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

-40.3 -40.3 -39.8 -39.8 -39.8 -39.6

droSim1

-46.1 -46.1 -45.7 -45.7 -45.6 -45.4

droSec1

-47.1 -47.1 -46.6 -46.4 -46.4 -46.4

droYak2

-39.9 -39.9 -39.4 -39.4 -39.2 -39.2

droEre2

-35.4 -35.4 -35.1 -35.1 -35.0 -34.7

droAna3

-46.4 -46.4 -46.4 -46.4 -45.8 -45.8

dp4

-17.4 -17.2 -17.2 -17.2 -17.2 -17.0

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

-15.7

droMoj3

-16.7 -16.7 -16.7 -16.0 -16.0 -16.0

droGri2

-21.7 -21.3 -21.1 -21.1 -21.0 -20.9

Generated: 01/05/2013 at 05:11 PM