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

-46.2 -46.0 -46.0 -46.0 -45.9 -45.9

droSim1

-46.9 -46.8 -46.8 -46.7 -46.6 -46.6

droSec1

-46.0 -45.9 -45.7 -45.6 -45.6 -45.6

droYak2

-37.2 -37.1 -36.9 -36.9 -36.9 -36.8

droEre2

-38.4 -38.1 -38.0 -37.8 -37.8 -37.8

droAna3

-41.4 -41.0 -41.0 -41.0 -41.0 -40.8

dp4

-5.5 -5.4 -5.4 -5.3 -5.0 -4.9

droPer1

-15.7 -15.7 -15.6 -15.6 -15.5 -15.5

droWil1

-16.5 -16.2 -16.0 -16.0 -16.0 -15.9

droVir3

-2.5 -1.8 -1.7

droMoj3

-1.7 -1.0

droGri2

-3.5 -3.2 -2.9 -2.8 -2.6 -2.5

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