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

-44.5 -44.3 -44.2

droSim1

-43.1 -42.9 -42.6 -42.4 -42.4 -42.2

droSec1

-44.4 -44.1 -43.9 -43.6

droYak2

-43.6

droEre2

-37.0 -36.0

droAna3

-32.4 -31.5 -31.5 -31.4

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-31.2 -31.2 -31.2 -31.1 -31.1 -31.1

droVir3

-39.8 -39.7 -39.3 -39.2 -39.2 -39.0

droMoj3

-35.7 -35.5

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:33 PM