Secondary structure and small RNA-seq evidence for dme-mir-976

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19452913-19453039 + AAC------------------G-----GCGGTG-GTGGGCAT--------------------------CG-----CCATGCAGTGCCGCGGCATTGGTGAGGC-CATCTCCAATGG-ATTAGTTCT---CA------ACATTGGATTAGTTATCATCAATGCCGGTGCACTGCACC--TAACAACATC---------------GCGCCGG
droSim1 chrX:15018511-15018617 + -----------------------------------------------------------------------------ATGCAGTGTCGTGGCATTGGTGAGGA-CATCTCCAATGG-ATTGGTTCT---CA------TCATTGGATTAGTTATCATCAATGCCGGTGCACTGCACTGCTGTCAACTTC---------------GCGCAAT
droSec1 super_8:1735239-1735349 + TCC------------------G------------------------------------------------------CATGCAGTGCCGTGGCATTGGTGAGGA-CATCTCCAATGG-CTTAGTTCT---CA------TCATTGGATTAGTTATCATCAATGCCGGTGCACTGCAGC--TGTCAACTTC---------------GCGCAAT
droYak2 chrX:11885798-11885920 - AGA------------------G--------GTGAGTGAGAAT--------------------------CG------CATGCAGTGCCACGACATTGGTGAGGG-CATCTCCAATGG-----GGACCCGGCA------TCATTGGATTAGTTCTCATTAATGCCGGAGCACTGCACC--TACCAACTTC---------------GCACGGT
droEre2 scaffold_4690:9688892-9689017 + TCC------------------A-----GAGGTGTGCCAGAAT--------------------------CG------CATGCAGTGCCTCGACATTGGTGAGGG-CATCTCCAATGG--GGAGCCAG---CA------TCATTGGATTAGTTCTCATTAATGCCGGAGCATGGCACC--TACGAACTGA---------------GCATTTG
droAna3 scaffold_13417:2467561-2467679 - GCT------------------A-----CCGATG-------------------------------------CTCCCCGAAGGAGCGCCTCGACATTGGTGAGTT-CATCTCCAATGG--TCAGTAGC---CC------GCATTGGATTAGTTCTCATTGATGGCGAAGCGAGT--CC--TACCCCCACA---------------CCAGCGA
dp4 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7956743-7956912 + CTCTCCCCTTCCTTCTTACACA-----GGATTATG-TAGGAT--------------------------TA------T-GGCAACACCTCGATATTGGTGAGTTCCAGCTCCAATGTTATTGGAGCCCAACATTGAACACATTGGATTAGTTCTCATCGATGGCGAAGTGTTT-GTGAGCAATATCGTATATTGTGCGTGCAGTGTATTGT
droVir3 scaffold_13042:906708-906880 - ATC------------------GTTATCGTTATC-GTTATCGTTATCAGAATTAATTATCGTTGAAGTGCGTTCTTTGGTGCAGCCCCTCGCGATTGATGATAG-CATCTCCAATGA-----GCATA---TC------ACATTGGATTAGTTCTCATCGATGCCGATGCGCTGTACCAGCAACAACAAC---AGGAATAGCAACGGAAACA
droMoj3 scaffold_6328:2900970-2901098 - TAT------------------C-----GTTATC-GCTAGCGA--------------------------CGCTTC-GGGTGCAGCCCCTCGCGATTGATGAAAG-CATCTCCAATGA-----GTATT---TC------GCATTGGATTAGTTCTCATCGATGTCGATGCGCTGTATCAGCAACAACAAC---------------AACATGA
droGri2 Unknown ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19452913-19453039 + AAC------------------G-----GCGGTG-GTGGGCAT--------------------------CG-----CCATGCAGTGCCGCGGCATTGGTGAGGC-CATCTCCAATGG-ATTAGTTCT---CA------ACATTGGATTAGTTATCATCAATGCCGGTGCACTGCACC--TAACAACATC---------------GCGCCGG
droSim1 chrX:15018511-15018617 + -----------------------------------------------------------------------------ATGCAGTGTCGTGGCATTGGTGAGGA-CATCTCCAATGG-ATTGGTTCT---CA------TCATTGGATTAGTTATCATCAATGCCGGTGCACTGCACTGCTGTCAACTTC---------------GCGCAAT
droSec1 super_8:1735239-1735349 + TCC------------------G------------------------------------------------------CATGCAGTGCCGTGGCATTGGTGAGGA-CATCTCCAATGG-CTTAGTTCT---CA------TCATTGGATTAGTTATCATCAATGCCGGTGCACTGCAGC--TGTCAACTTC---------------GCGCAAT
droYak2 chrX:11885798-11885920 - AGA------------------G--------GTGAGTGAGAAT--------------------------CG------CATGCAGTGCCACGACATTGGTGAGGG-CATCTCCAATGG-----GGACCCGGCA------TCATTGGATTAGTTCTCATTAATGCCGGAGCACTGCACC--TACCAACTTC---------------GCACGGT
droEre2 scaffold_4690:9688892-9689017 + TCC------------------A-----GAGGTGTGCCAGAAT--------------------------CG------CATGCAGTGCCTCGACATTGGTGAGGG-CATCTCCAATGG--GGAGCCAG---CA------TCATTGGATTAGTTCTCATTAATGCCGGAGCATGGCACC--TACGAACTGA---------------GCATTTG
droAna3 scaffold_13417:2467561-2467679 - GCT------------------A-----CCGATG-------------------------------------CTCCCCGAAGGAGCGCCTCGACATTGGTGAGTT-CATCTCCAATGG--TCAGTAGC---CC------GCATTGGATTAGTTCTCATTGATGGCGAAGCGAGT--CC--TACCCCCACA---------------CCAGCGA
droWil1 scaffold_181096:7956743-7956912 + CTCTCCCCTTCCTTCTTACACA-----GGATTATG-TAGGAT--------------------------TA------T-GGCAACACCTCGATATTGGTGAGTTCCAGCTCCAATGTTATTGGAGCCCAACATTGAACACATTGGATTAGTTCTCATCGATGGCGAAGTGTTT-GTGAGCAATATCGTATATTGTGCGTGCAGTGTATTGT
droVir3 scaffold_13042:906708-906880 - ATC------------------GTTATCGTTATC-GTTATCGTTATCAGAATTAATTATCGTTGAAGTGCGTTCTTTGGTGCAGCCCCTCGCGATTGATGATAG-CATCTCCAATGA-----GCATA---TC------ACATTGGATTAGTTCTCATCGATGCCGATGCGCTGTACCAGCAACAACAAC---AGGAATAGCAACGGAAACA
droMoj3 scaffold_6328:2900970-2901098 - TAT------------------C-----GTTATC-GCTAGCGA--------------------------CGCTTC-GGGTGCAGCCCCTCGCGATTGATGAAAG-CATCTCCAATGA-----GTATT---TC------GCATTGGATTAGTTCTCATCGATGTCGATGCGCTGTATCAGCAACAACAAC---------------AACATGA

Small RNA-sequencing read pileup

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

Secondary Structure

dm3

dG=-28.6,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droSim1

dG=-28.4,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.7,  p-value=0.009901

droSec1

dG=-27.8,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.0,  p-value=0.009901

droYak2

dG=-26.6,  p-value=0.009901

droEre2

dG=-26.9,  p-value=0.009901 dG=-26.2,  p-value=0.009901

droAna3

dG=-21.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-24.1,  p-value=0.009901 dG=-24.0,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-23.3,  p-value=0.009901

droVir3

dG=-21.0,  p-value=0.009901 dG=-20.0,  p-value=0.009901

droMoj3

dG=-21.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:17 PM