Secondary structure and small RNA-seq evidence for dme-mir-4956

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:6979754-6979901 - GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1 chrX:5492772-5492919 - GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1 super_24:199934-200081 - GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2 chrX:14374793-14374940 + GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2 scaffold_4690:15890244-15890391 - GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droAna3 scaffold_13117:2326296-2326455 - CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
dp4 chrXL_group1a:6391512-6391662 - CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1 super_25:931278-931428 + CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1 scaffold_180777:2984533-2984680 + CAGTGCCAATTCCCTTGGCG---------GTGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTATG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3 scaffold_12928:60655-60799 - CAGCGCCAATTCCCTTG------------GCGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACATG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3 scaffold_6359:1380681-1380818 - C-----CAATTCCCTCG------------GCGGCAACATCTGCAACATG---CCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGATG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2 scaffold_14853:6692716-6692854 - CAGCGCCAATTCACTCGGCG---------G---A---CTCTGCAACATG---CCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTATG------AACGATCCACGCAACAGCAACACCAATTTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:6979754-6979901 - GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACCTG
droSim1 chrX:5492772-5492919 - GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACTTG
droSec1 super_24:199934-200081 - GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACTTG
droYak2 chrX:14374793-14374940 + GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG---A---ACGATCCCCGGGCAAGCAACACCAACCTG
droEre2 scaffold_4690:15890244-15890391 - GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG---A---ACGATCCCCGGGCAAGCAACACCAACCTG
droAna3 scaffold_13117:2326296-2326455 - CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTTA---ATGACCAGCGGCCGAGCAACACCAACCTG
dp4 chrXL_group1a:6391512-6391662 - CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1 super_25:931278-931428 + CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAGTGCCAACAATCTAGGGGGCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATGA------ACGATCCTCGGGCAAGCAACACCAACTTGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CAGTGCCAATAATCTT---GGCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
...................................................................AGCAATCTATGCGGACTGTCGCT................................................................2312.00220
............................................................................TGCGGACTGTCGCTGGGCAGC.........................................................2111.00101
............................................................................TGCGGACTGTCGCTGGGCAGCG........................................................2211.00101
..................................................................TAGCAATCTATGCGGACTGTCG..................................................................2211.00110

Secondary Structure

dm3

dG=-36.3,  p-value=0.009901

droSim1

dG=-36.3,  p-value=0.009901

droSec1

dG=-36.3,  p-value=0.009901

droYak2

dG=-38.6,  p-value=0.009901

droEre2

dG=-38.6,  p-value=0.009901

droAna3

dG=-30.7,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.0,  p-value=0.009901

dp4

dG=-33.4,  p-value=0.009901

droPer1

dG=-33.4,  p-value=0.009901

droWil1

dG=-19.4,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.7,  p-value=0.009901

droVir3

dG=-25.7,  p-value=0.009901 dG=-23.6,  p-value=0.009901

droMoj3

dG=-18.5,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-17.5,  p-value=0.009901 dG=-17.5,  p-value=0.009901 dG=-16.8,  p-value=0.009901

droGri2

dG=-22.5,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-20.8,  p-value=0.009901

Generated: 03/07/2013 at 05:57 PM