Secondary structure and small RNA-seq evidence for dme-mir-210

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:18022237-18022366 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSim1 chrX_random:4635946-4636075 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSec1 super_8:332193-332322 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droYak2 chrX:16646312-16646441 + CCATG-----------------------------------------------TCGCGAA-----CCGAAAGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCATA
droEre2 scaffold_4690:8350125-8350254 + CCACG-----------------------------------------------TCGCGAA-----CCAAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCACA
droAna3 scaffold_13335:1603991-1604112 - GC--G------------------------------------------------------------TTAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACCAATCAACTGACCA--C-------------------------------------------------CAG----------ATC
dp4 chrXL_group3a:1970441-1970623 - ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAG------TT---TC
droPer1 super_11:2708510-2708698 + ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACAAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGT-TTCATTCCA--
droWil1 scaffold_181096:12033222-12033334 + CAATC-----------------------------------------------GCAAAAG-----CATAACGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCAGAAAACGACCAG--------------------------------------------------------------------------------
droVir3 scaffold_12928:1257190-1257317 - T---A-----------------------------------------------TATTTAA-----ACGAGCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGAGAAACAGCGAAT-ATT----------------------------------------------------------TAACTATTTTTCC---
droMoj3 scaffold_6473:13732313-13732476 + CCACATATACAGAGCATATATGTATATGCATATATCATACAAGTATATAGAATCCAGATCCATTGGGAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGATGCCAGAGAAGCAACA---------------------------------------------------------------------------------
droGri2 scaffold_15203:8453543-8453644 + ----------------------------------------------------------------------GGAGCTTATTGGAGCTGCTGGCCACTGCACAAGATTAGATTCAAAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGATA----ACAT-----C----------------------------------------------------------AAGCCAT---------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:18022237-18022366 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSim1 chrX_random:4635946-4636075 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droSec1 super_8:332193-332322 + CCACG-----------------------------------------------TCCGGAA-----CCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-----C----------------------------------------------------------CAGCCATTGTTCCATC
droYak2 chrX:16646312-16646441 + CCATG-----------------------------------------------TCGCGAA-----CCGAAAGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCATA
droEre2 scaffold_4690:8350125-8350254 + CCACG-----------------------------------------------TCGCGAA-----CCAAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAA-----C----------------------------------------------------------CAGCCATCGTCCCACA
droAna3 scaffold_13335:1603991-1604112 - GC--G------------------------------------------------------------TTAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACCAATCAACTGACCA--C-------------------------------------------------CAG----------ATC
dp4 chrXL_group3a:1970441-1970623 - ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAG------TT---TC
droPer1 super_11:2708510-2708698 + ATATG-----------------------------------------------T---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAA---ACTAAACAAACAAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGT-TTCATTCCA--
droWil1 scaffold_181096:12033222-12033334 + CAATC-----------------------------------------------GCAAAAG-----CATAACGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCAGAAAACGACCAG--------------------------------------------------------------------------------
droVir3 scaffold_12928:1257190-1257317 - T---A-----------------------------------------------TATTTAA-----ACGAGCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGAGAAACAGCGAAT-ATT----------------------------------------------------------TAACTATTTTTCC---
droMoj3 scaffold_6473:13732313-13732476 + CCACATATACAGAGCATATATGTATATGCATATATCATACAAGTATATAGAATCCAGATCCATTGGGAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTCA--AGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGATGCCAGAGAAGCAACA---------------------------------------------------------------------------------
droGri2 scaffold_15203:8453543-8453644 + ----------------------------------------------------------------------GGAGCTTATTGGAGCTGCTGGCCACTGCACAAGATTAGATTCAAAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGATA----ACAT-----C----------------------------------------------------------AAGCCAT---------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CCACGTCCGGA-----ACCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTTAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAG-------CCAGCCA-----------------------------------------TTGTTCCA---TCSizeHit CountTotal NormTotalGSM343915
Embryo
.......................................................................CTTGTGCGTGTGACAGCGGCTAT............................................................................................23132.003232
........................................................................TTGTGCGTGTGACAGCGGCTAT............................................................................................22129.002929
........................................................................TTGTGCGTGTGACAGCGGCT..............................................................................................20111.001111
.......................................................................CTTGTGCGTGTGACAGCGGCTA.............................................................................................22110.001010
.......................................................................CTTGTGCGTGTGACAGCGGCT..............................................................................................2115.0055
........................................................................TTGTGCGTGTGACAGCGGCTA.............................................................................................2114.0044
...................................AGCTGCTGGCCACTGCACAAGA.................................................................................................................................2212.0022
...................................AGCTGCTGGCCACTGCACAAGAT................................................................................................................................2312.0022
...................................AGCTGCTGGCCACTGCACAAGATT...............................................................................................................................2411.0011
........................................................................TTGTGCGTGTGACAGCGGC...............................................................................................1911.0011
.......................................................................CTTGTGCGTGTGACAGCGGC...............................................................................................2011.0011
dp4
ATATGT---GATTTAGCTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTTAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAAACTAAACAAACCAAAAAGGAAGTTGAACGCCTAATGCAATCGATGAGTGTTGGGTTGCTTCAGTTTCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.......................................................................CTTGTGCGTGTGACAGCGGCTAT............................................................................................23153563.00535632353540
.......................................................................CTTGTGCGTGTGACAGCGGCT..............................................................................................21147134.0047134847126
........................................................................TTGTGCGTGTGACAGCGGCTAT............................................................................................22142465.00424652542440
........................................................................TTGTGCGTGTGACAGCGGCT..............................................................................................20122563.0022563822555
.......................................................................CTTGTGCGTGTGACAGCGGCTA.............................................................................................22118745.0018745618739
........................................................................TTGTGCGTGTGACAGCGGCTA.............................................................................................21118036.0018036718029
........................................................................TTGTGCGTGTGACAGCGGC...............................................................................................19115366.0015366015366
.......................................................................CTTGTGCGTGTGACAGCGGC...............................................................................................2014416.00441654411
.......................................................................CTTGTGCGTGTGACAGCGG................................................................................................1912266.00226602266
.......................................................................CTTGTGCGTGTGACAGCGGCTATT...........................................................................................2411867.00186701867
........................................................................TTGTGCGTGTGACAGCGGCTATT...........................................................................................2311631.00163101631
........................................................................TTGTGCGTGTGACAGCGG................................................................................................1811549.00154901549
.......................................................................CTTGTGCGTGTGACAGCG.................................................................................................181153.001530153
.........................................................................TGTGCGTGTGACAGCGGCTAT............................................................................................21149.0049049
..........................................................................GTGCGTGTGACAGCGGCTAT............................................................................................20130.0030030
...................................AGCTGCTGGCCACTGCACAAGA.................................................................................................................................22129.0029227
...................................AGCTGCTGGCCACTGCACAAGAT................................................................................................................................23128.0028226
.........................................................................TGTGCGTGTGACAGCGGCT..............................................................................................19123.0023023
.........................................................................TGTGCGTGTGACAGCGGCTA.............................................................................................20120.0020020

Secondary Structure

dm3

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droSim1

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droSec1

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droYak2

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droEre2

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droAna3

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

dp4

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droPer1

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droWil1

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droVir3

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droMoj3

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droGri2

dG=-28.4,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901

Generated: 03/07/2013 at 04:53 PM