Secondary structure and small RNA-seq evidence for dme-mir-977

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19453040-19453168 + GGA-------AT--------------------------------------CCCAACACAACGA-ATCAACAA-----------------------A-----------------CAAGGTATGCTTTAGATAACTCGAATATCACATCTTC---------A--GTGTTCGAAATCTGATGAGATA-TTCACGTTGTCTAAATCATGTTTTGTACGAAAC--------------------TACAACTAA
droSim1 chrX:15018618-15018753 + GGA-------AT--------------------------------------ACCAACTCCGGAGTGCC-------------------------GAAAATGCA----TCC-----CAAGGTATGGTTTAGATAACTCGAATATCACATTTTC---------A--GTGTTCGATATCTGATGAGATA-TTCACGTTGTCTAAACCATGGTTTGTTTTTGAA--------------------AACTACTCA
droSec1 super_8:1735350-1735483 + GGA-------AT--------------------------------------ACCAACTCCGGAGTGCC-------------------------GAAAATTCA----TCC-----CAAGGTATGGTTTAGATAACTCGAATATCACATCTTC---------A--GTGTTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGGTTTGTTTGAAA----------------------ACTACTCA
droYak2 chrX:11885613-11885797 - TCCTATTCCTATTCC----------------GATTCC-GATTCGGAATCAACCAAGTGCGGACAGCT-------------------------CAGAGTTCA----CCC-----CAAGGTATGGCCTAGATAACACGGGTATCACATCTTT---------AT-GCATTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGTTTTGTAAGGAAATGCACTCTGCTCATCAGTTAAACTACTAA
droEre2 scaffold_4690:9689018-9689184 + GGG-------ATCGG----------------GATCCCGGATTCGG-----------------A-GTCAACAAACTCTTGTCAAACAAACGAGCAGAATTCA----ACC-----CAAGGTATGGCCTAGATAACTCGGGTATCACATCTTT---------AT-GCATTCGATATCTGGTGAGATAATTCACGTTGTCTAAACCATGTTTTGTAAGAAAT--------------------AACGCCTTA
droAna3 scaffold_13417:2467442-2467560 - GGC-------ACACG----------------CGTACC---------------------------------------------------------------------GC-----CGAGGTTCGGCCTCGATCACGAGAACGTCGCATCTTA---------GT-TACATTTCCATATGATGAGATA-TTCACGTCGTCGAAACCGTGTCTCGGCTTGGCC--------------------ACCAATCGC
dp4 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7956913-7957043 + GAT-------GT--------------------------------------GACACCGTGGACG-ATCAACAA-----------------------AATTCA---------------TATACAATTTCAATAACGTAGATATCGCATCGTTTTTTTTTACC--ATATTTGATAAGAGATGAGATA-TTCACGTTGTTGAAGTTGTGAAGGAATTAA-----------------------------AAA
droVir3 scaffold_13042:906546-906707 - GGA-------AC--------------------------------------CGGAACAGAAACA-GGAAAAAG-----------------------AAATTGTGTTCCCCCTGGCCCAGCCCAGTTGCGATTGCGCGGACATCTCATCGTA---------TAAACATTCGATAACCAACGAGATA-TTCACGTTATCGAGACTGAGACGTCGGCAAAG------ACTGCAAGATTGTGCGACAAGTGA
droMoj3 scaffold_6328:2900856-2900969 - GTT-------AAACGAAATGAACCAGTTCGTTGTTC--------------------------------------------------------------------------TGGCCCAGCCCGGTTCCGATTGCGCGGACATCTCATCGTC---------TGACCATTCGATAACCGATGAGATA-TTCACGTTATCGAGACTGCG------------------------------------------
droGri2 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19453040-19453168 + GGA-------AT--------------------------------------CCCAACACAACGA-ATCAACAA-----------------------A-----------------CAAGGTATGCTTTAGATAACTCGAATATCACATCTTC---------A--GTGTTCGAAATCTGATGAGATA-TTCACGTTGTCTAAATCATGTTTTGTACGAAAC--------------------TACAACTAA
droSim1 chrX:15018618-15018753 + GGA-------AT--------------------------------------ACCAACTCCGGAGTGCC-------------------------GAAAATGCA----TCC-----CAAGGTATGGTTTAGATAACTCGAATATCACATTTTC---------A--GTGTTCGATATCTGATGAGATA-TTCACGTTGTCTAAACCATGGTTTGTTTTTGAA--------------------AACTACTCA
droSec1 super_8:1735350-1735483 + GGA-------AT--------------------------------------ACCAACTCCGGAGTGCC-------------------------GAAAATTCA----TCC-----CAAGGTATGGTTTAGATAACTCGAATATCACATCTTC---------A--GTGTTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGGTTTGTTTGAAA----------------------ACTACTCA
droYak2 chrX:11885613-11885797 - TCCTATTCCTATTCC----------------GATTCC-GATTCGGAATCAACCAAGTGCGGACAGCT-------------------------CAGAGTTCA----CCC-----CAAGGTATGGCCTAGATAACACGGGTATCACATCTTT---------AT-GCATTCGATATCTGGTGAGATA-TTCACGTTGTCTAAACCATGTTTTGTAAGGAAATGCACTCTGCTCATCAGTTAAACTACTAA
droEre2 scaffold_4690:9689018-9689184 + GGG-------ATCGG----------------GATCCCGGATTCGG-----------------A-GTCAACAAACTCTTGTCAAACAAACGAGCAGAATTCA----ACC-----CAAGGTATGGCCTAGATAACTCGGGTATCACATCTTT---------AT-GCATTCGATATCTGGTGAGATAATTCACGTTGTCTAAACCATGTTTTGTAAGAAAT--------------------AACGCCTTA
droAna3 scaffold_13417:2467442-2467560 - GGC-------ACACG----------------CGTACC---------------------------------------------------------------------GC-----CGAGGTTCGGCCTCGATCACGAGAACGTCGCATCTTA---------GT-TACATTTCCATATGATGAGATA-TTCACGTCGTCGAAACCGTGTCTCGGCTTGGCC--------------------ACCAATCGC
droWil1 scaffold_181096:7956913-7957043 + GAT-------GT--------------------------------------GACACCGTGGACG-ATCAACAA-----------------------AATTCA---------------TATACAATTTCAATAACGTAGATATCGCATCGTTTTTTTTTACC--ATATTTGATAAGAGATGAGATA-TTCACGTTGTTGAAGTTGTGAAGGAATTAA-----------------------------AAA
droVir3 scaffold_13042:906546-906707 - GGA-------AC--------------------------------------CGGAACAGAAACA-GGAAAAAG-----------------------AAATTGTGTTCCCCCTGGCCCAGCCCAGTTGCGATTGCGCGGACATCTCATCGTA---------TAAACATTCGATAACCAACGAGATA-TTCACGTTATCGAGACTGAGACGTCGGCAAAG------ACTGCAAGATTGTGCGACAAGTGA
droMoj3 scaffold_6328:2900856-2900969 - GTT-------AAACGAAATGAACCAGTTCGTTGTTC--------------------------------------------------------------------------TGGCCCAGCCCGGTTCCGATTGCGCGGACATCTCATCGTC---------TGACCATTCGATAACCGATGAGATA-TTCACGTTATCGAGACTGCG------------------------------------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGAATACCAACTCCGGAGTGCCGAAAATGCATC-----CCAAGGTATGGTTTAGATAACTCGAATATCACATTTTCAGTGTTCGATATCTGATGAGATATTCACGTTGTCTAAACCATGGTTTGTTTTTGAAAACTACTCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
---------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-20.8,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droSim1

dG=-26.5,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.7,  p-value=0.009901

droSec1

dG=-26.9,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.2,  p-value=0.009901

droYak2

dG=-20.1,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.1,  p-value=0.009901

droEre2

dG=-18.4,  p-value=0.009901 dG=-18.1,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.5,  p-value=0.009901 dG=-16.6,  p-value=0.009901

droAna3

dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-29.3,  p-value=0.009901 dG=-29.3,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-28.8,  p-value=0.009901

droVir3

dG=-22.5,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.9,  p-value=0.009901

droMoj3

dG=-26.7,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:18 PM