Secondary structure and small RNA-seq evidence for dme-mir-31b

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:8887323-8887479 - TCGCTCCACGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAACATTTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droSim1 chrX:7083953-7084109 - TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droSec1 super_34:250169-250325 - TTGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droYak2 chrX:12425680-12425836 + TTTCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTTTGATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--TAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droEre2 scaffold_4690:6225295-6225451 + TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACACTATCAACGTTG
droAna3 scaffold_13047:712420-712562 - AT---CCTCG------------AAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGAGGATCGAGCGAGTCATCGACCGAGACG---------------------------A----------------ATT--CCAAA------GCGGCTATGCCTCATCTAGTCAATTACATTACTTTGACACTTTCCACGAGG
dp4 chrXL_group1e:8162325-8162445 - GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droPer1 super_13:404315-404435 + GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droWil1 scaffold_181150:794468-794638 + TCACGAAT-----GTG---ATGAAAACAACTAGTGGATTTGGCAAGATGTCGGAATAGCTGAAAGTCACACAAAATCA----------------------TAAAATGTTTGCCGTTTTGTTATTGT-TGTGAA-----T-TTTATTGATTTCAAAAATTACGGCTATGCCTCATCTAGTCAATTGCATTAGTTTGATTAAGTCAAC--TG
droVir3 scaffold_12726:2775742-2775905 - TTGCAGCACATATATATAAATATAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAAG--TC----------------------ATA-AAT----CCAGAATTTCTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAAAAGCAACG---
droMoj3 scaffold_6473:5711141-5711289 + GTGGTCCTCG----------------CAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAA-TATC----------------------ATAGAAT----CCAGAATTTATATT-T-TGTGTA-----T-TTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAGCAGCAAC---C
droGri2 scaffold_15203:6378282-6378443 - TCGACCACCAT--TTGCACCCGCAAACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGACAG-CACAA--GATC----------------------ACA-AAT----CAAGAAACTTTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGAC---ATCAACAACG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:8887323-8887479 - TCGCTCCACGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAACATTTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droSim1 chrX:7083953-7084109 - TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droSec1 super_34:250169-250325 - TTGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droYak2 chrX:12425680-12425836 + TTTCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTTTGATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--TAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droEre2 scaffold_4690:6225295-6225451 + TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACACTATCAACGTTG
droAna3 scaffold_13047:712420-712562 - AT---CCTCG------------AAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGAGGATCGAGCGAGTCATCGACCGAGACG---------------------------A----------------ATT--CCAAA------GCGGCTATGCCTCATCTAGTCAATTACATTACTTTGACACTTTCCACGAGG
dp4 chrXL_group1e:8162325-8162445 - GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droPer1 super_13:404315-404435 + GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droWil1 scaffold_181150:794468-794638 + TCACGAAT-----GTG---ATGAAAACAACTAGTGGATTTGGCAAGATGTCGGAATAGCTGAAAGTCACACAAAATCA----------------------TAAAATGTTTGCCGTTTTGTTATTGT-TGTGAA-----T-TTTATTGATTTCAAAAATTACGGCTATGCCTCATCTAGTCAATTGCATTAGTTTGATTAAGTCAAC--TG
droVir3 scaffold_12726:2775742-2775905 - TTGCAGCACATATATATAAATATAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAAG--TC----------------------ATA-AAT----CCAGAATTTCTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAAAAGCAACG---
droMoj3 scaffold_6473:5711141-5711289 + GTGGTCCTCG----------------CAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAA-TATC----------------------ATAGAAT----CCAGAATTTATATT-T-TGTGTA-----T-TTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAGCAGCAAC---C
droGri2 scaffold_15203:6378282-6378443 - TCGACCACCAT--TTGCACCCGCAAACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGACAG-CACAA--GATC----------------------ACA-AAT----CAAGAAACTTTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGAC---ATCAACAACG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCGCTCCTCGTTAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAGCACAGCGGATCGAGCCTCTTATCGTCCGAAAAAATGTGATTATTTTTGAAAAGCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTGSizeHit CountTotal NormTotalGSM343915
Embryo
............................TGGCAAGATGTCGGAATAGCTGA..........................................................................................................231499.00499499
............................TGGCAAGATGTCGGAATAGCTG...........................................................................................................22169.006969
............................TGGCAAGATGTCGGAATAGCT............................................................................................................21149.004949
..........................TTTGGCAAGATGTCGGAATAGCT............................................................................................................23128.002828
............................TGGCAAGATGTCGGAATAGC.............................................................................................................2019.0099
............................TGGCAAGATGTCGGAATAG..............................................................................................................1912.0022
...........................TTGGCAAGATGTCGGAATAGCT............................................................................................................2212.0022
....................................................................................AAAATGTGATTATTTTTGAAAAGC.................................................2411.0011
.................................AGATGTCGGAATAGCTGA..........................................................................................................1811.0011
..................................................................................AAAAAATGTGATTATTTTTGAAAAGC.................................................2611.0011
..........................TTTGGCAAGATGTCGGAATAGC.............................................................................................................2211.0011
......................................................................................AATGTGATTATTTTTGAAAAGC.................................................2211.0011
..........................TTTGGCAAGATGTCGGAATAG..............................................................................................................2111.0011
................................AAGATGTCGGAATAGCTGA..........................................................................................................1911.0011
dp4
GTGTCCT------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAGCA----------------------------AAAAGAAGATGAT--TTGAAATGCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
............................TGGCAAGATGTCGGAATAGCTGA..........................................................................................................231677.00677454223
............................TGGCAAGATGTCGGAATAGCTG...........................................................................................................221319.0031971248
............................TGGCAAGATGTCGGAATAGCT............................................................................................................211114.0011413101
............................TGGCAAGATGTCGGAATAGC.............................................................................................................20118.0018216
................................AAGATGTCGGAATAGCTGA..........................................................................................................1912.00220
...........................TTGGCAAGATGTCGGAATAGCT............................................................................................................2211.00101
...........................TTGGCAAGATGTCGGAATAGCTG...........................................................................................................2311.00110
...............................CAAGATGTCGGAATAGCT............................................................................................................1811.00101
...........................TTGGCAAGATGTCGGAATAGC.............................................................................................................2111.00101
..........................TTTGGCAAGATGTCGGAATAGCT............................................................................................................2311.00110
............................TGGCAAGATGTCGGAATAG..............................................................................................................1911.00101
.....................................................GCA----------------------------AAAAGAAGATGAT--TTGAAATGC.................................................2511.00110

Secondary Structure

dm3

dG=-29.0,  p-value=0.009901 dG=-28.9,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droSim1

dG=-29.9,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droSec1

dG=-29.9,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droYak2

dG=-29.9,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-29.3,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droEre2

dG=-29.0,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901

droAna3

dG=-27.6,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-26.9,  p-value=0.009901

dp4

dG=-21.6,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.7,  p-value=0.009901

droPer1

dG=-21.6,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.7,  p-value=0.009901

droWil1

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.1,  p-value=0.009901 dG=-29.0,  p-value=0.009901

droVir3

dG=-27.0,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-25.2,  p-value=0.009901

droMoj3

dG=-27.1,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.6,  p-value=0.009901

droGri2

dG=-26.6,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-26.2,  p-value=0.009901

Generated: 03/07/2013 at 05:29 PM