Oatp58Dc_in3- Best orthologs

Oatp58Dc_in3	chr2R:18113752-18113821 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 18113753-18113774
   star strand at position 18113776-18113796
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:18113737-18113836 -		1	GATGGATTGGTTTTGGTAAGTT------ATATAGAAG-------------GATATA--TATAATA-ATCGGAGGT-------------------------------------TAACGTATAATTATCC-----------TTTTAT--T---ACTGCGCAGGTCTTCTTACCATCG
droSim1	chr2R:16713489-16713586 -	LASTZ	4	GATGGATTGGTTTCGGTAACTT------ATATTAAAA-------------GATACA--TACGAGA-CTCGGAAGT-------------------------------GAGATA--------AATGGTCG-----------CTTTAT--T---ACTCTGCAGGTCTCCTTACCATCG
droSec1	super_9:1424074-1424171 -	LASTZ	1	GATGGATTGGTTTTGGTAAGAT------ATATGAAAA-------------GATACA--AACGAGA-CTCGGAAGT-------------------------------GAGCTA--------AATGGTCC-----------CTTTAT--T---ACTGTGCAGGTCTTCTTACCATCG
droYak2	chr2R:17860970-17861071 -	LASTZ	5	GATGGATTGGTTTTGGTAAGAT------CTATAGAAA-------------GATATATTTATGTTA-CTCAGAAGT-------------------------------------TAAGGTATAATTGCCA-----------TTTTGT--A---AATGTTCAGGTCTTCTTACCATCG
droEre2	scaffold_4845:12253086-12253177 -	LASTZ	5	GATGGATTGGTTTTGGTAAGAT------ATATA---------------------------TGTTA-CTCGGC---TTAATAATC----------------------AGGTTT--------AATTTTAC-----------TTTTAT--A---ACTGTGCAGGTCTTCTCACCATCG
droEug1	scf7180000409672:6008742-6008837 -	LASTZ	4	GATGGATTGGGTTCGGTAAGAT------GTTTACAGG-------------AAGA-----TATGTT-CTCAAACAA--------------A----AATACTATAGTT-----------------CGACC--------------ATA--T---ACCCCTCAGGTCTTCTTACCATAG
droBia1	scf7180000302143:2603202-2603295 +	LASTZ	5	GGTGGATTGGGTTTGGTAAGAC------ATATACAAG-------------AATA-----AAGTGT-CCCAGAAAG-----------------------------------------------------TAAAAAAATATTTTCCTATG---TTTGATAAGGTCTTCTCACCATTG
droTak1	scf7180000415243:306616-306705 -	LASTZ	5	GATGGATTGGGTTTGGTAAGAT------ATGGACAAG-------------AATT-----AAGTTT-GTCAGAAAA---------------------------------------ATGTA---GAGCCC-----------TTTTCT-------TTATTTAGGTCTCCTAACCATCG
droEle1	scf7180000491282:187924-188020 +	LASTZ	5	GATGGATTGGTTTTGGTAAGAC------TTGTACA-------TTTACTGGAAAA-------------------GT-----TTTCCCCGTT----TCT---GGGACT----------------------TATAAAACTG-----------T-TTGCCTTAGGTCTTCTCACCATCG
droRho1	scf7180000779898:29354-29438 -	LASTZ	5	GATGGATTGGATTTGGTAAGAT------ATTTACTGG-------------TAAA-----GGGTTT-CTCAGATCA-----------------------------------------------------TGTAACACTG-----------C-CTGCTTCAGGTCTTCTCACCATCG
droFic1	scf7180000454066:2005007-2005107 -	LASTZ	4	GGTGGATTGGGTTTGGTAAGAT------ATACCATATTG--------CATTACATA--TAAGTAC-ATCAGAAGA-------------------------------------TATAATAT----TTTA-----------AATCAT--A---ATTTAATAGGTCTCCTTACCATTG
droKik1	scf7180000302471:1382481-1382572 +	LASTZ	5	GGTGGATTGGCTTTGGTAAGCT------CTTAAGTAA-------------AATATA--T---ACTCTTCAA-GGATTGA----------A-------------------------------------------AATGCTTTTCCT--A---TATAAATAGGCCTGCTCACCATTG
droAna3	scaffold_13266:2121470-2121555 -	LASTZ	5	GATGGATTGGCTTTGGTACGTA------GTCACCAAAGAACATT--------------TAT---T-TTCAA--GT-------------------------------------TATTA-------------T-GAAATA-----------T-CCCTTTTAGGCTTGTTGACCATTG
droBip1	scf7180000396384:456386-456471 +	LASTZ	5	GATGGATTGGCTTTGGTAAGTA------TTCCCCAAAGGACATT--------------TAATTG------AATCT---------------------TATTATA------------------------------AACTA-----------T-CTTTTTTAGGTCTGTTAACCATTG
dp4	chr3:15036317-15036415 +	LASTZ	5	GCTGGATGGGAATAGGTAAGCC------TTAACTTTGGG--------CAC-----CTTTACGTAG-CTC--------------------------CTTCTCTCGGT------TAT-----------CT--C-TGA-----ATATC--T---TCTGGATAGGGTTGCTAACAATTG
droPer1	super_4:4021493-4021585 -	LASTZ	5	GCTGGATAGGATTCGGTAAGAG------CAGCATTCCGA--------TGG-----ATTTCTATC-----------------------GAT----TCCATTACAGCT------TAT-----------CG--------------GCT--A---CTCCCCCAGGTCTCCTCACCATTG
droWil1	scaffold_180697:335215-335309 +	LASTZ	5	GTTGGATTGGCTTTGGTATGATTAAAGACTCATTAATATATATTGACTTGAAAT-------------------GG-----------------------------------------------TTGCAA-----------ATTTGT--GAT-TTCTGACAGGTCTTCTAACAATTG
droVir3	scaffold_10324:576498-576590 -	LASTZ	4	GCTGGATAGGATTTGGTGAGTG--AATGAGCGGAAATCT-------------------AAAGTA------------------------------GCTTCTCTTAT-----------------TCATCT-----------TTTTCT--T-TCTGCCAACAGGCCTACTAACTATTG
droMoj3	scaffold_6496:2396237-2396342 -	LASTZ	4	GTTGGATGGGTTTGGGTAAAT-------ATATATAAA--------------ATATA--TATAA---TAAAAAAAT-----TATGT----AAAGAACTTCTCAAATTAAAGTA--------AAT--------------C-----------C-CACTTCCAGGTCTGTTTACAATCG
droGri2	scaffold_15245:8292349-8292444 -	LASTZ	4	GCTGGATTGGATTTGGTAAATA------AAATAAACCGG--------CGA-----CT-TAAGTGT---T------------------AAT----CTCACAATA-------------------------AAAAACAT----AATTT--A---CCTTGCCAGGATATTTTACGGTTA

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	GATGGATTGGTTTTGGTAAGTT------ATATAGAAG-------------GATATA--TATAATA-ATCGGAGGT-------------------------------------TAACGTATAATTATCC-----------TTTTAT--T---ACTGCGCAGGTCTTCTTACCATCG
droSim1	GATGGATTGGTTTCGGTAACTT------ATATTAAAA-------------GATACA--TACGAGA-CTCGGAAGT-------------------------------GAGATA--------AATGGTCG-----------CTTTAT--T---ACTCTGCAGGTCTCCTTACCATCG
droSec1	GATGGATTGGTTTTGGTAAGAT------ATATGAAAA-------------GATACA--AACGAGA-CTCGGAAGT-------------------------------GAGCTA--------AATGGTCC-----------CTTTAT--T---ACTGTGCAGGTCTTCTTACCATCG
droYak2	GATGGATTGGTTTTGGTAAGAT------CTATAGAAA-------------GATATATTTATGTTA-CTCAGAAGT-------------------------------------TAAGGTATAATTGCCA-----------TTTTGT--A---AATGTTCAGGTCTTCTTACCATCG
droEre2	GATGGATTGGTTTTGGTAAGAT------ATATA---------------------------TGTTA-CTCGGC---TTAATAATC----------------------AGGTTT--------AATTTTAC-----------TTTTAT--A---ACTGTGCAGGTCTTCTCACCATCG
droEug1	GATGGATTGGGTTCGGTAAGAT------GTTTACAGG-------------AAGA-----TATGTT-CTCAAACAA--------------A----AATACTATAGTT-----------------CGACC--------------ATA--T---ACCCCTCAGGTCTTCTTACCATAG
droBia1	GGTGGATTGGGTTTGGTAAGAC------ATATACAAG-------------AATA-----AAGTGT-CCCAGAAAG-----------------------------------------------------TAAAAAAATATTTTCCTATG---TTTGATAAGGTCTTCTCACCATTG
droTak1	GATGGATTGGGTTTGGTAAGAT------ATGGACAAG-------------AATT-----AAGTTT-GTCAGAAAA---------------------------------------ATGTA---GAGCCC-----------TTTTCT-------TTATTTAGGTCTCCTAACCATCG
droEle1	GATGGATTGGTTTTGGTAAGAC------TTGTACA-------TTTACTGGAAAA-------------------GT-----TTTCCCCGTT----TCT---GGGACT----------------------TATAAAACTG-----------T-TTGCCTTAGGTCTTCTCACCATCG
droRho1	GATGGATTGGATTTGGTAAGAT------ATTTACTGG-------------TAAA-----GGGTTT-CTCAGATCA-----------------------------------------------------TGTAACACTG-----------C-CTGCTTCAGGTCTTCTCACCATCG
droFic1	GGTGGATTGGGTTTGGTAAGAT------ATACCATATTG--------CATTACATA--TAAGTAC-ATCAGAAGA-------------------------------------TATAATAT----TTTA-----------AATCAT--A---ATTTAATAGGTCTCCTTACCATTG
droKik1	GGTGGATTGGCTTTGGTAAGCT------CTTAAGTAA-------------AATATA--T---ACTCTTCAA-GGATTGA----------A-------------------------------------------AATGCTTTTCCT--A---TATAAATAGGCCTGCTCACCATTG
droAna3	GATGGATTGGCTTTGGTACGTA------GTCACCAAAGAACATT--------------TAT---T-TTCAA--GT-------------------------------------TATTA-------------T-GAAATA-----------T-CCCTTTTAGGCTTGTTGACCATTG
droBip1	GATGGATTGGCTTTGGTAAGTA------TTCCCCAAAGGACATT--------------TAATTG------AATCT---------------------TATTATA------------------------------AACTA-----------T-CTTTTTTAGGTCTGTTAACCATTG
dp4	GCTGGATGGGAATAGGTAAGCC------TTAACTTTGGG--------CAC-----CTTTACGTAG-CTC--------------------------CTTCTCTCGGT------TAT-----------CT--C-TGA-----ATATC--T---TCTGGATAGGGTTGCTAACAATTG
droPer1	GCTGGATAGGATTCGGTAAGAG------CAGCATTCCGA--------TGG-----ATTTCTATC-----------------------GAT----TCCATTACAGCT------TAT-----------CG--------------GCT--A---CTCCCCCAGGTCTCCTCACCATTG
droWil1	GTTGGATTGGCTTTGGTATGATTAAAGACTCATTAATATATATTGACTTGAAAT-------------------GG-----------------------------------------------TTGCAA-----------ATTTGT--GAT-TTCTGACAGGTCTTCTAACAATTG
droVir3	GCTGGATAGGATTTGGTGAGTG--AATGAGCGGAAATCT-------------------AAAGTA------------------------------GCTTCTCTTAT-----------------TCATCT-----------TTTTCT--T-TCTGCCAACAGGCCTACTAACTATTG
droMoj3	GTTGGATGGGTTTGGGTAAAT-------ATATATAAA--------------ATATA--TATAA---TAAAAAAAT-----TATGT----AAAGAACTTCTCAAATTAAAGTA--------AAT--------------C-----------C-CACTTCCAGGTCTGTTTACAATCG
droGri2	GCTGGATTGGATTTGGTAAATA------AAATAAACCGG--------CGA-----CT-TAAGTGT---T------------------AAT----CTCACAATA-------------------------AAAAACAT----AATTT--A---CCTTGCCAGGATATTTTACGGTTA

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

GATGGATTGGTTTCGGTAACTT------ATATTAAAA-------------GATACA--TACGAGA-CTCGGAAGT-------------------------------GAGATA--------AATGGTCG-----------CTTTAT--T---ACTCTGCAGGTCTCCTTACCATCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................ACATA--------AATGGTCG-----------TTTTA...............................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

GATGGATTGGTTTTGGTAAGAT------ATATGAAAA-------------GATACA--AACGAGA-CTCGGAAGT-------------------------------GAGCTA--------AATGGTCC-----------CTTTAT--T---ACTGTGCAGGTCTTCTTACCATCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............ATAAGAT------ATAxGAAAA-------------GAT..........................................................................................................................	18	1	1.00	0.00	0.00	1.00
..............GGAGAGAT------ATATGAAAA-------------G............................................................................................................................	18	7	0.14	0.00	0.00	0.14
...................GAT------ATATGAAAA-------------GACATA--.....................................................................................................................	18	7	0.14	0.00	0.14	0.00
GATxxTTTGGTTTTGGTAAG...........................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
......TTGGTTTTGGTAAGAT------ATATG..............................................................................................................................................	21	1	1.00	1.00	0.00	0.00
.................................ACAA-------------GATACA--AACGAGA-A............................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

GATGGATTGGTTTTGGTAAGAT------CTATAGAAA-------------GATATATTTATGTTA-CTCAGAAGT-------------------------------------TAAGGTATAATTGCCA-----------TTTTGT--A---AATGTTCAGGTCTTCTTACCATCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.ATGGGCTGGTTTTGGTAAG...........................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...GGATTGCTTTAGGTAAGAT------...................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GATGGATTGGTTTTGGTAAGAT------ATATA---------------------------TGTTA-CTCGGC---TTAATAATC----------------------AGGTTT--------AATTTTAC-----------TTTTAT--A---ACTGTGCAGGTCTTCTCACCATCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................TTAC-----------TTTTAT--A---ACTGTGTT................	19	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................TTAC-----------TTGTAT--A---ACTGTGG.................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................TAC-----------TTTTAT--A---ACTGTGCT................	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

GATGGATTGGGTTCGGTAAGAT------GTTTACAGG-------------AAGA-----TATGTT-CTCAAACAA--------------A----AATACTATAGTT-----------------CGACC--------------ATA--T---ACCCCTCAGGTCTTCTTACCATAG

Size

Hit Count

Total Norm

droBia1

GGTGGATTGGGTTTGGTAAGAC------ATATACAAG-------------AATA-----AAGTGT-CCCAGAAAG-----------------------------------------------------TAAAAAAATATTTTCCTATG---TTTGATAAGGTCTTCTCACCATTG

Size

Hit Count

Total Norm

droTak1

GATGGATTGGGTTTGGTAAGAT------ATGGACAAG-------------AATT-----AAGTTT-GTCAGAAAA---------------------------------------ATGTA---GAGCCC-----------TTTTCT-------TTATTTAGGTCTCCTAACCATCG

Size

Hit Count

Total Norm

droEle1

GATGGATTGGTTTTGGTAAGAC------TTGTACA-------TTTACTGGAAAA-------------------GT-----TTTCCCCGTT----TCT---GGGACT----------------------TATAAAACTG-----------T-TTGCCTTAGGTCTTCTCACCATCG

Size

Hit Count

Total Norm

droRho1

GATGGATTGGATTTGGTAAGAT------ATTTACTGG-------------TAAA-----GGGTTT-CTCAGATCA-----------------------------------------------------TGTAACACTG-----------C-CTGCTTCAGGTCTTCTCACCATCG

Size

Hit Count

Total Norm

droFic1

GGTGGATTGGGTTTGGTAAGAT------ATACCATATTG--------CATTACATA--TAAGTAC-ATCAGAAGA-------------------------------------TATAATAT----TTTA-----------AATCAT--A---ATTTAATAGGTCTCCTTACCATTG

Size

Hit Count

Total Norm

droKik1

GGTGGATTGGCTTTGGTAAGCT------CTTAAGTAA-------------AATATA--T---ACTCTTCAA-GGATTGA----------A-------------------------------------------AATGCTTTTCCT--A---TATAAATAGGCCTGCTCACCATTG

Size

Hit Count

Total Norm

droAna3

GATGGATTGGCTTTGGTACGTA------GTCACCAAAGAACATT--------------TAT---T-TTCAA--GT-------------------------------------TATTA-------------T-GAAATA-----------T-CCCTTTTAGGCTTGTTGACCATTG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

GATGGATTGGCTTTGGTAAGTA------TTCCCCAAAGGACATT--------------TAATTG------AATCT---------------------TATTATA------------------------------AACTA-----------T-CTTTTTTAGGTCTGTTAACCATTG

Size

Hit Count

Total Norm

dp4

GCTGGATGGGAATAGGTAAGCC------TTAACTTTGGG--------CAC-----CTTTACGTAG-CTC--------------------------CTTCTCTCGGT------TAT-----------CT--C-TGA-----ATATC--T---TCTGGATAGGGTTGCTAACAATTG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GCTGGATAGGATTCGGTAAGAG------CAGCATTCCGA--------TGG-----ATTTCTATC-----------------------GAT----TCCATTACAGCT------TAT-----------CG--------------GCT--A---CTCCCCCAGGTCTCCTCACCATTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................AGAG------CAxCATTCCGC--------TGG-----AT......................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GTTGGATTGGCTTTGGTATGATTAAAGACTCATTAATATATATTGACTTGAAAT-------------------GG-----------------------------------------------TTGCAA-----------ATTTGT--GAT-TTCTGACAGGTCTTCTAACAATTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................................................................................TAACAGGTCTTCTAGCAA...	18	1	2.00	0.00	0.00	2.00	0.00

droVir3

GCTGGATAGGATTTGGTGAGTG--AATGAGCGGAAATCT-------------------AAAGTA------------------------------GCTTCTCTTAT-----------------TCATCT-----------TTTTCT--T-TCTGCCAACAGGCCTACTAACTATTG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GTTGGATGGGTTTGGGTAAAT-------ATATATAAA--------------ATATA--TATAA---TAAAAAAAT-----TATGT----AAAGAACTTCTCAAATTAAAGTA--------AAT--------------C-----------C-CACTTCCAGGTCTGTTTACAATCG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GCTGGATTGGATTTGGTAAATA------AAATAAACCGG--------CGA-----CT-TAAGTGT---T------------------AAT----CTCACAATA-------------------------AAAAACAT----AATTT--A---CCTTGCCAGGATATTTTACGGTTA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:21:46 EDT

Oatp58Dc_in3

chr2R:18113752-18113821 -

Candidate

mirtron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup