dme-mir-2497- Best orthologs

dme-mir-2497	chr2L:16678250-16678317 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 16678250-16678274
   star strand at position 16678297-16678317
   mutations
   read mismatches

Notes: "Orthologs does not look confident from droWil1 - droGri2 due to loss of splice acceptor site. The miRNA is only present in dm3. droRho1 othologous intron may be too large for LASTZ to span the entire region, hence two disjoint hits were reported."

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:16678235-16678332 +		1	GATAAGCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATG-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATCATTAACA-ACA-TTTACAATGT--TTGCAGGCTGTCAACGTTGAT
droSim1	chr2L:16366233-16366322 +	LASTZ	5	GATAAGCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT
droSec1	super_7:325110-325199 +	LASTZ	5	GATAAGCATGTTATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------CTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT
droYak2	chr2R:4424626-4424717 -	LASTZ	5	GATAAGCACGTCATCGTAAGCTTTGCTAT--------------------------------------------ATA-----T-----------GTAG------------------AT------------------------------------------------------------------GTGAATTTCGAGCTTCAATTCTTTT-------C---TATTCT--CTTCAGGCTGTCAATGTTAAT
droEre2	scaffold_4845:19748460-19748547 +	LASTZ	5	GATAAGCACGTTATTGTAAGCTGCGCCA----------------------------------------------TA-----T-------------AG------------------TT------------------------------------------------------------------CGTAAATTCGAGCTTCAATTATGTT-------C---TATTCT--CTCCAGGCTGTCAATGTTAAT
droEug1	scf7180000408961:253912-254004 +	LASTZ	5	AATAAGCAACTTATTGTAGGCAACATAAT--------------------------------------------TTA-----A-------------TA------------------AT----------------------GT-------------------------------------------TGAATCTCAGATTCTAATCCTACT-------TTT-ACTTCC--TTTTAGGCAGTCAATATGGAT
droBia1	scf7180000301468:836914-837003 +	LASTZ	5	GATAAGCAAGTCATTGTAAGCTACTAAAC--------------------------------------------T--GCCTGT---TTAT----AT-------------------------------------CCAAATTACT---------------------------------------------------------GACTATA---------ATTCTCGTCC--AACCAGGCTGTCAATGTAAAT
droTak1	scf7180000415914:402900-403000 +	LASTZ	5	GATAAGCAAGTTATTGTAAGCTACACATT--------------------------------------------TTA--TCTT---TTGCAACCAA-------------------------------------AGAG--AGCC------------------------------------------TA-TTCTAATAC-----------T--CTATTC---CACGCAACCCACAGGCAGTCAATGTGAAT
droEle1	scf7180000490579:668430-668616 -	LASTZ	5	AATAAACAAGTTATTGTGAGTCCAAAT--TTAAGGCTTTTTTAAGTACGAAAACTATCATCA-TTAATCCGTTAC----------ATTT--------------------------TTGACATGGGCTAGCTTTAACTAGGCTGAAAATTGAATATTATTACGATTACTAATATATATACTAATAC--------------GAACTTACT--TTG-TC---TTTTCT--CCTCAGGCGGTCAACGTGAAC
droRho1	scf7180000777347:13383-13513 -	LASTZ	5	AATAAACAAGTTATTGTAAGTAAGGAATT--AAGGCTTCTTTGAGTAA-----------TCA-T--AT-----TCG-----A-------------CAAGAGCAATTCACATATTTTTGACATGTTTTG----------------------------------------------------------------ACCT---ACTTCATCG------CT---ATATTT--TTCCAGGCTGTCAACGTTAAT
droFic1	scf7180000449814:1574-1709 -	LASTZ	5	AACAAACAAGTCATCGTAAGTAATCAAGG------CTTTCTTCATCAGAAAGGTTATTTTTAGCCAAA-----ATA-----CAGGATTT----TT-------------------------------------GGATTAAACTAA-----TAA--------------------------------TA-TTTTTACAT-----------T--TTGTACT--GCTTGT--CCCCAGGCTGTTAATGTAAAT
droKik1	scf7180000302382:508886-508975 +	LASTZ	5	GACAAGCAAGTGATTGTAAGTTAAGCGAA--------------------------------------------TTC-----A-------------AG------------------AT------------------------------------------------------------------TTTCTAGCCCTAGTACGACCCTTCT-------C---GTTTCT--GACCAGGCTGTCAACGTGAAT
droAna3	scaffold_12916:15881689-15881781 -	LASTZ	5	GAAAAGCAAGTGATTGTAAGATGTAAACTCTTAGACCCTCCTAACTG----------------------------------------------CT-------------------------------------ACA---AGCT---------------------------------------------------------AATACTTTT-------G---CTTTGA--ATCCAGGCTGTTAACGTGAAC
droBip1	scf7180000396717:120661-120753 -	LASTZ	5	GAAAAGCAAGTGATTGTAAGTTTCGAACTCTAAGACCCAAGTAGGTG----------------------------------------------CC-------------------------------------ACAAACTATA---------------------------------------------------------AGT---TTT-------G---CTTTCA--ATCCAGGCTGTTAACGTGAAC
dp4	chr4_group3:8422191-8422279 +	LASTZ	5	CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TTAATC--TTCTAGGCTGTCGAATTAAAT
droPer1	super_1:9873274-9873362 +	LASTZ	5	CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TGAATC--TTCTAGGCTGTCGAATTAAAT
droWil1	scaffold_181132:892502-892596 -	MAF	5	GACAAAGAAGTGATTGTAGGTGTCAATGA-------T------------------------------------T--------------T----CA-------------------------------------AACTAACATC--------AA------------------------------TTTTTTATTAAC-----GTCTTTATT-------T---TTTCCT--ATTCAGGCTATCAATGTCAAT
droVir3	Unknown	MAF	0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	MAF	0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	GATAAGCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATG-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATCATTAACA-ACA-TTTACAATGT--TTGCAGGCTGTCAACGTTGAT
droSim1	GATAAGCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT
droSec1	GATAAGCATGTTATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------CTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT
droYak2	GATAAGCACGTCATCGTAAGCTTTGCTAT--------------------------------------------ATA-----T-----------GTAG------------------AT------------------------------------------------------------------GTGAATTTCGAGCTTCAATTCTTTT-------C---TATTCT--CTTCAGGCTGTCAATGTTAAT
droEre2	GATAAGCACGTTATTGTAAGCTGCGCCA----------------------------------------------TA-----T-------------AG------------------TT------------------------------------------------------------------CGTAAATTCGAGCTTCAATTATGTT-------C---TATTCT--CTCCAGGCTGTCAATGTTAAT
droEug1	AATAAGCAACTTATTGTAGGCAACATAAT--------------------------------------------TTA-----A-------------TA------------------AT----------------------GT-------------------------------------------TGAATCTCAGATTCTAATCCTACT-------TTT-ACTTCC--TTTTAGGCAGTCAATATGGAT
droBia1	GATAAGCAAGTCATTGTAAGCTACTAAAC--------------------------------------------T--GCCTGT---TTAT----AT-------------------------------------CCAAATTACT---------------------------------------------------------GACTATA---------ATTCTCGTCC--AACCAGGCTGTCAATGTAAAT
droTak1	GATAAGCAAGTTATTGTAAGCTACACATT--------------------------------------------TTA--TCTT---TTGCAACCAA-------------------------------------AGAG--AGCC------------------------------------------TA-TTCTAATAC-----------T--CTATTC---CACGCAACCCACAGGCAGTCAATGTGAAT
droEle1	AATAAACAAGTTATTGTGAGTCCAAAT--TTAAGGCTTTTTTAAGTACGAAAACTATCATCA-TTAATCCGTTAC----------ATTT--------------------------TTGACATGGGCTAGCTTTAACTAGGCTGAAAATTGAATATTATTACGATTACTAATATATATACTAATAC--------------GAACTTACT--TTG-TC---TTTTCT--CCTCAGGCGGTCAACGTGAAC
droRho1	AATAAACAAGTTATTGTAAGTAAGGAATT--AAGGCTTCTTTGAGTAA-----------TCA-T--AT-----TCG-----A-------------CAAGAGCAATTCACATATTTTTGACATGTTTTG----------------------------------------------------------------ACCT---ACTTCATCG------CT---ATATTT--TTCCAGGCTGTCAACGTTAAT
droFic1	AACAAACAAGTCATCGTAAGTAATCAAGG------CTTTCTTCATCAGAAAGGTTATTTTTAGCCAAA-----ATA-----CAGGATTT----TT-------------------------------------GGATTAAACTAA-----TAA--------------------------------TA-TTTTTACAT-----------T--TTGTACT--GCTTGT--CCCCAGGCTGTTAATGTAAAT
droKik1	GACAAGCAAGTGATTGTAAGTTAAGCGAA--------------------------------------------TTC-----A-------------AG------------------AT------------------------------------------------------------------TTTCTAGCCCTAGTACGACCCTTCT-------C---GTTTCT--GACCAGGCTGTCAACGTGAAT
droAna3	GAAAAGCAAGTGATTGTAAGATGTAAACTCTTAGACCCTCCTAACTG----------------------------------------------CT-------------------------------------ACA---AGCT---------------------------------------------------------AATACTTTT-------G---CTTTGA--ATCCAGGCTGTTAACGTGAAC
droBip1	GAAAAGCAAGTGATTGTAAGTTTCGAACTCTAAGACCCAAGTAGGTG----------------------------------------------CC-------------------------------------ACAAACTATA---------------------------------------------------------AGT---TTT-------G---CTTTCA--ATCCAGGCTGTTAACGTGAAC
dp4	CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TTAATC--TTCTAGGCTGTCGAATTAAAT
droPer1	CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TGAATC--TTCTAGGCTGTCGAATTAAAT
droWil1	GACAAAGAAGTGATTGTAGGTGTCAATGA-------T------------------------------------T--------------T----CA-------------------------------------AACTAACATC--------AA------------------------------TTTTTTATTAAC-----GTCTTTATT-------T---TTTCCT--ATTCAGGCTATCAATGTCAAT

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																		None	None	None
UNAFold Image																		None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

GATAAGCACGTCATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------GTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..TAACCAGGTCATCGTAAGC...................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droSec1

GATAAGCATGTTATCGTAAGCATTGCAAA--------------------------------------------ATA-----T-------------AG------------------TT------------------------------------------------------------------CTTAAATTCGCTCTTCAATTATTTA-------C---TATTGA--TTGCAGGCTGTCAACGTTGAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................................................................................................................................................................TATTGA--TTGCAGGAGGTC.........	18	1	2.00	0.00	2.00	0.00
.......................................................................................................................................................................................................ATTTATTTA-------C---TTTTGA--TT...................	18	1	1.00	0.00	1.00	0.00

droYak2

GATAAGCACGTCATCGTAAGCTTTGCTAT--------------------------------------------ATA-----T-----------GTAG------------------AT------------------------------------------------------------------GTGAATTTCGAGCTTCAATTCTTTT-------C---TATTCT--CTTCAGGCTGTCAATGTTAAT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GATAAGCACGTTATTGTAAGCTGCGCCA----------------------------------------------TA-----T-------------AG------------------TT------------------------------------------------------------------CGTAAATTCGAGCTTCAATTATGTT-------C---TATTCT--CTCCAGGCTGTCAATGTTAAT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

AATAAGCAACTTATTGTAGGCAACATAAT--------------------------------------------TTA-----A-------------TA------------------AT----------------------GT-------------------------------------------TGAATCTCAGATTCTAATCCTACT-------TTT-ACTTCC--TTTTAGGCAGTCAATATGGAT

Size

Hit Count

Total Norm

droBia1

GATAAGCAAGTCATTGTAAGCTACTAAAC--------------------------------------------T--GCCTGT---TTAT----AT-------------------------------------CCAAATTACT---------------------------------------------------------GACTATA---------ATTCTCGTCC--AACCAGGCTGTCAATGTAAAT

Size

Hit Count

Total Norm

droTak1

GATAAGCAAGTTATTGTAAGCTACACATT--------------------------------------------TTA--TCTT---TTGCAACCAA-------------------------------------AGAG--AGCC------------------------------------------TA-TTCTAATAC-----------T--CTATTC---CACGCAACCCACAGGCAGTCAATGTGAAT

Size

Hit Count

Total Norm

droEle1

AATAAACAAGTTATTGTGAGTCCAAAT--TTAAGGCTTTTTTAAGTACGAAAACTATCATCA-TTAATCCGTTAC----------ATTT--------------------------TTGACATGGGCTAGCTTTAACTAGGCTGAAAATTGAATATTATTACGATTACTAATATATATACTAATAC--------------GAACTTACT--TTG-TC---TTTTCT--CCTCAGGCGGTCAACGTGAAC

Size

Hit Count

Total Norm

droRho1

AATAAACAAGTTATTGTAAGTAAGGAATT--AAGGCTTCTTTGAGTAA-----------TCA-T--AT-----TCG-----A-------------CAAGAGCAATTCACATATTTTTGACATGTTTTG----------------------------------------------------------------ACCT---ACTTCATCG------CT---ATATTT--TTCCAGGCTGTCAACGTTAAT

Size

Hit Count

Total Norm

droFic1

AACAAACAAGTCATCGTAAGTAATCAAGG------CTTTCTTCATCAGAAAGGTTATTTTTAGCCAAA-----ATA-----CAGGATTT----TT-------------------------------------GGATTAAACTAA-----TAA--------------------------------TA-TTTTTACAT-----------T--TTGTACT--GCTTGT--CCCCAGGCTGTTAATGTAAAT

Size

Hit Count

Total Norm

droKik1

GACAAGCAAGTGATTGTAAGTTAAGCGAA--------------------------------------------TTC-----A-------------AG------------------AT------------------------------------------------------------------TTTCTAGCCCTAGTACGACCCTTCT-------C---GTTTCT--GACCAGGCTGTCAACGTGAAT

Size

Hit Count

Total Norm

droAna3

GAAAAGCAAGTGATTGTAAGATGTAAACTCTTAGACCCTCCTAACTG----------------------------------------------CT-------------------------------------ACA---AGCT---------------------------------------------------------AATACTTTT-------G---CTTTGA--ATCCAGGCTGTTAACGTGAAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........AGTGATTGAAAGATGAAAA.............................................................................................................................................................................................................................	19	1	4.00	3.00	1.00	0.00	0.00
.................AAGGTxTAAACTCTTAGACC...................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.ATAAGCAAGTGAATGTA......................................................................................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
....AGCAAGCGATAGTAAGAT..................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........AGTGATGGTAAGATGAAA..............................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.GAAAGCAAGTGATGGTAA.....................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droBip1

GAAAAGCAAGTGATTGTAAGTTTCGAACTCTAAGACCCAAGTAGGTG----------------------------------------------CC-------------------------------------ACAAACTATA---------------------------------------------------------AGT---TTT-------G---CTTTCA--ATCCAGGCTGTTAACGTGAAC

Size

Hit Count

Total Norm

dp4

CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TTAATC--TTCTAGGCTGTCGAATTAAAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.........CTGAAAGTAAGTACTGGA.............................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CAAAAGCAGCTGATAGTGAGTACTGGAAG--------------------------------------------C--ATTTAT---ATCT----CT-------------------------------------GGAAAGCACT---------------------------------------------------------AATTCTTTT-------T---TGAATC--TTCTAGGCTGTCGAATTAAAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........GCTGGGAGTGAGTACTGG..............................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

GACAAAGAAGTGATTGTAGGTGTCAATGA-------T------------------------------------T--------------T----CA-------------------------------------AACTAACATC--------AA------------------------------TTTTTTATTAAC-----GTCTTTATT-------T---TTTCCT--ATTCAGGCTATCAATGTCAAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......AACTGATTGTTGGTGTCA...............................................................................................................................................................................................................................	18	1	2.00	0.00	1.00	0.00	1.00
.............................................................................................AA-------------------------------------AACGAACATC--------AA------------------------------TTTTTT............................................................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:28:33 EDT

dme-mir-2497

chr2L:16678250-16678317 +

Known_mirbase

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