAGGACGACAGCGAAGACT---GCAAC-AGGACGACTCTTGGT
droYak2 chr2R:18832811-18832950 - AACCGCGTTTATTTGCCAAAATG------------------------------------------C---------------------------------------TGCTCCGAGCTCTACCACTTCTGCTCACACTCTGTGTGTTGGTCCTCTCCAACGACGACACGGAT----GCAGATGAAGAAGAG---GAAGAGGACGA------CGACT---GCAAC-AAGGCGACTCTTGGT
droEre2 scaffold_4845:20234099-20234238 - AACCACGTTTATTTGCCATAATG------------------------------------------C---------------------------------------TGCTCCGAACTCTGCTC------CTTACGCTCTTCGTGTTTGTCCTTGCCAAAAACGATACGATT----GCAGAAGTAGAGGAA---GAGTCGGACGAGGACGAAGGAT---GCAAC-AAGGCGACTCTTGGT
droAna3 scaffold_13266:15204126-15204261 - ATTTAAGA-GCTTTTCCCTTCAAAGCCT----------------------------------------------------------------------------------------------AAACAGTTGACACAAAATGTGGCTACCCTTCTTGCTAGTGGCACTGCC----TTGGGGGACTGTGGTGGG---GGGAGGTCCTCTGACATTGGCCAATCTTAGCCGAATCATTGGA
dp4 chr3:14089101-14089284 - AAGCA-ATTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTT----------------------------------------------AGTAACTCCCAGAACAACAAAATGAA---CAAAGCTCGATCCGCGTTC---GCCGC-CGCCCTTCTTTTGCT
droPer1 super_4:1228949-1229132 + AAGCA-ATTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTT----------------------------------------------AGTAGCTCCCAGAACAACAAAATGAA---CAAAGCTCGATCCGCGTTC---GCCGC-CGCCCTTCTTTTGCT
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6496:24343095-24343103 - AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC
droGri2 scaffold_15112:3934700-3934745 - ATATTCAATATGCT-------------------------------------------GAGCACATC---------------------------------------TTCTGAAAGCATTTCAGACTTTC--------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:18872718-18872857 - ATGCACATTTATTTGGCATCATGCTTCTGCGATCTCTACCAATTTTCCTTGCACTCT------TTGTCCTTTCCAAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAACGACTGCAACCGGACGACTCTTGGT
droSim1 chr2R:17459524-17459663 - ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCAGGTGAAGATTCGGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droSec1 super_9:2164747-2164886 - ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCAGGTGAAGATTCAGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droYak2 chr2R:18832811-18832950 - AACCGCGTTTATTTGCCAAAATGCTGCTCCGAGCTCTACCACTTCTGCTCACACTCTGTGTGTTGGTCCTCTCCAACGACGACACGGATGCAGATGAAGAAGAGGAAGAGGACGAC------GACTGCAACAAGGCGACTCTTGGT
droEre2 scaffold_4845:20234099-20234238 - AACCACGTTTATTTGCCATAATGCTGCTCCGAACTCTGCTCCTT------ACGCTCTTCGTGTTTGTCCTTGCCAAAAACGATACGATTGCAGAAGTAGAGGAAGAGTCGGACGAGGACGAAGGATGCAACAAGGCGACTCTTGGT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATCCACATTTATTTGGCATCATGCTTCTGCGAGCT----------CTACCACTTCTCCTTGCACTCTTTGTCC-------------------------------------------TTTCCAAAAGCGACACTGATGCAGGTGAAGAT--------TCGGAGGAGGACGACAGC-----GAA------------GACTGCAACAGGACGACTCTTGGTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AAGCA-ATTAGTTTGCCATTTGCCA-------TCTTATCGGGGTAATACCCAATC-----CAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGA------------------AATTTTAGTAACTCCCAG---AACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-38.7 -38.3 -38.2 -37.9 -37.8 -37.8

droSim1

-31.8 -31.8 -31.7 -31.3 -31.3 -31.3

droSec1

-29.2 -29.2 -28.8 -28.8 -28.7 -28.7

droYak2

-30.9 -30.8 -30.3 -30.2 -30.1 -30.1

droEre2

-26.7 -26.7 -26.7 -26.7 -26.7 -26.7

droAna3

-26.7 -26.4 -26.3 -26.3 -26.3 -26.1

dp4

-15.1 -14.8 -14.8 -14.8 -14.7 -14.7

droPer1

-15.9 -15.9 -15.3 -15.3 -15.3 -15.2

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

-5.0 -4.8

Generated: 01/05/2013 at 05:21 PM