Secondary structure and small RNA-seq evidence for dme-mir-4951

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:17142422-17142602 + TTTGAA-AATCC-CTTCCTTTTCG----TACGT---ACAA-AAAAGCATCAGGT-TTTCGGGTGAGGTTTC--TGATGCTTTG---TCTCTTAAGTTTTTCCTAACAATT--------------------------------------AAA--C-----CCTATGTCGGTATTA-CGAATACCA-T------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAACAA-C------G-
droSim1 chr3R:4327111-4327287 - TTTCAAAAATCC-CTTCCTTTTCG----TACGT---ACAA-AAAAGCATCAGGT-TTTCGGGTGAGGTTTC--TGATGCTTTG---TCTCTTAAGTTTTCCCTAAAAATA--------------------------------------AGA--C-----CCTATGTCGGTATTT-CGAATACCA-T------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droSec1 super_6:4348795-4348971 - TTTCAAAAATCC-CTTCCTTTTCG----TACGT---ACAA-AAAAGCATCAGGT-TTTCGGGTGAGGTTTC--TGATGCTTTG---TCTCTTAAGTTTTCCCTAACAATT--------------------------------------AGA--C-----CCTATGTCGGTATTT-CGAATACCA-T------CAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAA-T-TTCAATAAA-------------
droYak2 chr3R:5943432-5943618 + TTAAAAAAATTCATTTACTTTACG----TGCGT---ACAAAAAAAGCATCAGGT-TTTCGGGTGAGGTTTC--TGATGCTTTG---TCTCTTAAGTTTTTCCTAACAACT--------------------------------------AGT--C-----CCTATGTTGGTACTA-CGAATACCA-AAT----CAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAA-T-TTCAATATAAAAAC------A-
droEre2 scaffold_4770:4529493-4529670 - T---------AT----------TGTACGTAAGC---ATTA-TTAAGCATCAGGT-TTTCGGGTGAGGTTTC--TGATGCTTCG---TCTCTTAAGTTTTCCATAACAATT--------------------------------------GGT--C-----CCTATGTTGGTATTA-CAAATACCA-TAC----CAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAA-T-TTCAATAAAAAAATGTTGTCGA
droAna3 scaffold_13340:3794779-3794949 + T---------CT-CTACATTAATA----TTATC---ATGG-AAAAGCATCAGTTTTTTCGGGTGAGGTTATACTGATGCTTAG---TCATTTCAATTGCCCAAAATAATT--------------------------------------GAA--T-----TTT-AATTGGTATTTTTCAATACCC-A------AGACTAACCTCACCCACCAAATATATGAACAAAGAGATATAAA-T-TTCAATAAA-------------
dp4 chr2:5640393-5640558 + C---------CC-CGTCAATATTG----TAATT---AAAATAAAAGCATCCGAG-CTTCGGGTGAGGTTAT--GGATGCATTTTGATCTCTGCACTTATCTCCAA--------------------------AA-------------------CC-----CC--CTTTTGTATGGAAACATACCA-C-C----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAA-------------
droPer1 super_19:1368761-1368939 + C---------CC-CGTCAATATTG----TAATT---AAAATAAAAGCATCCGAG-CTTCGGGTGAGGTTAT--GGATGCATTTTGATCTCTGCACTTATCTCCAA--------------------------AA-------------------CC-----CC--TTTTTGTATGGAAACATACCA-C-C----CAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAA-T-TTCAATAAACACAAAACCACG-
droWil1 scaffold_181130:16134997-16135163 + T---------AA-AT--CTTACTG----TTATC-----CA-AAAATCATCACGG-TTTCGGGTGAGGTTAG--TGATGACTTTTCCTTTTT----------CAAACAACTAA--AATTTTAATTCCAA---AA-------------------AC-----CC--TTTCGGTATAG-ACAATACCA-A------AAAAAAACCTCACCCACCAAATATATGAACAAAGAGAAACAAA-TTTTCA------------------
droVir3 scaffold_12822:1191963-1192168 - CTT--------------AATGTCG----TACGACTTA-TG-AGAAGCATCTAG--TTTCGGGTGAGGTTTTA-TGATGCAATTCTCGCTCT---ATCC-------CATCTTG--AACATACGTTCCAAAAT--AAATACATAATAAAAAAATCC-----CCTGCTTTGGTATTT-AAGCTACCA-ACCA---AAAAAAACCTCACCCACCAAATGTATGAACAAAGAGATAAAAAATTTTCAATACACCA-T------G-
droMoj3 scaffold_6540:33813435-33813629 - C---------CTCCTCCCAAGTTG----TACAGCTTG-TG-AGATGCATCAGAT-TTTCGGGTGAGGTTTTA-TGATGCAGTACTC--CAT---GTCCC-------ACTCCGAATACTAAAAT----------AA----------AAAGAATCCTTCTCCC--ATTTGGTATTA-AAGCCACCCAC-C----AAAAAAACCTCACCCACCAAACATATGAACAAAGAGATACAAAATATTCAATACAACAAC--------
droGri2 scaffold_15074:2653282-2653451 + T---------G----------TCG----TACGACT-AATG-AAATGCATCTAGT-TTTCGGGTGAGGTTTT--AGATGCGTT---------------TCCCCCAGAAAAT-----------------------A--------------AAA--C-ACT-CC-TTTTTGGTATTT-AAACTACAA-AAAAAAAAAAAAAACCTCACCCACCAAATATATGAACAAAGAGATAAAAT-A-TTCAATAAACCAACAAACCCG-

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:17142422-17142602 + TTTGAA-AATCC-CTTCCTTTTCGTACGT------ACAA-AAAAGCATCAGGTT-TTCGGGTGAGGTT--TCTGATGCTTTGTCTCTTAAGTTTTTCCTAACAATTAAACCCTATGTCGGTATTA-CGAATACCA--TCAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAATTTCAATAAA-CAACG-------
droSim1 chr3R:4327111-4327287 - TTTCAAAAATCC-CTTCCTTTTCGTACGT------ACAA-AAAAGCATCAGGTT-TTCGGGTGAGGTT--TCTGATGCTTTGTCTCTTAAGTTTTCCCTAAAAATAAGACCCTATGTCGGTATTT-CGAATACCA--TCAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAATTTCAATAAA-------------
droSec1 super_6:4348795-4348971 - TTTCAAAAATCC-CTTCCTTTTCGTACGT------ACAA-AAAAGCATCAGGTT-TTCGGGTGAGGTT--TCTGATGCTTTGTCTCTTAAGTTTTCCCTAACAATTAGACCCTATGTCGGTATTT-CGAATACCA--TCAAAAAACCTCACCCACCAAATGTATGACCAGAGAGATAAAAATTTCAATAAA-------------
droYak2 chr3R:5943432-5943618 + TTAAAAAAATTCATTTACTTTACGTGCGT------ACAAAAAAAGCATCAGGTT-TTCGGGTGAGGTT--TCTGATGCTTTGTCTCTTAAGTTTTTCCTAACAACTAGTCCCTATGTTGGTACTA-CGAATACCAAATCAAAAAACCTCACCCACCAAAAGTATGAACAGAGAGATAAAAATTTCAATATAAAAACA-------
droEre2 scaffold_4770:4529493-4529670 - TAT---------------TGTACGTAAGC------ATTA-TTAAGCATCAGGTT-TTCGGGTGAGGTT--TCTGATGCTTCGTCTCTTAAGTTTTCCATAACAATTGGTCCCTATGTTGGTATTA-CAAATACCATACCAAAAAACCTCACCCACCAAATGTATGAACAGAGAGATAAAAATTTCAATAAAAAAATGTTGTCGA
droAna3 scaffold_13340:3794779-3794949 + TCTC----------------TACATTAATATTATCATGG-AAAAGCATCAGTTTTTTCGGGTGAGGTTATACTGATGCTTAGTCATTTCAATTGCCCAAAATAATTGAATTTTA-ATTGGTATTTTTCAATACCC--AAGACTAACCTCACCCACCAAATATATGAACAAAGAGATATAAATTTCAATAAA-------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTTCAAAAATCCCTTCCTTTTCGTACGTACAA-AAAAGCATCAGGTTTTCGGGTGAGGTTTCTGATGCT--TTG-TCTCTTAAGTTTTCCCTAAAAATAAGACCCTATGTCGGTATT-TCGAATACCATCAAAA-AACCTCACCCACCAAATGTATGACCAGAGAGATAAAAATTTCAATAAA-----SizeHit CountTotal NormTotalGSM343915
Embryo
............................................................................................AAAAATAAGACCCTATGTCGGT..........................................................................2212.0022
dp4
C---------CCCGTCAATATTGTAATTAAAATAAAAGCATCCGAGCTTCGGGTGAGGTTATGGATGCATTTTGATCTCTGCACTTATCTCCAA------AACCCCCTTT-TGTATGGAAACATACCACCCAAATAACCTCACCCACCAAAT-TATGAACAAAGAGAAAAAAATTTCAATAAA-----SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
........................................................................TGATCTCTGCACTTATCTC.................................................................................................1911.00110

Secondary Structure

dm3

dG=-26.3,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901

droSim1

dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-25.7,  p-value=0.009901

droSec1

dG=-28.6,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-24.8,  p-value=0.009901

droYak2

dG=-26.3,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-24.7,  p-value=0.009901

droEre2

dG=-27.6,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-22.5,  p-value=0.009901

droAna3

dG=-27.3,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.0,  p-value=0.009901

dp4

dG=-26.8,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-23.6,  p-value=0.009901

droPer1

dG=-26.8,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-23.6,  p-value=0.009901

droWil1

dG=-22.7,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-18.49,  p-value=0.009901

droVir3

dG=-26.4,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-19.8,  p-value=0.009901

droMoj3

dG=-24.4,  p-value=0.009901 dG=-24.3,  p-value=0.009901 dG=-24.2,  p-value=0.009901 dG=-24.2,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droGri2

dG=-21.8,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-20.4,  p-value=0.009901

Generated: 03/07/2013 at 05:54 PM