Secondary structure and small RNA-seq evidence for dme-mir-4955

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:2438757-2438956 - T--T-GCTGATGTCAA-----ATCACCGATTTGCTTCCCCT-TTT----------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATC------------------------TCTGTCTCTGTCTAACGCTTA-----ATTGTTGCT-CAATTGCGAATTAATGTC------------------------------------------------------TGGGGCTTTTTTT---CTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAC------------------------AACCTGCCAGCCGT-TTAAAGC
droSim1 chrX:1743323-1743545 - T--T-GCTGATGTCAA-----ATCACCGATTTGTTTCCCTT-TTT----------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCT-CAATTGCGAATTAATGTC-------------------------------------------------------GGGGCTTTTTTT---CTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAC------------------------AACCTGCCAGCCGT-TTAAAGC
droSec1 super_10:2212704-2212927 - T--TTGCTGATGTCAA-----ATCACCGATTTGTTTCCCCT-TTT----------------------------------TCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAACTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCT-CAATTGCGAATTAATGTC-------------------------------------------------------GGGGCTTTTTTT---CTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAC------------------------AACCTGCCAGCCGT-TTAAAGC
droYak2 chrX:5905985-5906183 + T--T-GCTGATGTG-------TTCACCGATTTGTTTCCCCT-TTT----------------------------------TCCGTGCGCCGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTC----------------------------CCTGTCTCTGTCTTACGCTTAATTTAATTGTCGCT-CAATTGCGAATTAATGTC------------------------------------------------------GGGGGCTTTTTTT---CTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAA------------------------AACCTGCCAGCCGT-TCAAAGC
droEre2 scaffold_4644:2389120-2389318 - T--T-GCTGATGTG-------TTCACCGATTTGTTTCCCCT-TTT----------------------------------TCCGTGCGCTGAGAAAAAAATCCCCAGAAACCTAATATCAGGATGCTCTCTGTCTC----------------------CCTGTCTCTGTCTCACGGCAA-----ATTGTTGCT-TAATTGCGAATTAATGTC-------------------------------------------------------GGGGCTTTTTTT---CTCCGTGCAGTGCCATAGCCGTA------------------------------------------------------------A-CCAC------------------------AACCTGCCGACCGT-TTAAAGC
droAna3 scaffold_12929:2354513-2354742 - G--T-GTTTCTTCCAA-----ATCTTCACTTCTCTTCTCTTTTCTTTTCTTTCCTTCTTCTGTTTTTTTTTTTTGTTGGTCCCTGCACGGAGAAGAAGTTGTTAGGACA-------TT-----------------------A----------------------------------------------------GAGTGGACCTTAG---TGTGGTTAATAGATCATATGACTCATTGTCCTTGCAATT--ATTTCACAACTCGCT-CCAC-TTTTCT---CTCTGTGCAGTGCCATAACCGTA------------------------------------------------------------A-CCAC------------------------AACCTGCCAGCCGT-TCAAAAA
dp4 chrXL_group3a:2134676-2134849 - TTTC-GCTGATTCGGGAATATATTCTCCACCCCCCCACCCT-CTACCA--TTTC-------------------------CTCTTCTGCTGACCTA----------------------CACGATTTTCCCCCTC----------------------------TCTCTT---------------------------------------------------------------------------AACGATCTTAACGCTCCACTCTTT-CTGT--CTCTCTCGATTTTTGCAGTGCCATAGCCGTA------------------------------------------------------------AAACAC------------------------TGTCTTCCTACCGT-TTACCGT
droPer1 super_13:248212-248305 - T--C-TCTGG--------------------------------------------------------------------------------------------------------------------------C------------------------TCTGTCTCTGTCTCAGGCGTA-----ACAGGTGCGTTGAGTGCATTTCAATTGT-------------------------------------------------------ATGGATA---------ATTGTGCTGTATTGTAATTGAA------------------------------------------------------------ATCCAC------------------------AA--------------------
droWil1 scaffold_181096:12164007-12164188 - T--C-GCTGATTTTGGAAAACATTTCTTATTTGCTCTCCTT-TAATTTATGTTTTT---------------------------------------------------------------------------------------------------------------------TTTTT-----GTTGTTGTT-CTTTTGTATATTTTT----------------------------------------------------------TATGT--TTATT---TTGTTTGCAGTGCCATAA-CATAATAATAGTTAATACTTATTGTGTTCACACAAAAATTTTGGGCCGCCGAATCGAAAACGAAT-------------------------------------------ATCAAAAC
droVir3 scaffold_12928:1476007-1476072 - T--T-T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTT---TTACTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CCTTTTT-C--TTTCTTTATCACGTCTAAACGC---------------AT
droMoj3 scaffold_6473:13536163-13536218 + C--G-T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTC---TCTCTTGCAGTGCCATAAACATCGTA-------------------------------------------------------------AT-------------------------TTTTTTCATTTAT-TTACGTC
droGri2 scaffold_15203:8273975-8274075 + AATA-GCTGAA-----------------ATTTGTTTTCCTC-A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCTTGCAGTGCCATAAACATCGTA---------------------------------------------------------A-CCTTTTTTCTTTTTTTTTCTTACGTCAAAACGCATCGATCGCATCAGAGG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:2438757-2438956 - T-TGCTGATGTCAAATCACCGATTTGCTTCCCCTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATCT------------------------CTGTCTCTGTCTAACGCTTA-----ATTGTTGCTCAATTGCGAATTAATGTCTGGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droSim1 chrX:1743323-1743545 - T-TGCTGATGTCAAATCACCGATTTGTTTCCCTTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droSec1 super_10:2212704-2212927 - TTTGCTGATGTCAAATCACCGATTTGTTTCCCCTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAACTGTCTGTCCCTGTCTGACGCTTA-----ATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCAGCCGTTTAAAGC
droYak2 chrX:5905985-5906183 + T-TGCTGATGTG--TTCACCGATTTGTTTCCCCTTTTTCCGTGCGCCGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTC----------------------------CCTGTCTCTGTCTTACGCTTAATTTAATTGTCGCTCAATTGCGAATTAATGTCGGGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCAAAACCTGCCAGCCGTTCAAAGC
droEre2 scaffold_4644:2389120-2389318 - T-TGCTGATGTG--TTCACCGATTTGTTTCCCCTTTTTCCGTGCGCTGAGAAAAAAATCCCCAGAAACCTAATATCAGGATGCTCTCTGTCTC----------------------CCTGTCTCTGTCTCACGGCAA-----ATTGTTGCTTAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAACCACAACCTGCCGACCGTTTAAAGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TT--GCTGATG-------------TCAAATCACCGATTTGTTTCCCTTTTTTCCGTGCGCGGAGAAAAAAATCCCCAGAAACATAATATCAGGATGCTCTCTATATCTATCTCAGTCTGGGCCCAAGTGTCTGTCCCT--GTCTGACGCTTAATTGTTGCTCAATTGCGAATTAATGTC-GGGGCTTTTTTTCTCCGTGCAGTGCCATAGCCGTAA-CCACAACCTGCCAGCCGTTTAAAGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTTCGCTGATTCGGGAATATATTCTCCACCCCCCCACCCTCTAC-CATTTCCTCTTCTGCTGACCTA----------------------CACGATTTTCCCCCTCTC------------------------TCTTAACGATCTTAACGCTCCACTCTTTC---------------------TGTCTCTCTCGATTTTTGCAGTGCCATAGCCGTAAAACACTGTCTTCCTACCGTTTACCGTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..........................................................................................................................................................................................................TGCCATAGCCGTAAAACA......................1811.00110
...............................................................................................................................................................C---------------------TGTCTCTCTCGATTTTTGCAG........................................2211.00110

Secondary Structure

dm3

dG=-46.2,  p-value=0.009901 dG=-46.0,  p-value=0.009901 dG=-45.9,  p-value=0.009901 dG=-45.8,  p-value=0.009901 dG=-45.6,  p-value=0.009901 dG=-38.74,  p-value=0.009901

droSim1

dG=-46.8,  p-value=0.009901 dG=-46.7,  p-value=0.009901 dG=-46.5,  p-value=0.009901 dG=-46.5,  p-value=0.009901 dG=-46.4,  p-value=0.009901 dG=-45.0,  p-value=0.009901

droSec1

dG=-45.6,  p-value=0.009901 dG=-45.5,  p-value=0.009901 dG=-45.2,  p-value=0.009901 dG=-45.2,  p-value=0.009901 dG=-45.2,  p-value=0.009901 dG=-41.4,  p-value=0.009901

droYak2

dG=-36.8,  p-value=0.009901 dG=-36.7,  p-value=0.009901 dG=-36.5,  p-value=0.009901 dG=-36.5,  p-value=0.009901 dG=-36.4,  p-value=0.009901

droEre2

dG=-38.0,  p-value=0.009901 dG=-37.4,  p-value=0.009901 dG=-37.4,  p-value=0.009901 dG=-37.4,  p-value=0.009901

droAna3

dG=-37.3,  p-value=0.009901 dG=-36.9,  p-value=0.009901 dG=-36.9,  p-value=0.009901 dG=-36.7,  p-value=0.009901 dG=-36.6,  p-value=0.009901

dp4

dG=-3.8,  p-value=0.009901 dG=-2.8,  p-value=0.019802 dG=-2.8,  p-value=0.009901

droPer1

dG=-13.7,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-9.3,  p-value=0.009901

droWil1

dG=-0.6,  p-value=0.009901 dG=-0.5,  p-value=0.009901 dG=-0.4,  p-value=0.009901 dG=-0.1,  p-value=0.009901 dG=-0.1,  p-value=0.009901

droVir3

dG=0.0,  p-value=1.0 dG=0.5,  p-value=1.0 dG=1.0,  p-value=1.0 dG=1.0,  p-value=1.0

droMoj3

dG=0.0,  p-value=1.0 dG=1.0,  p-value=1.0

droGri2

dG=0.0,  p-value=1.0 dG=1.0,  p-value=1.0

Generated: 03/07/2013 at 06:12 PM