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

-26.2 -26.2 -26.2 -26.2 -26.2 -26.2

droSim1

-24.1 -24.1 -23.7 -23.7 -23.2 -23.2

droSec1

-25.2 -25.2 -25.2 -25.2

droYak2

-23.5 -23.5 -23.5 -23.5 -23.5 -23.5

droEre2

-22.4 -22.4 -22.4 -22.4 -22.4 -22.4

droAna3

-19.5 -19.5 -19.5 -19.4 -19.4 -19.4

dp4

-0.1 0.0 0.5

droPer1

-0.1 0.0 0.5

droWil1

-21.7 -21.7 -21.7 -21.7 -21.7 -21.7

droVir3

-24.1 -24.1 -23.8 -23.8 -23.5 -23.5

droMoj3

-31.0 -30.4 -30.3

droGri2

-25.7 -25.7 -25.7 -25.7 -25.3 -25.3

Generated: 01/05/2013 at 05:32 PM