Secondary structure and small RNA-seq evidence for dme-mir-4957

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:15213971-15214085 - CTTTTTTTT--------------CTCTGCTC----GT-----------------------T--GTA--------TTTTACGCA--CTCTGCTGGCAGCG---CTGTCGGC---GTCGCTGCCAGCTGCCAGCAGCGAGCGGTACACTT--------GCAACTATC-----CTGT-GCACCCTACAATT
droSim1 chrX:11736931-11737042 - CTTTTTTTTTTTT----------CTCTGCTC----GT-----------------------T--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---AGCGCTGCCA-------GCAGCGAGCGGTACACTT--------GCAACTATC-----CTGC-GCACCCTACAATT
droSec1 super_56:101687-101796 - CTTTTTTTTT--T----------CTCTGCTC----GT-----------------------T--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---AGCGGTGCCA-------GCAGCGAGCGGTACACTT--------GCAACTATC-----CTGC-ACACCCTACAATT
droYak2 chrX:9414156-9414285 - TTTTTTT----------------CTCTGCTC----GTTTTTCTCTCTTTTTCTTCTCGCCT--GCA--------TTTTACGCA--CTCTGCTAGCAGCG---ACGCCGAC---TGCGCTGCCA-------ACAGCAAGCGGTACACTT--------GCAACTATT-----CTAT-GCACCCTACAATT
droEre2 scaffold_4690:11807313-11807440 + TTTTTT-----------------CTCCGCTC----GTTTTTCTCTCCTTTTCTGCTCGCCT--GCA--------TTTTACGCA--CTCTGCTGGCAGCG---ACGCCGAC---TGCGCTGCAA-------ACAGCGAGCGGTACACTT--------GCAACTATT-----CTGT-GCACCCTACAATT
droAna3 scaffold_13117:1427273-1427395 - ATTTTTCTTC---CCATGCAACC-TGTGTCC----AT-----------------------TGTACG--------TTTTACGCA--CTCTCC--CCAGCA---ACACCGCC---GCCGATAGCG-------ACTGCGACGAGTACGTTG--------GCAGCGGCACTTGACTCT-TTTTGCGGCAATT
dp4 chrXL_group1e:12152468-12152588 - CTTTAGCTTT---TTG--------------CGTTTGCGTTTGCCCCGATTTCAATGCA-AT--GTG--------TTGTACGCA--CACGGGTT---TTT---ATCTCAGC---TGTGGGATGA-------ACGGC--CCGAGACACTT--------GC--CGATG-----CGGC-GA-CCC--CAGGC
droPer1 super_14:1456573-1456693 + CTTTAGCTTT---TTG--------------CGTTTGCGTTTGCCCCGATTTCAATGCA-AT--GTG--------TTGTACGCA--CACGGGTT---TTT---ATCTCAGC---TGTGGGATGA-------ACGGC--CCGAGACACTT--------GC--CGATG-----CGGC-GA-CCC--CAGGC
droWil1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12928:4095173-4095244 - CTCTTTATTG---CAA--------------------------------TGCGAC-----------------------TACGCATGATTTAGGCGCAGGT---TGGTCG----------------------------------ACACTT--------GCATTGGTT-----GC--------AAGTACTT
droMoj3 scaffold_6680:3750941-3751063 - TTTGTTTTTG---TTT-----------TCTT----TT-----------------------T--GTAGCCTAGGAATTTACC-----TCTTGTGGCATATCAGCTGTTGGC---TTTGGTTGCA-------AACACACG--TTGACTTTTCACACACAGAATTCTG-----TTGAAATGTTTAACACTT
droGri2 scaffold_14853:566008-566117 + CTCTTTTATT----------------------------------GCAATGAGACTGCG-AC--GCA--------TGATTTGGG--CGCAGG-------T---CTATCACCACTTGCACTGACG-------ACTGCTTTTGCTTTTGCT--------ACTACTTTT-----ACTT-GCCAGCGGAACTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:15213971-15214085 - CTTTT----TTTTCTCTGCTCGTTGTATTTTACGCACTCTGCTGGCAGCGCTGTCGGCGTCGCTGCCAGCTGCCAGCAGCGAGCGGTACACTTGCAACTATCCTGTGCACCCTACAATT
droSim1 chrX:11736931-11737042 - CTTTTTTTTTTTTCTCTGCTCGTTGCATTTTACGCACTCTGCTGGCAGCGACGCCGACAGCGC-------TGCCAGCAGCGAGCGGTACACTTGCAACTATCCTGCGCACCCTACAATT
droSec1 super_56:101687-101796 - CTTTTT--TTTTTCTCTGCTCGTTGCATTTTACGCACTCTGCTGGCAGCGACGCCGACAGCGG-------TGCCAGCAGCGAGCGGTACACTTGCAACTATCCTGCACACCCTACAATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTTTTTTTTTTTTC-------------------TCTGCTCGTTGCATTTTACGCACTCTGCTGG-CAGCGACGCCGACAGCGCTG-------------------CCAGCAGCGAGCGGTACACTTGCAACTATCCTGCGCACCCTACAATTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTTTAGCTTTTTGCGTTTGCGTTTGCCCCGATTTCAATGCAATGTGTTGTACGCACACGGGTTTTTATC----------------TCAGCTGTGGGATGAACGGC---------CCGAGACACTTGC--CGATGCGGCGACCC---CAGGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
................................................................TTATC----------------TCAGCTGTGGGATGA...................................................2011.00110
......CTTTTTGCGTTTGCGTTTGCC............................................................................................................................2111.00101

Secondary Structure

dm3

-35.9 -35.9 -35.1 -35.1 -35.1 -35.1

droSim1

-35.3 -34.5 -34.5

droSec1

-31.2 -30.4 -30.4

droYak2

-19.7 -19.0 -18.9 -18.9

droEre2

-24.9 -24.9 -24.4 -24.4 -24.4 -24.3

droAna3

-18.3 -18.1 -18.0 -17.9 -17.9 -17.9

dp4

-27.0 -27.0 -26.0 -26.0 -26.0 -26.0

droPer1

-27.0 -27.0 -26.0 -26.0 -26.0 -26.0

droWil1

No secondary structure predictions returned

droVir3

-12.4

droMoj3

-16.9 -16.6 -16.5 -16.2 -16.2 -16.1

droGri2

-14.4 -14.1 -14.1 -14.0 -13.7 -13.7

Generated: 01/05/2013 at 05:24 PM