Secondary structure and small RNA-seq evidence for dme-mir-4976

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:2723022-2723155 - ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTC---CGCG---TCTGGTCCACG
droSim1 chr2R:1535693-1535826 - ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTC---CGCG---TCTGGTCCACG
droSec1 super_1:401443-401575 - ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTT---CGCG---TCTGGTCCACG
droYak2 chr2L:15457678-15457811 - ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTC---CGCG---TCTGGTCCACG
droEre2 scaffold_4929:19824507-19824640 + ACATCATCGATTATGGTCGATGGCGGCGTC---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTC---CGCG---TCCGGTCCACG
droAna3 scaffold_13266:9050244-9050380 - ACATCATCGATTATTGTCGATGTTGGCGTT---TCCTG---CTC------------------------------------------------------------------------------CAAGTTATCGTCAAGCGGGTTTGTGTTGTCGCCATTTAGCTCCGTAGATGTCAGCCACCGGTGGAAGGCGTCATCCAGCTC---CTCGGGGTCATGTCCACT
dp4 chr3:994566-994696 - ACATCATCGATTATTGTCGATGCTGCTGTT---TCCTG---CTC------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTC---CTTG---CC---ACCGCT
droPer1 super_2:1175582-1175712 - ACATCATCGATTATTGTCGATGCTGCTGTT---TCCTG---CTC------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTC---CTTG---CC---ACCGCT
droWil1 scaffold_180745:52392-52526 + ACATCATCGATTATCGTTGATGCTGATGTTTTTTCCTG---CTC------------------------------------------------------------------------------CAAGCTAACGTCCAGTGTATTGGTATTTTCAACATTCAGCTCTGTGGATGTTAGCCAACGATGAAATGCATCATCATCTTGTTCCA-----TC---ATCTTC
droVir3 scaffold_12875:15675057-15675224 - ACATCATCGATTATTGTTGATGCTGGCGTT---TCCTG---TTCGACAGCAACTGCTGCTGCTGCTGC---------------------------------------TGCCGCAGCTGCTGCCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTCAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTCAGCTTC---CTCA--------ATTTCC
droMoj3 scaffold_6496:8124753-8124946 + ACATCATCGATTATTGTTGATGCTGGTGTT---TCCTGCTGCTGAACGGCAAgTGtTGgTGgTGgTggGtgGGgTggGGgTGtTGgTGgTGgTGgTTgTGgTTgTGgTTgTGgTGgTGgTGTCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTC---------------------------
droGri2 scaffold_15245:12478490-12478641 - ACATCATCGATTATTGTTGATGCTGATGTT---TCCTG---CTCAATTGTAGCTTCTGCTGCAGCTGC---------------------------------------AGCTGCTGCTGCTGCCAAGTTATCGTCAAACATATTTGTACTGTCAATATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCATC---------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:2723022-2723155 - ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACG
droSim1 chr2R:1535693-1535826 - ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACG
droSec1 super_1:401443-401575 - ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTTCGCGTCTGGTCCACG
droYak2 chr2L:15457678-15457811 - ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTCCGCGTCTGGTCCACG
droEre2 scaffold_4929:19824507-19824640 + ACATCATCGATTATGGTCGATGGCGGCGTCTCCCGCTCCAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTCCGCGTCCGGTCCACG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
ACATCATCGATTATTGTCGATGCTGCTGTTTCCTGCTCCGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTGCC---ACCGCTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-52.3 -52.1

droSim1

-52.3 -52.1

droSec1

-53.1 -53.1 -53.0 -53.0 -52.9 -52.9

droYak2

-52.4 -51.5

droEre2

-58.4 -58.3 -57.5 -57.4

droAna3

-25.7 -25.3 -25.2 -25.2 -25.1 -25.0

dp4

-30.6 -30.4 -30.1 -29.8 -29.8 -29.8

droPer1

-30.6 -30.4 -30.1 -29.8 -29.8 -29.8

droWil1

-28.4 -27.8 -27.8 -27.6

droVir3

-48.9 -48.9 -48.6 -48.6 -48.6 -48.6

droMoj3

-48.6 -48.6 -48.5 -48.5 -48.3 -48.3

droGri2

-41.9 -41.6 -41.4 -41.4 -41.3 -41.2

Generated: 01/05/2013 at 05:27 PM