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 + GAGAGCCCCAGCAGAGTGAGTA-------GCGA---------------------------------------------------------------------------------TGGGG-GTCAGATGG-----------------------------------------------------------CCGTGGAA----GATATGTGACGATTGCC--------------------------------------------------------------------------------------------------CCCTTAC----------T---------------------ACTATCGTC---TGCTCAACAGGAAAGCAAACTACAT

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

-26.5 -26.3 -25.8

droSim1

-13.9 -13.9 -13.9 -13.8 -13.8 -13.8

droSec1

-15.7 -15.6 -15.4 -15.1 -14.9 -14.8

droYak2

-21.2

droEre2

-11.7 -11.4 -11.2 -10.9 -10.9

droAna3

-23.0 -23.0 -22.5 -22.5 -22.2 -22.2

dp4

-25.0 -24.6 -24.4 -24.0

droPer1

-20.5 -19.9 -19.9 -19.7

droWil1

-19.5 -19.5 -19.5 -19.3 -19.3 -19.3

droVir3

-49.1 -48.9 -48.9 -48.8 -48.7 -48.7

droMoj3

-12.9 -12.6 -12.1 -12.1 -11.9

droGri2

-46.7 -46.5 -46.4 -46.4 -46.2 -46.2

Generated: 01/05/2013 at 05:20 PM