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

-33.1 -33.1 -32.9 -32.9 -32.7 -32.7

droSim1

-34.4 -34.4 -34.3 -34.3 -33.9 -33.8

droSec1

-35.4 -35.4 -34.9 -34.7 -34.6 -34.6

droYak2

-32.1 -32.1 -32.0 -31.5 -31.2 -31.2

droEre2

-31.9 -31.9 -31.9 -31.9 -31.6 -31.5

droAna3

-33.2 -33.1 -32.9 -32.8 -32.7 -32.6

dp4

-30.6 -30.3 -30.2 -29.9 -29.9 -29.8

droPer1

-30.6 -30.3 -30.2 -29.9 -29.9 -29.8

droWil1

-23.6 -23.6 -23.5 -23.3 -23.3 -23.2

droVir3

-34.9 -34.9 -34.7 -34.7 -34.5 -34.3

droMoj3

-29.5 -29.4 -29.3 -29.3 -29.2 -29.2

droGri2

-25.2 -24.8 -24.5 -24.2

Generated: 01/05/2013 at 05:23 PM