Secondary structure and small RNA-seq evidence for dme-mir-971

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:12956090-12956215 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droSim1 zec46h04.g1:44-170 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droSec1 super_21:701218-701343 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droYak2 chrX:7229770-7229895 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAAAC---
droEre2 scaffold_4690:13914734-13914859 - TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droAna3 scaffold_13117:3891784-3891909 + TGCATGTGAGAAAA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTT----ATCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCTG--------------------------GAGCACATATTAAAAA-----
dp4 chrXL_group3a:1391638-1391748 - AGCATGTGAGAGAGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTG----TTGGTAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droPer1 super_52:413307-413417 + AGCATGTGAGAGAGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTG----TTGGTAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droWil1 scaffold_181096:6691507-6691601 - AC-----------A--------TTAAACGGCCCAATA--CGCTCGCTGTAAATTGTAGCAATCAAAGCGTTGCCTTTTGCCTC---ACAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droVir3 scaffold_12928:4279754-4279849 - ------------------------------------------CCGCTGTAAAATGTAATCATCAGAGCGTC-CT------CTC--AACCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCC--------------------------AAGGTCCGACCGTAAATCATA
droMoj3 scaffold_6328:350121-350240 + ---------------------------------------CGACCGCTGTAAATTGTAATCATCAAAGCGTC-TG------CTA--AATCGCTTGGTGTTACTTCTTACAGTGAGCGCGGCGCTCGAAACTACAGTGAAACTAGCATAAAGTGAACAAGGAAAGGAAA-----
droGri2 scaffold_14853:994421-994540 - CACG--------AA--------CT---TGAATGACGTCACGCCCGCTGTAATATGTAATCATCAAAGCGTG-TATT----TT---ACTCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCACAC-----------------------GTCCAGCGGAGGAGAGTG---

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:12956090-12956215 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droSim1 zec46h04.g1:44-170 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droSec1 super_21:701218-701343 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droYak2 chrX:7229770-7229895 + TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCTCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAAAC---
droEre2 scaffold_4690:13914734-13914859 - TGCATGTGAGAGAA--------TTCCGTGGCTGGCAT--CGCCCGCTGTAAATTGTAATCATCAAAGCGTT-TT------CTCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCC--------------------------GTACACAGAAAGAAAACC---
droAna3 scaffold_13117:3891784-3891909 + TGCATGTGAGAAAA--------TTCCGTGGCTGGCAT--CGTTCACTGTAAATTGTAACCATCAAAGCGTT-TTTT----ATCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGAGCCAGCTG--------------------------GAGCACATATTAAAAA-----
dp4 chrXL_group3a:1391638-1391748 - AGCATGTGAGAGAGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTG----TTGGTAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droPer1 super_52:413307-413417 + AGCATGTGAGAGAGCGGCTCCTTTCCCTGGACCCCAT--CGCTCGCTGTAAATTGTAATGGCCAAAGCTTT-TTTG----TTGGTAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droWil1 scaffold_181096:6691507-6691601 - AC-----------A--------TTAAACGGCCCAATA--CGCTCGCTGTAAATTGTAGCAATCAAAGCGTTGCCTTTTGCCTC---ACAGCTTGGTGTTACTTCTTACAGTGAGTGTG------------------------------------------------------
droVir3 scaffold_12928:4279754-4279849 - ------------------------------------------CCGCTGTAAAATGTAATCATCAGAGCGTC-CT------CTC--AACCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCC--------------------------AAGGTCCGACCGTAAATCATA
droMoj3 scaffold_6328:350121-350240 + ---------------------------------------CGACCGCTGTAAATTGTAATCATCAAAGCGTC-TG------CTA--AATCGCTTGGTGTTACTTCTTACAGTGAGCGCGGCGCTCGAAACTACAGTGAAACTAGCATAAAGTGAACAAGGAAAGGAAA-----
droGri2 scaffold_14853:994421-994540 - CACG--------AA--------CT---TGAATGACGTCACGCCCGCTGTAATATGTAATCATCAAAGCGTG-TATT----TT---ACTCGCTTGGTGTTACTTCTTACAGTGAGTGCGACGGCCACAC-----------------------GTCCAGCGGAGGAGAGTG---

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TGCATGTGAGAGAA--------TTCCGTGGCTGGCATCGCTCGCTGTAAATTGTAATCATCAAAGCGTTTTC--TCAGAGCCGCTTGGTGTTACTTCTTACAGTGAGTGTGCCAGTCCGTACACAGAAAGAAAACCSizeHit CountTotal NormTotalGSM343915
Embryo
....................................................................................TTGGTGTTACTTCTTACAGTGA..............................221133.00133133
....................................................................................TTGGTGTTACTTCTTACAGTG...............................2115.0055
dp4
AGCATGTGAGAGAGCGGCTCCTTTCCCTGGACCCCATCGCTCGCTGTAAATTGTAATGGCCAAAGCTTTTTTGTTGGTAGCAGCTTGGTGTTACTTCTTACAGTGAGTGTG-------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
....................................................................................TTGGTGTTACTTCTTACAGTGA..............................221144.0014410935
..........................................GCTGTAAATTGTAATGGCCAAAGC......................................................................24114.0014104
....................................................................................TTGGTGTTACTTCTTACAGTG...............................2118.00826
...................................................................................CTTGGTGTTACTTCTTACAGTGA..............................2318.00862
..........................................GCTGTAAATTGTAATGGCCAAAG.......................................................................2315.00505
..........................................GCTGTAAATTGTAATGGCCAAA........................................................................2215.00505
..........................................GCTGTAAATTGTAATGGCCA..........................................................................2014.00404
..........................................GCTGTAAATTGTAATGGCCAA.........................................................................2112.00202
....................................................................................TTGGTGTTACTTCTTACAGT................................2011.00110
....................................................................................TTGGTGTTACTTCTTACAG.................................1911.00101
..........................................GCTGTAAATTGTAATGGCCAAAGCT.....................................................................2511.00110
...................................................................................CTTGGTGTTACTTCTTACAGT................................2111.00110
........................................................................................TGTTACTTCTTACAGTGA..............................1811.00110
...........................................CTGTAAATTGTAATGGCCAAAGCT.....................................................................2411.00101
...................................................................................CTTGGTGTTACTTCTTACAGTG...............................2211.00110

Secondary Structure

dm3

dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droSim1

dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droSec1

dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droYak2

dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droEre2

dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901

droAna3

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

dp4

dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droPer1

dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droWil1

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

droVir3

dG=-20.8,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droMoj3

dG=-23.8,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.8,  p-value=0.009901

droGri2

dG=-27.4,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.6,  p-value=0.009901

Generated: 03/07/2013 at 07:16 PM