Secondary structure and small RNA-seq evidence for dme-mir-4969

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:17624220-17624408 - TATATATATGTTTTTGTATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCTGCCATTG----------TTTGG---TTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--TGCGACATCATCATAATAATCATCGCCTTT
droSim1 chr3R:17429869-17430050 - TGTTTTTG--------TATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---TTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTAA--------ATCAATACCACCCCG-------CCGA--AGCGACATCATCATAATAATCATCGCCTGC
droSec1 super_0:17996591-17996767 - TATATATATGTTTTTATATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---TTGATA--------------------------------------AGGAAGCCTGGCGCACTATTACCTGGCTCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--AGCGACA------------TCATCGCCTTT
droYak2 chr3R:18444204-18444378 - G---------------TATGGATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---CTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCCCTCTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--ACCGACATCATCATAATAATCATCGCCAGC
droEre2 scaffold_4820:10462895-10463063 + TGTAT--------------GAATTTTTCGGCGTGGCGGTAA------------ATTGAATGATGAGTGG-GAGG--ATGTCGCAGCCATTG----------TTTGG---CTGATA--------------------------------------AGGGAGCCTGGCGCACTATTACCTGGCCCTGTGAA-------------------------------------------A-CGAGAGC--------CCACCTGTCA--------ATCAATACCACCCCG-------CCGA--ACCGACATCATCATAGTAATCAT-------
droAna3 scaffold_13417:705028-705198 + TGTATATGTGTGGGTGTAGAGGTGTGT--------AGGTGT------------GCAGGTGTACGGTTGT-GTGT--GTGTGGCATTCGTTGCT-ACTTATGTTTAA-GCTTCGTA--------------------------------------TTTAAGCTTTTTGCACGATTTCCT----CTAACAA-------------------------------------------A-TGGATTT--------TCACTTGTT------------------GCCCAGCCAG---ACG---AACGAAGCCATCACAAAAAT----------
dp4 chr4_group3:1192892-1193069 - TATATGGCCTATCCAGCAGGAATTTATCCAGCGGATGGTAG------------CTAGAGATGC-AGTTG-GAGG--GGG---GCACCATAG----------TTTGG---AGTAGC--------------------------------------CAAA---------------TGCCAGGCGATAAGGC-------------------------------ATGAAAAATACAA-CTAATAA--------ACATAAACCAGTCTTCTTTTAAAA--------G-------CTGC------TCATCATCATCATCATCATGATCATC
droPer1 super_7:2291330-2291534 - CATAAAAGGGTCTGAGTATCTGAGCGT----C------------------------------TGGGTGG-AACC--TCTGTGCTGCTAATG----------TT-AG---CTGATCCCTCTCCTCCCTCCCACTCGGTCCCTGCCCCCGCTCCCTTGGTGGCTGTTGCACTTTCCCCCGGGGCTCTGGA------------GTGTGCACACTTTTGGCA---------TAATA-CAACAAAATTGATTTG----------------------------------------------CAGCATGCATCATTATCAACATCGTCGTT
droWil1 scaffold_181089:335812-335995 + TTTTTTGAAATGTTTGTAAATGTGTGT----G----TGTTT------------GTGTGTGAAGAAGAA-TGTGTGTATGTGCTGACTAG--TTCAATAATG----C---C--------------------------------------------CAGAGAATGTTACAAGTTTAATGGAAGTTTTCAA-------------------------------------------ATAGAAAAG--------CTAAAAGGAA--------TTTAATTTTAGACAT-------CAGTTTCGAAGCATCGGCATCACAATCATCCCCATT
droVir3 scaffold_12963:15197471-15197651 + TATATATATAGATATATATATATATATATGCTGGGT----------------------TATATGA--------------------CTTTTG----------GG-TG---CTGATAAGAGGCG----TTCAGCTCAGTGC---------------CAGAGCCCAGCGGCTAATTGACAGCCCCACGGG-----------------CCATGCGGTTA---------AATTAAAA-CGAAAAA--------TCATTTGCCA--------GCA-GCAACAGC-AG----CAGCAGC--AGCGGCAGCAGC-----------------A
droMoj3 scaffold_6496:7093711-7093898 - TAGCAACTCGTTTCTGTTGCTGTATGT----GTAGCTGTAGCTGTATCTGTAGCTGTATCTGTGGCTG-TATCTGTATCTGGCAGCTGG----CAGCAGTA----G---C--------------------------------------------TGGTAGCTGCTGCTGGCTC--------TGTTGCT------GCCAGAGTATCTGTATCTGTGGCGCGTCAT-----------------------------TGT------------------------T-------GTGC--GTTGCCGTTGCCATCGTAACCAACGCCGTC
droGri2 scaffold_15126:1496468-1496644 - TACATCCACATCGCTGCTTCGGCTTAT----GTTGTGGTAA------------GTCATTAGAT--GCAG-ATGA--TTGGCGTCATCATCG----------CCTGCT--TCCACA--------------------------------------TCATAGTCAAGGGTATTCTTTTCTGCCGTCTC--AATGAGCGCTAGCG--------CCGATGAGATATCAA-----------------------------CGA------------------------G-------GTGC------TCTTCATCATCATCATCATCGTCATC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:17624220-17624408 - TATATATATGTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCTGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGATGCGACATCATCATAATAATCATCGCCTTT
droSim1 chr3R:17429869-17430050 - T--------GTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTAAATCAATACCACCCCGCCGAAGCGACATCATCATAATAATCATCGCCTGC
droSec1 super_0:17996591-17996767 - TATATATATGTTTTTATATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGAAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAAGCGACATCA------------TCGCCTTT
droYak2 chr3R:18444204-18444378 - ---------------GTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGCTGATAAGGGAGCCTGGCGCACTATTACCTGGCCCTCTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAACCGACATCATCATAATAATCATCGCCAGC
droEre2 scaffold_4820:10462895-10463063 + T--------------GTATGAATTTTTCGGCGTGGCGGTAAATTGAATGATGAGTGGGAGGATGTCGCAGCCATTGTTTGGCTGATAAGGGAGCCTGGCGCACTATTACCTGGCCCTGTGAAACGAGAGCCCACCTGTCAATCAATACCACCCCGCCGAACCGACATCATCATAGTAATCAT-------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
T--------GTTTTTGTATGGATTTTTCGGCGTGGCGGTAAATTGAATGATG-AGTGGGAGGATGTCGCAGCCATTGTTTGGTTGATAAGGGAGCCTGGCGCACTATTACCTGGCTCTCTGAAACGAGAG-CCCACCT-GTAAATCAATACCACCCCGC----CGAAGCGA--CATCATCATAATAATCATCGCCTGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATATGGCCTATCCAGCAGGAATTTATCCAGCGGATGGTAGCTAGAG--ATGCAGTTGGAGGGGGGC---ACCATAGTTTGGAGTAGCC---------------AAATGCCAGGCGATAAGGCATGAAAAATACAACTAATAAACATAAACCAGTCTTCTTTTAAAAGCTGCTCATCATCATCATCATCATGATCATCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-55.8 -55.6 -55.4 -55.2 -55.2 -55.0

droSim1

-55.0 -54.8 -54.6 -54.4 -54.2 -54.1

droSec1

-54.5 -54.3 -54.1 -54.0 -53.9 -53.9

droYak2

-57.2 -57.0 -56.9 -56.9 -56.8 -56.7

droEre2

-55.7 -55.5 -55.3 -55.1 -55.0 -54.9

droAna3

-34.4 -34.4 -34.2 -34.2 -34.2 -34.1

dp4

-33.3 -33.2 -33.2 -33.1 -33.0 -32.8

droPer1

-42.8 -42.8 -42.6 -42.5 -42.5 -42.4

droWil1

-21.1 -20.7 -20.6 -20.6 -20.4 -20.4

droVir3

-43.7 -43.6 -43.3 -43.2 -43.2 -43.1

droMoj3

-58.8 -58.8 -58.8 -58.8 -58.5 -58.5

droGri2

-43.4 -43.4 -43.4 -43.4 -43.2 -43.2

Generated: 01/05/2013 at 05:26 PM