Secondary structure and small RNA-seq evidence for dme-mir-2499

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19451026-19451151 + CTTTGGGCGTTCGCCTCCTTGCTGT------GGGTGTGGT--------TGCGTGCGTAGACGTCAGCGCAATGCCTTTGTTTGGCGGCATGCG-G---ATGACAT-----------------TCACGTCCGTATCCGCACACACATCCGCATCCATATA-----------------------------TC------
droSim1 chrX:15016847-15016968 + CTTTGGGCGTTCGCCTCCTTGCTGT------GGG--TGGG--------TGCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCATGTG-G---ATGACGT-----------------TCATGTCCACATCCGCACACACATCCGCATCCATA-------------------------------TC------
droSec1 super_8:1733318-1733439 + CTTTGGGCGTTCGCCTCCGTGCTGT------GGG--TGGG--------TGCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCATGTG-G---ATGACGT-----------------TCATGTCCACATCCGCACACACATCCGCATCCATA-------------------------------TC------
droYak2 chrX:11887438-11887559 - CTTTGGGCGCTCTCCTCCTTGCTGT------GAG--CGGG--------TGCGTGCGTTGACGTCAGCGCAATGCCTTTGTTTGTCGGCATGCG-G---ATGGCGT-----------------ACACGTCCACATCCGCACACACACACGCATCTGTA-------------------------------TC------
droEre2 scaffold_4690:9687367-9687488 + CTTTGGGCGCTCCTTTCCTGGCTGT------GAG--TGGG--------TGCGTGCGTTTATGTCAGCGCAATGCTTTTGTTTGGCGGCATGCG-G---ATGGCAT-----------------ACACGTCCACATCCGCACACACATCCGCATCCGTA-------------------------------TC------
droAna3 scaffold_13417:2469661-2469798 - CGA-----------CTT----CTGTGTGT--GTGTGCGTG--------TGTTGGCGTTGGCGTCAGCGCAATGCCATTGTTTGCCGGCATGCG-G---CTGGCGT-----------------GCACGTCTACATCCGCACCTGCATCCACAT------AGCAGCTGCAACAACAAACACGGCACTCCGTC------
dp4 chrXL_group1e:12520639-12520746 - TTTTTGA-------------GT-----GTGTGTT--TGTATTTATTTATTTTTGTGTGGACTTCACTGCATTGTCATTGATTGGCGGC-----------TGTCGT-----------------GCAGGACAATGT--GAAACATCATTCGACA-CAAA-------------------------------TC------
droPer1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_13042:909712-909778 - A----------------------------------------------------------------------GGCCATTGTT--ATGGCAGGTGGGCAGGTGTCAT-----------------CAATAGCCGCATCC--AGGCACATCCGCATCCACA-------------------------------T-------
droMoj3 scaffold_6328:2902676-2902778 - CTGTGGGCTTTAGGCCAATTGATAT------GGT--CGTG--------T------------------------------------GGCATGAG-G---CAGGTGTCAGCAGGTGGCAGCAATTCGGAACCAT-TGTGTGCCCACATCCGCATTTGCA-A-----------------------------GC------
droGri2 scaffold_15081:2046312-2046418 - TGTTGCA-------------GTTGC------ATT--TGAA--------TGTAGGTGTTGTCATTA-------------TTTTGAGGGCATGCG-G---CAGGTGTCAACG------------CCACGTCCTCATTTGCATCCGCTTCCGCATCCGCA-------------------------------TCCGCTGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19451026-19451151 + C----TTTGGGCGTTCGCCTCCTTGCTGTGGGTGTGGTTGCGTGCGTAGACGTCAGCGCAATGCCTTTGTTTGGCGGCATGCGGATGACATTCACGTCCGTATCCGCACACACATCCGCATCC------------------------ATATATC
droSim1 chrX:15016847-15016968 + C----TTTGGGCGTTCGCCTCCTTGCTGTGGG--TGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCATGTGGATGACGTTCATGTCCACATCCGCACACACATCCGCATCC--------------------------ATATC
droSec1 super_8:1733318-1733439 + C----TTTGGGCGTTCGCCTCCGTGCTGTGGG--TGGGTGCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCATGTGGATGACGTTCATGTCCACATCCGCACACACATCCGCATCC--------------------------ATATC
droYak2 chrX:11887438-11887559 - C----TTTGGGCGCTCTCCTCCTTGCTGTGAG--CGGGTGCGTGCGTTGACGTCAGCGCAATGCCTTTGTTTGTCGGCATGCGGATGGCGTACACGTCCACATCCGCACACACACACGCATCT--------------------------GTATC
droEre2 scaffold_4690:9687367-9687488 + C----TTTGGGCGCTCCTTTCCTGGCTGTGAG--TGGGTGCGTGCGTTTATGTCAGCGCAATGCTTTTGTTTGGCGGCATGCGGATGGCATACACGTCCACATCCGCACACACATCCGCATCC--------------------------GTATC
droAna3 scaffold_13417:2469661-2469798 - CGACTTCTGTGTG-------------TGTGTG--CGTGTGTTGGCGTTGGCGTCAGCGCAATGCCATTGTTTGCCGGCATGCGGCTGGCGTGCACGTCTACATCCGCACCTGCATCCACATA-GCAGCTGCAACAACAAACACGGCACTCCGTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTTTG-----GGCGTTCGCCTCCTTGCTGTGGGT--GGGTGCAGGCGTGGACGTCAGCACAATGCCTTTGTTTGGCGGCATG--TGGATGACGTTCATGTCCACATCCGCACACA---CATCCGCATCC--ATATCSizeHit CountTotal NormTotalGSM343915
Embryo
...............................................................................ATG--TGGATGACGTTCATGTCCA.................................2211.0011
dp4
TTTTTGAGTGTGTGTTTGTATTTAT-----------TTATTTTTGTGTGGACTTCACTGCATTGTCATTGATTGGCGGCTGTCGTGCAGGACA---------ATG--TGAA---ACATCATTCG---ACACAAATCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-28.1,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.3,  p-value=0.009901

droSim1

dG=-37.1,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.6,  p-value=0.009901 dG=-36.4,  p-value=0.009901 dG=-36.4,  p-value=0.009901

droSec1

dG=-37.1,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.6,  p-value=0.009901 dG=-36.4,  p-value=0.009901 dG=-36.4,  p-value=0.009901

droYak2

dG=-29.3,  p-value=0.009901 dG=-29.3,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.6,  p-value=0.009901

droEre2

dG=-27.2,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.8,  p-value=0.009901

droAna3

dG=-33.6,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901

dp4

dG=-15.5,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.0,  p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

dG=-15.7,  p-value=0.009901 dG=-11.5,  p-value=0.009901

droMoj3

dG=-10.3,  p-value=0.009901

droGri2

dG=-16.3,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-14.5,  p-value=0.009901

Generated: 03/07/2013 at 04:58 PM