Secondary structure and small RNA-seq evidence for dme-mir-4942

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:23332312-23332452 + TATGACATCTGCCTGTT-----------ATGAA-------TACATATATT-TTTATGTTTG--AG-TCAACATC--GA------------------------------------------GTTGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGGCATCGA----AATATGTCCATATCTAATATATAGTTCCATTCTGTTTTATT
droSim1 chr3L:22456065-22456207 + AATGACAGCTGCCTGTT-----------ATAAG-------TAATTGTATT-TTTATGTTTG--AGCTAAACATC--GA-----------------------------------------TTATGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGCCATCAA----AGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT
droSec1 super_41:217199-217341 + AATGACATCTGCCTGTT-----------GTAAG-------TAATTGTATT-TTTATGTTTG--AGCTAAACATC--GA-----------------------------------------TTATGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGCCATCAA----AGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT
droYak2 chr3L:23917805-23917956 + TATGATATCTGAATATTTAGTTTTTCTTTTGC---------ATATTTATT-TTTAATATTG--AGCTTCACATA--TA-----------------------------------------TATTGCCGATGTTTAC---AAAACATCGATGACATTGTT----------TTTGGCATCGT----CATATGCCCATCACTAATATATAGTCCCCTTCTGTTTCATT
droEre2 scaffold_4784:22817455-22817604 - GGC---ATCTGTATAGG-----------ATGAA-------TAAATTAATT-TTTAAGTTTG--ACCACAACTTT--CA-----------------------------------------TTTTGCCGATGTTTAG---AAAACATCGATGACACCGCA-----TCATCGTTGTCATCGACTTACATATGTACATCTCTAATATATAGTATCATTCTGTTTTATT
droAna3 scaffold_12916:14167403-14167537 + TGCT---------CGTT-----------AGAGA-------TGAT-AAACA-TCGATGTTGGCTTGCCAAACATC--GA-----------------------------------------TGTCAACGATGTTTTC---AAAACATCGATGACATCGAT----------GTTAACATCGA----TGTTTCTCCACCTCTGACCACTGGAGTGAATTATTTTTAGT
dp4 chrXL_group1e:10317112-10317245 + TCAAACATATTATTTTT--------ATTGTAAATATCCTA----------------GTTAT--GGTGTAAATCT--GA-----------------------------------------AAATATCGATGTTTGAGAAAAAACATCGATGACATCCAT----------GTTAACATCGA----TGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------
droPer1 super_69:203478-203603 - CATATT-----ATTATT-----------GTAAATATCCTA----------------TTTAT--AGTGTAAATCT--GA-----------------------------------------AAATATCGATGTTTGAGAAAAAACATCGATGACATCCAT----------GTTAACATCGA----TGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------
droWil1 scaffold_181155:90645-90784 - TATTGTTTCCGCCTCTT-----------CTGAT-------CAATCTATTT-CTAATTTATT--TGCT-AACTT---CTTCTCGACTACGTACATATCTACTACGTACAACTCTAGTCAGATATATCCATATCCTATAACG-----------------------------------------------------------AAATCCAACTGCATTCTTAATCGTG
droVir3 scaffold_13036:829247-829384 - TTTATCGTTTATATTTGAAATT------ATTAA-------TTAAATTATT-ATTATTTTTA--AGTAATACAAA-----------------------------------------------------------------ATAAATTAAGGAAATAAAAGTGCAAATTTGTTGTTTTCAA----AG-ATACATTTAATTAATTTTTATTTTTTTTTTATTTTATT
droMoj3 scaffold_6500:19787300-19787437 - TATTATG---AGCTGAA-----------ATAAA-------TATAAAAATA-TTTA--ATTA--AATTCAACAAAATGATGTC------------------------------------------TAGATATTAAA---AAAAAAAAAAAAAATAAAAT----------ATATATATATA----TATATATATATATAT-ATATATATATATATTTTTTTTTTTT
droGri2 scaffold_14853:4224791-4224937 - TATATC-TATGCGTCTGTAGATACT----TGCA-------TAAGTGTATCATCTATGTACG--GTTTACATATA--GT-----------------------------------------GT---ATGGTTTATAA---AAAATATTTCTCAATACGCC----------GTTAGTACAAA----AAAAAAGTAGTGTATAAAAAATGCTTGCACTTTGTTTTAGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:23332312-23332452 + TATGACATCTGCCTGTT-----------ATGAA-------TACATATATT-TTTATGTTTG--AG-TCAACATC--GA------------------------------------------GTTGCCGATGTTTGG---AAAACATCGATGACATCGCT----------GTTGGCATCGA----AATATGTCCATATCTAATATATAGTTCCATTCTGTTTTATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AATGACAGCTGCCTGTTATAAGTAATTGTATTTTTATGTTTGAGCTAAACATCGATTATGCCGATGTTTGG---AAAACATCGATGACATCGCTGTTGCCATCAAAGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATTSizeHit CountTotal NormTotalGSM343915
Embryo
.............................................................................................................................ATAGTTCCATTCTGTTATAT.2011.0011
dp4
TCAAACATATTATTTTTATT---GTAAATATCCTAGTTATGGTG-TAAATCTGAAAA-TATCGATGTTTGAGAAAAAACATCGATGACATCCATGTTAACATCGATGTTTGTCCAGCTTTAGCTTGCATCCCTAGCTTG-------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-29.2 -29.1 -28.9 -28.8 -28.7 -28.6

droSim1

-21.8 -21.7 -21.7 -21.6 -21.2 -21.2

droSec1

-21.8 -21.7 -21.7 -21.6 -21.2 -21.2

droYak2

-16.6 -16.5 -16.5 -16.4 -16.4 -16.3

droEre2

-19.6 -19.5 -19.4 -19.3 -19.2 -19.1

droAna3

-49.8 -49.7 -49.6 -49.5 -49.4 -49.3

dp4

-25.2 -24.7 -24.3

droPer1

-25.4 -24.9 -24.6 -24.5

droWil1

-6.7 -6.5 -6.3 -6.2 -6.2 -6.1

droVir3

-10.6 -10.5 -10.5 -10.4 -10.4 -10.3

droMoj3

-16.4 -15.8 -15.8 -15.6 -15.5 -15.5

droGri2

-14.2 -14.0 -14.0 -14.0 -14.0 -13.9

Generated: 01/05/2013 at 05:21 PM