Secondary structure and small RNA-seq evidence for dme-mir-963

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:5641975-5642093 + TACAACTAA----------------------TTTTTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTCGA---TCGAAACATCTGTATATACCTTTGTTCCGATT-GGACA-AAAGTG--CGTCTTC--------------TA--GTT
droSim1 chr2L:5435040-5435157 + TACTACTGA----------------------TT-TTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTAGA---TCGAAACATCTGTATATACCTTTGATCCGGTT-GGACA-AAAGTG--CATCTTC--------------TA--GTG
droSec1 super_5:3719693-3719811 + TACTACTGA----------------------TTTTTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTAGA---TAGAAACATCTGTATATACCTTTGATCCGGTT-GGACA-AAAGTG--CATCTTC--------------TA--GTG
droYak2 chr2L:13551185-13551307 - CACTACTGC---A------------------TTGTTCTTGGTCTAATCTAAAACAAGGTACATATCAGGTTGTTTCCTATATTGGATGATCGAAACATCTGTATATACCTTTGTTCCGAAT-GGACG-AAAGAG--CATCTTC--------------AA--GTT
droEre2 scaffold_4929:5730368-5730489 + CAGTGCTGC----------------------TTGTTCTTAGTCTAATCTAAAACAAGGTACATATCAGGTTGTTTCCTGTATTGGATGATCGAAACATCTGTATATACCTTTGTTCCGAAT-GGACG-AAAGAG--CATCTTC--------------TA--GTT
droAna3 scaffold_12916:11085426-11085560 + TAATTA--GTTAAAAA---------------GTGTTCTTGATTTAATCTAAAACAAGGTACATATCTGGTTGTTTCCTATATTCAAAGTTTGAAACATCTGTATCTACCTTTGTTTCGATT-AAACT-AAAGAG--CTACT---AAGA---ATACGAGT--GTT
dp4 chr4_group4:3181623-3181668 - AAGAAGAGGA--AAA--------GATAATGT-GA-------------TTAATACAA-------------------------GTGGCTGATTGGA----------------------------------------------------------------------
droPer1 super_10:2200549-2200594 - AAGAAGAGGA--AAA--------GATAATGT-GA-------------TTAATACAA-------------------------GTGGCTGATTGGA----------------------------------------------------------------------
droWil1 scaffold_180708:8625051-8625198 - CATAGTTAAT--TGA--------GTTAATTG-AATTCTAATTCTAGTCTAAAACAAGGTACATATCAGGTTGTTTCGTATATTTGAAGCCTGAAACATCTGTATCTACCTTTGTTTCGAATAGGACT-AAAGAG--TTTTCTTTAAGCCCAACACATTT--GTT
droVir3 scaffold_12963:3616326-3616465 + TGGAGTTAATGTACGGATGGGCA--------TAAACAACAATCTAATCTGAAACAAGGTACATATCAGAGTGTTTCTTAAATTTGATTATTGAAACCTCTGTATATACCTTTCATTGGATT-AAACT-GATAAGCACATGTTT--------------CAAAAGT
droMoj3 scaffold_6500:14019361-14019489 + TGGAGTGCGC--A------------------CTG-AATCGGTCTAATCTAAAACAAGGTACATATCAGAGTGTTTCCCGTATTCGAGTTTTGAAACCTCTGTATATACCTTTCATTAGATT-CAACCGAAAGTC--CATA----AATATT---GA--TA--TAT
droGri2 scaffold_15252:3148184-3148306 + GCAAAATAA-----------------------------CAGTCTAATCCAAAACAAGGTACATATTAGAGCGTTTCCTATCTTTGAGTATTGAAACCTCTGTATATACCTTCA-TTCGATT-CGACT-GATAATCTCATT----AAAATC---ATTTCA--GTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:5641975-5642093 + TACAACTAA--------------TTTTTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTCGA---TCGAAACATCTGTATATACCTTTGTTCCGATT-GGACA-AAAGTG--CGTCTTC--------------TA--GTT
droSim1 chr2L:5435040-5435157 + TACTACTGA--------------TT-TTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTAGA---TCGAAACATCTGTATATACCTTTGATCCGGTT-GGACA-AAAGTG--CATCTTC--------------TA--GTG
droSec1 super_5:3719693-3719811 + TACTACTGA--------------TTTTTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTAGA---TAGAAACATCTGTATATACCTTTGATCCGGTT-GGACA-AAAGTG--CATCTTC--------------TA--GTG
droYak2 chr2L:13551185-13551307 - CACTACTGC-------------ATTGTTCTTGGTCTAATCTAAAACAAGGTACATATCAGGTTGTTTCCTATATTGGATGATCGAAACATCTGTATATACCTTTGTTCCGAAT-GGACG-AAAGAG--CATCTTC--------------AA--GTT
droEre2 scaffold_4929:5730368-5730489 + CAGTGCTGC--------------TTGTTCTTAGTCTAATCTAAAACAAGGTACATATCAGGTTGTTTCCTGTATTGGATGATCGAAACATCTGTATATACCTTTGTTCCGAAT-GGACG-AAAGAG--CATCTTC--------------TA--GTT
droAna3 scaffold_12916:11085426-11085560 + TAAT--TAGTTAAAAA-------GTGTTCTTGATTTAATCTAAAACAAGGTACATATCTGGTTGTTTCCTATATTCAAAGTTTGAAACATCTGTATCTACCTTTGTTTCGATT-AAACT-AAAGAG--CTACT---AAGA---ATACGAGT--GTT
droWil1 scaffold_180708:8625051-8625198 - CATAGTTAATTGAGTTAATT---GAATTCTAATTCTAGTCTAAAACAAGGTACATATCAGGTTGTTTCGTATATTTGAAGCCTGAAACATCTGTATCTACCTTTGTTTCGAATAGGACT-AAAGAG--TTTTCTTTAAGCCCAACACATTT--GTT
droVir3 scaffold_12963:3616326-3616465 + TGGAGTTAATGTACGGATGGGCATAAACAACAATCTAATCTGAAACAAGGTACATATCAGAGTGTTTCTTAAATTTGATTATTGAAACCTCTGTATATACCTTTCATTGGATT-AAACT-GATAAGCACATGTTT--------------CAAAAGT
droMoj3 scaffold_6500:14019361-14019489 + TGGAGTGC--GC----------ACTG-AATCGGTCTAATCTAAAACAAGGTACATATCAGAGTGTTTCCCGTATTCGAGTTTTGAAACCTCTGTATATACCTTTCATTAGATT-CAACCGAAAGTC--CATA----AATATT---GA--TA--TAT
droGri2 scaffold_15252:3148184-3148306 + GCAAAATAA---------------------CAGTCTAATCCAAAACAAGGTACATATTAGAGCGTTTCCTATCTTTGAGTATTGAAACCTCTGTATATACCTTCA-TTCGATT-CGACT-GATAATCTCATT----AAAATC---ATTTCA--GTT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TACTACTGATT-TTCTTAGTCTAATCTAAAACAAGGTAAATATCAGGTTGTTTCCTGTATTAGATCGAAACATCTGTATATACCTTTGATCCGGTTGGACAAAAGTGCATCTTCTAGTGSizeHit CountTotal NormTotalGSM343915
Embryo
..............................ACAAGGTAAATATCAGGTTGTTTC.................................................................24119.001919
dp4
A---------------------------AGAAGAGGAAAAGATAATGTGATT--------------AATACAAGTG-------------GCTGATTGGA--------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

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

droSim1

dG=-15.1,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-14.7,  p-value=0.009901 dG=-14.7,  p-value=0.009901 dG=-14.7,  p-value=0.009901

droSec1

dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-15.8,  p-value=0.009901

droYak2

dG=-16.6,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-16.6,  p-value=0.009901

droEre2

dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901

droAna3

dG=-15.2,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-14.6,  p-value=0.009901 dG=-14.6,  p-value=0.009901

dp4

dG=-0.1,  p-value=0.009901 dG=0.0,  p-value=0.009901 dG=0.5,  p-value=0.009901

droPer1

dG=-0.1,  p-value=0.009901 dG=0.0,  p-value=0.009901 dG=0.5,  p-value=0.009901

droWil1

dG=-18.2,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.2,  p-value=0.009901

droVir3

dG=-19.9,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droMoj3

dG=-19.8,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.1,  p-value=0.009901

droGri2

dG=-16.1,  p-value=0.009901 dG=-16.1,  p-value=0.009901 dG=-16.1,  p-value=0.009901 dG=-16.1,  p-value=0.009901 dG=-15.5,  p-value=0.009901

Generated: 03/07/2013 at 07:10 PM