Secondary structure and small RNA-seq evidence for dme-mir-4969

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:17624220-17624408 - TATATATATGTTTTTGTATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCTGCCATTG----------TTTGG---TTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--TGCGACATCATCATAATAATCATCGCCTTT
droSim1 chr3R:17429869-17430050 - TGTTTTTG--------TATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---TTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTAA--------ATCAATACCACCCCG-------CCGA--AGCGACATCATCATAATAATCATCGCCTGC
droSec1 super_0:17996591-17996767 - TATATATATGTTTTTATATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---TTGATA--------------------------------------AGGAAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--AGCGACA------------TCATCGCCTTT
droYak2 chr3R:18444204-18444378 - G---------------TATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---CTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCCCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--ACCGACATCATCATAATAATCATCGCCAGC
droEre2 scaffold_4820:10462895-10463063 + TGTAT--------------GAATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---CTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCCCTGTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--ACCGACATCATCATAGTAATCAT-------
droAna3 scaffold_13417:705028-705198 + TGTATATGTGTGGGTGTAGAGGTGTGT--------AGGTGT------------GCAGGTGTACGGTTGT-GTGT--GTGTGGCATTCGTTGCT-ACTTATGTTTAA-GCTTCGTA--------------------------------------TTTAAGCTTTTTGCACGATTTCCT----CTAACAA-------------------------------------------A-TGGATTT--------TCACTTGTT------------------GCCCAGCCAG---ACG---AACGAAGCCATCACAAAAAT----------
dp4 chr4_group3:1192892-1193069 - TATATGGCCTATCCAGCAGGAATTTATCCAGCGGATGGTAG------------CTAGAGATGC-AGTTG-GAGG--GGG---GCACCATAG----------TTTGG---AGTAGC--------------------------------------CAAA---------------TGCCAGGCGATAAGGC-------------------------------ATGAAAAATACAA-CTAATAA--------ACATAAACCAGTCTTCTTTTAAAA--------G-------CTGC------TCATCATCATCATCATCATGATCATC
droPer1 super_7:2291330-2291534 - CATAAAAGGGTCTGAGTATCTGAGCGT----C------------------------------TGGGTGG-AACC--TCTGTGCTGCTAATG----------TT-AG---CTGATCCCTCTCCTCCCTCCCACTCGGTCCCTGCCCCCGCTCCCTTGGTGGCTGTTGCACTTTCCCCCGGGGCTCTGGA------------GTGTGCACACTTTTGGCA---------TAATA-CAACAAAATTGATTTG----------------------------------------------CAGCATGCATCATTATCAACATCGTCGTT
droWil1 scaffold_181089:335812-335995 + TTTTTTGAAATGTTTGTAAATGTGTGT----G----TGTTT------------GTGTGTGAAGAAGAA-TGTGTGTATGTGCTGACTAG--TTCAATAATG----C---C--------------------------------------------CAGAGAATGTTACAAGTTTAATGGAAGTTTTCAA-------------------------------------------ATAGAAAAG--------CTAAAAGGAA--------TTTAATTTTAGACAT-------CAGTTTCGAAGCATCGGCATCACAATCATCCCCATT
droVir3 scaffold_12963:15197471-15197651 + TATATATATAGATATATATATATATATATGCTGGGT----------------------TATATGA--------------------CTTTTG----------GG-TG---CTGATAAGAGGCG----TTCAGCTCAGTGC---------------CAGAGCCCAGCGGCTAATTGACAGCCCCACGGG-----------------CCATGCGGTTA---------AATTAAAA-CGAAAAA--------TCATTTGCCA--------GCA-GCAACAGC-AG----CAGCAGC--AGCGGCAGCAGC-----------------A
droMoj3 scaffold_6496:7093711-7093898 - TAGCAACTCGTTTCTGTTGCTGTATGT----GTAGCTGTAGCTGTATCTGTAGCTGTATCTGTGGCTG-TATCTGTATCTGGCAGCTGG----CAGCAGTA----G---C--------------------------------------------TGGTAGCTGCTGCTGGCTC--------TGTTGCT------GCCAGAGTATCTGTATCTGTGGCGCGTCAT-----------------------------TGT------------------------T-------GTGC--GTTGCCGTTGCCATCGTAACCAACGCCGTC
droGri2 scaffold_15126:1496468-1496644 - TACATCCACATCGCTGCTTCGGCTTAT----GTTGTGGTAA------------GTCATTAGAT--GCAG-ATGA--TTGGCGTCATCATCG----------CCTGCT--TCCACA--------------------------------------TCATAGTCAAGGGTATTCTTTTCTGCCGTCTC--AATGAGCGCTAGCG--------CCGATGAGATATCAA-----------------------------CGA------------------------G-------GTGC------TCTTCATCATCATCATCATCGTCATC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:17624220-17624408 - TATATATATGTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCTGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGATGCGACATCATCATAATAATCATCGCCTTT
droSim1 chr3R:17429869-17430050 - T--------GTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTAAATCAATACCACCCCGCCGAAGCGACATCATCATAATAATCATCGCCTGC
droSec1 super_0:17996591-17996767 - TATATATATGTTTTTATATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGAAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAAGCGACATCA------------TCGCCTTT
droYak2 chr3R:18444204-18444378 - ---------------GTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGCTGATAAGGGAGCCTGGCGCACTATTACCTGGCCCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAACCGACATCATCATAATAATCATCGCCAGC
droEre2 scaffold_4820:10462895-10463063 + T--------------GTATGAATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGCTGATAAGGGAGCCTGGCGCACTATTACCTGGCCCTGTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAACCGACATCATCATAGTAATCAT-------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
T--------GTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATG-AGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAG-CCCACCT-GTAAATCAATACCACCCCGC----CGAAGCGA--CATCATCATAATAATCATCGCCTGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATATGGCCTATCCAGCAGGAATTTATCCAGCGGATGGTAGCTAGAG--ATGCAGTTGGAGGGGGGC---ACCATAGTTTGGAGTAGCC---------------AAATGCCAGGCGATAAGGCATGAAAAATACAACTAATAAACATAAACCAGTCTTCTTTTAAAAGCTGCTCATCATCATCATCATCATGATCATCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-44.6,  p-value=0.009901 dG=-44.2,  p-value=0.009901 dG=-44.0,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.7,  p-value=0.009901 dG=-40.1,  p-value=0.009901

droSim1

dG=-42.4,  p-value=0.009901 dG=-42.0,  p-value=0.009901 dG=-41.7,  p-value=0.009901 dG=-41.5,  p-value=0.009901 dG=-41.5,  p-value=0.009901 dG=-36.3,  p-value=0.009901

droSec1

dG=-42.9,  p-value=0.009901 dG=-42.5,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-42.0,  p-value=0.009901 dG=-35.8,  p-value=0.009901

droYak2

dG=-45.2,  p-value=0.009901 dG=-44.9,  p-value=0.009901 dG=-44.8,  p-value=0.009901 dG=-44.5,  p-value=0.009901 dG=-44.5,  p-value=0.009901 dG=-37.8,  p-value=0.009901

droEre2

dG=-44.7,  p-value=0.009901 dG=-44.3,  p-value=0.009901 dG=-44.0,  p-value=0.009901 dG=-44.0,  p-value=0.009901 dG=-43.8,  p-value=0.009901 dG=-40.6,  p-value=0.009901

droAna3

dG=-28.3,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-27.7,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-24.8,  p-value=0.009901

dp4

dG=-21.9,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droPer1

dG=-32.2,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-25.2,  p-value=0.009901

droWil1

dG=-14.8,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droVir3

dG=-34.0,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droMoj3

dG=-47.6,  p-value=0.009901 dG=-47.6,  p-value=0.009901 dG=-47.3,  p-value=0.009901 dG=-47.3,  p-value=0.009901 dG=-47.2,  p-value=0.009901 dG=-42.4,  p-value=0.009901

droGri2

dG=-30.4,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.9,  p-value=0.009901 dG=-29.4,  p-value=0.009901

Generated: 03/07/2013 at 06:41 PM