Secondary structure and small RNA-seq evidence for dme-mir-997

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:15152661-15152905 - CAATTAA-TATGTAGTTTA---------------TGGAT-----CCTCTTTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAAGAGCGACAGTC-CTGGAGAAGTTATCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCC--------GTCTCTGAAAACGTCTTCAG-CAGAAGTTGTTTTTAGCGAAGTGAAACTCATT-CGATTTTGATCATACTA-ACGA---CATTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATA
droSim1 chr3R:6329088-6329350 + CAATAAA-TATGTAGTTTTGGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAACTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-ACGACATTTGTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATT
droSec1 super_25:615309-615568 + CAATAAA-TATGTAGTTTTAGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAACAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAATTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-A---CATTTGTGGAT------G-CTTG-----GATCGTCA----GTTTGGTGGAATATT
droYak2 chrU:8935876-8936155 - AAAATAAAAGTTGAATTTTGAAAAATAAA--ATTTCCAA-----TTTTTGACCATGATTTTTGAACGTTTGCCGAAAATCGT----GTTTCTGCGACTATAAATATCCGTATTTTGATCATAACTTTCGAAATATTGGTCCAATCA-TGGAATGCCACAC-CTCGTTGAGTTC-----------------------GTAATTAAATTTCCAATCGAACTGTGTTTA---------AAAA-TAAAAGTTGAATTTTGAAAAATAAAATTT--CCAATTTTTGACCATG---------ATTTTTGAAC------G-TTTGCCGAAAATCG--T----GTTTCTGCGACTATA
droEre2 scaffold_4784:21223629-21223900 - CAAGACG--------CCTTAAA-----GCGAGTTCAGCTTTACTGTTCTA-GAATGCAGTTTAT----ATACCCAAACTCGAAGGAGTTCCACA------------------------------------------------TTAAGAAGAGCAGCAGAAGCAGAAAAAAATGTCTGGACCCTTGAAATTCATTTTGCAAATGCATTTCCATT------GGCTCGGAAATCTTTCTCTGTCAGGTGTTGATTTTTTAAAAGTGGAGCTCATT-CGATTTTGAATATATAAAATAACAGTTCTTGATATGTATGAGTTG-----GATTTGCACCTTGTCTGACAGAAAAAC
droAna3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:15152661-15152905 - CAATTAATATGTAGTTTA---------------TGGATCCTCTTT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAAGAGCGACAGTC-CTGGAGAAGTTATCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCC--GTCTCTGAAAACGTCTTCAG-CAGAAGTTGTTTTTAGCGAAGTGAAACTCATTCGATTTTGATCATACTA-ACGACAT---TGGATG-------CTTGGATCGGCA----GTTTGGTGGAATATA
droSim1 chr3R:6329088-6329350 + CAATAAATATGTAGTTTTGGATACTCGCCAGTCAGGATGCTCTGT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCA--GTCTCTGAAAACTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTA-ACGACATTTGTGGATG-------CTTGGATCGGCA----GTTTGGTGGAATATT
droSec1 super_25:615309-615568 + CAATAAATATGTAGTTTTAGATACTCGCCAGTCAGGATGCTCTGT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAACAAAATTCATA-TGATGATGCATTTTCA--GTCTCTGAAAATTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTA-A---CATTTGTGGATG-------CTTGGATCGTCA----GTTTGGTGGAATATT
droEre2 scaffold_4784:21223629-21223900 - CAAGAC-------GCCTTAAA-----GCGAGTTCAGCTTTACTGTTCTAGAATGCAGTTTATATACCCAAACTCGAAGGAGTTCCACATTAAGAAGAGCAGCAGAAGCAGAAAAAAATGTCTGGACCCTTGAAATTCATTTTGCAAATGCATTTCCATTGGCTCGGAAATCTTTCTCTGTCAGGTGTTGATTTTTTAAAAGTGGAGCTCATTCGATTTTGAATATATAAAATAACAGTTCTTGATATGTATGAGTTGGATTTGCACCTTGTCTGACAGAAAAAC

Small RNA-sequencing read pileup

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

Secondary Structure

dm3

dG=-58.9,  p-value=0.009901 dG=-58.5,  p-value=0.009901 dG=-58.3,  p-value=0.009901 dG=-57.9,  p-value=0.009901

droSim1

dG=-61.6,  p-value=0.009901 dG=-61.0,  p-value=0.009901

droSec1

dG=-59.3,  p-value=0.009901 dG=-58.7,  p-value=0.009901

droYak2

dG=-28.1,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.7,  p-value=0.009901

droEre2

dG=-51.8,  p-value=0.009901 dG=-51.8,  p-value=0.009901 dG=-51.6,  p-value=0.009901 dG=-51.6,  p-value=0.009901 dG=-51.3,  p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 08:25 PM