Secondary structure and small RNA-seq evidence for dme-mir-4917

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:14093563-14093669 + GAGAGCCCCAGCAGAGTGAGTA-------GCGA---------------------------------------------------------------------------------TGGGG-GTCAGATGG-----------------------------------------------------------CCGTGGAA----GATATGTGACGATTGCC--------------------------------------------------------------------------------------------------CCCTTAC----------T---------------------ACTATCGTC---TGCTCAACAGGAAAGCAAACTACAT
droSim1 chrX_random:3764305-3764407 + GAGAGCCCC---AGAGTGAGTA-------GCGA---------------------------------------------------------------------------------TGGGG-GTCAGATG-------------------------------------------------------GATGGCCGTGGAT----GATATGTGACGATTGCC----------------------------------------------------------------------------------------------------CTTAC----------T------------------------ACGCTC---TGCCCAACAGGAAAGCAAGCTACAT
droSec1 super_20:697977-698075 + GAGAGCCCC---AGAGTGAGTA-------GCGA---------------------------------------------------------------------------------TGGGG-GTCAGATGG-----------------------------------------------------------CCGTGGAT----GATATGTGACGATTGCC----------------------------------------------------------------------------------------------------CTTAC----------T------------------------ACGCTC---TGCCCAACAGGAAAGCAAGCTACAT
droYak2 chrX:8347469-8347564 + GAGAGCCCC---AGAGTAAGTA-------GCCA---------------------------------------------------------------------------------GGGGG-ATCAGGAGG-----------------------------------------------------------CCGCGGAA----GGTATGTGATGATTCCC-----------------------------------------------------------------------------------------------------------------------------------------ATTACCCTC---CGATCCACAGGAAAGCAACCTACAT
droEre2 scaffold_4690:12836867-12836962 - GAGAGCCCC---AGAGTGAGTA-------CGCA---------------------------------------------------------------------------------GTCGG-GTCAGAAGG-----------------------------------------------------------CCGCGGAA----GATATGTGATGATTCCC-----------------------------------------------------------------------------------------------------------------------------------------ATTCCCCTC---CGATCAACAGGAAAGCAACCTACAC
droAna3 scaffold_13047:1616598-1616749 + GATACCCCG---AGAGTGAGTTAAATA-----GGTAGACTGGGTTTTACGGGTTTTGGGGATTAGGGTTAAGGGGTTTAAGGATCAGGGACTTGGCTA----------------GAAGG-ACCAA------------------------------------------------------------------AGGA-CTTA-----------------AGAA------------------------------------------------------------------------------------------------CTAAC----------A---------------------AAAATTCAC---CATTCCACAGGCAAGCACGGTACAC
dp4 chrXL_group1e:6144259-6144391 - GAAAACTCC---AGAGTGAGTTGAGTGAGGTT-----------------------------------------------------------------------------------GAGAGCCGGGGTG-------------------------------------------------------------CTCGGAA----GA----------CCATCCTC-------------------------------------------------------------------------ACTGATCCTATTCTAATCTT-------CCCCTCTTTCGTCTATATCTCTC--------------TCTCTC---TCGTCCGCAGGCAAGCGAACTATAC
droPer1 super_21:1109353-1109492 - GAAAACTCC---AGAGTGAGTG-------GTTG-----------------------------------------------------------------------------------AGAGCCGGGGTGC-----------------------------------------------------------TCGCAA------GA----------CCTTCCTC-------------------------------------------------------------------------ACTGATCCTATTCTAATCTT-------CCCCTCTTTCGTCTATATCTCTCTCTCTCTCTCTCTCTCGCTC---TCGTCCGCAGGCAAGCGAACTATAC
droWil1 scaffold_180702:2428501-2428590 + GAGAACACA---AGGGTGAGTG-------GGAG---------------------------------------------------------------------------------GAGAG-ATGAGAGGA-----------------------------------------------------------GAATGGA------------------------------------------------------------------------------------------------------------------------CTTTAAC-CGCCATTATT------------------------T--CTT---TCTTCCACAGGGAAGTGAACTACAA
droVir3 scaffold_12970:1543996-1544230 - GAAAACACA---CGAGTAAGTG-------GACAACTATC---------------------------ACTATACCCC-----------------------------------------------AG-TAACCCTGGAGACACCTTCGACCC-ATGCTAACTTGCTGATTTTCGAGGGCTATGTTTGTAG-----CC-ATAT-----------------GCTATGTTACGGCAGTTTTAAGCTAGGTTCAGG------GTA-TCCTCCCAGCCGGGCCCTCTCGACCAGCGCAATCCTGCTCTAATAAATTTC------TTCAA----------C------------------------ATTTTCTATCCAACAGCAGTCAAGCGAAATACAG
droMoj3 scaffold_6359:2739408-2739517 - GAAAACACA---AGAGTGAGTG-------ACAA---------------------------------------------------------------------------------GATTT-ATATATATT-----------------------------------------------------------TATAGGA-ATAT-----------------AATA------------------------------------------------------------------------------------------CTAATTCTTAT-CTACGTTATT------CCC------------GTCTCACTC---AATCAATTAGTCGAGCCGAATACAT
droGri2 scaffold_15081:1312788-1313066 - GAAAACAGA---GGAGTAAGTACGATC-----AGCTCGC---------------------------ATTATACCCCGTAAGAGAAGGTTCCCTAATGAAATGGACAAACAGAAATAGAA-ATCAATTT-----GAAAATCGGTGCAAGGTAAAATTAACTTGAT---CTCTCCAGCATAAATATATAT-----AT-ATAC-----------------GCTG------GACAG-ATTAAGTTCATTTTAGATGGTCGATAACACTTTCAACA--CCTTTTTAAATCAATTTCAAACTGCTTTTATTCAATTATT-------AACGTTTATCGTT------------------------T--TAT---CTGTCAACAGTCGAGCGAAATACAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:14093563-14093669 + GAGAGCCCCAGCAGAGTGAGTAGCGATGGGGGTCAGA----TGGCCGTGGAAGATATGTGACGATTGCCCCCTTACTACTATCG-TCTGCTCAACAGGAAAGCAAACTACAT
droSim1 chrX_random:3764305-3764407 + GAGAGCCCC---AGAGTGAGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGATATGTGACGATTGCC--CTTACTAC----GCTCTGCCCAACAGGAAAGCAAGCTACAT
droSec1 super_20:697977-698075 + GAGAGCCCC---AGAGTGAGTAGCGATGGGGGTCAGA----TGGCCGTGGATGATATGTGACGATTGCC--CTTACTAC----GCTCTGCCCAACAGGAAAGCAAGCTACAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAGAGCCCCA---GAGTG-----AGTAGCGATGGGGGTCAGATGGATGGCCGTGGATGATATGTGACGATTGC--CCTTACTAC----G----------------------------------------CTCTGCCCAACAGGAAAGCAAGCTACATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GAAAACTCCA---GAGTGAGTTGAGTGAGGTTGAGAGCCG----GGGTG-CTCGGAAG----------ACCAT--CCTCACTGA----TCCTATTCTAATCTTCCCCTCTTTCGTCTATATCTCTCTCTCTCTCGTCCGCAGGCAAGCGAACTATACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-26.5,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.8,  p-value=0.009901

droSim1

dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.8,  p-value=0.009901

droSec1

dG=-15.7,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.4,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-14.9,  p-value=0.009901

droYak2

dG=-21.2,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droEre2

dG=-11.7,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-9.0,  p-value=0.009901

droAna3

dG=-23.0,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-20.0,  p-value=0.009901

dp4

dG=-25.0,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.4,  p-value=0.009901 dG=-24.0,  p-value=0.009901

droPer1

dG=-20.5,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.7,  p-value=0.009901

droWil1

dG=-19.5,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901

droVir3

dG=-49.1,  p-value=0.009901 dG=-48.9,  p-value=0.009901 dG=-48.9,  p-value=0.009901 dG=-48.8,  p-value=0.009901 dG=-48.7,  p-value=0.009901

droMoj3

dG=-12.9,  p-value=0.009901 dG=-12.6,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-11.9,  p-value=0.009901

droGri2

dG=-46.7,  p-value=0.009901 dG=-46.5,  p-value=0.009901 dG=-46.4,  p-value=0.009901 dG=-46.2,  p-value=0.009901 dG=-46.2,  p-value=0.009901

Generated: 03/07/2013 at 06:58 PM