ID:

dvi_14400

Coordinate:

scaffold_13042:2264494-2264644 -

Confidence:

Candidate

Type:

Unknown

[View on UCSC Genome Browser {Cornell Mirror}]

Legend:

mature

star

mismatch in alignment

mismatch in read

Predicted structure

Flybase annnotation

exon [dvir_GLEANR_16119:3]; CDS [Dvir\GJ15679-cds]; intron [Dvir\GJ15679-in]

No Repeatable elements found

Sense Strand Reads

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ACCCATATCCAGTGTGCTGGAGGAGCTGCTCAAAAACACCGGCTATGATGGTAAGTAAGCAATTCCTTAAACCTAAGTTGGAATTGTTGGGAGCATGCGGCTTGACAGGCAGCTCACTGATTAGTTGCGTTCAAGGATTTTCCTGGCATCAACAATGCGGTTTAATAGTGTGAAAGATCCTGGAAGATGGAAAATCAATTCGGCAATTTGTTGGCCATTCTCGCTGAACTGCTTTCCCCATGTTTCTTGTA ************************************************.......(((((((((.............)))))))))..((((..((((((...(((........)))...))))))))))....(((((((.((.(((....((((.........))))....))))).))))))).............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060659 Argentina_testes_total	GSM1528803 follicle cells	M047 female body	SRR060658 140_ovaries_total	SRR060667 160_females_carcasses_total	SRR060676 9xArg_ovaries_total	SRR060681 Argx9_testes_total	SRR060678 9x140_testes_total	SRR060683 160_testes_total	SRR060660 Argentina_ovaries_total	SRR060682 9x140_0-2h_embryos_total	SRR060689 160x9_testes_total	SRR060684 140x9_0-2h_embryos_total
.........................................................................................................................................................AATGCGGTGTAATCGCGTGAA.............................................................................	21	3	1	2.00	2	1	0	0	0	1	0	0	0	0	0	0	0	0
...................GAGGAGCTGCTCAAAAACACCGGCTA..............................................................................................................................................................................................................	26	0	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0	0	0
.......................................................................................................................................................................................................................AATTCTCGCGGAAGTGCTTTCCCC............	24	3	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0
....ATATCCAGTGTGCTGGAGGAGCT................................................................................................................................................................................................................................	23	0	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0
..................................AACACCGGCTATGATGAT.......................................................................................................................................................................................................	18	1	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0
.............GTGCTGGAGGAGCTGCTCAAAAACACC...................................................................................................................................................................................................................	27	0	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0
................................................................................GAATTGTTGGGAGCATCTGGCT.....................................................................................................................................................	22	2	1	1.00	1	0	0	0	0	0	0	1	0	0	0	0	0	0
ACCCATATCCAGTGTGCTGGA......................................................................................................................................................................................................................................	21	0	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................................ATTCTCGCTGAACTGCTTTCCCCA...........	24	0	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0
................................................................................GAATTGTTGGGACCATGTGG.......................................................................................................................................................	20	2	2	0.50	1	0	0	0	0	0	0	0	1	0	0	0	0	0
.........................................................................................................................................................AATGCGGTGTAATCGCGTGA..............................................................................	20	3	3	0.33	1	0	0	0	0	0	0	0	0	1	0	0	0	0
.................................ATACACCGGCTAAGATTGT.......................................................................................................................................................................................................	19	3	14	0.07	1	0	0	0	0	0	0	0	0	0	0	1	0	0
.........................................................................................................................................................AATGCGGTGTAATCGCGTG...............................................................................	19	3	14	0.07	1	0	0	0	0	0	0	0	0	0	1	0	0	0
.................................................................................................................................................................................TGCTGGAAGATGGAAAAA........................................................	18	2	18	0.06	1	0	0	0	0	0	0	0	0	0	0	0	1	0
........................................................................................................................................................CAATGCGGTGTAATCGCG.................................................................................	18	3	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0
....................................................................AAACCTTAGTTGGATTGGT....................................................................................................................................................................	19	3	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	1

Anti-sense strand reads

TGGGTATAGGTCACACGACCTCCTCGACGAGTTTTTGTGGCCGATACTACCATTCATTCGTTAAGGAATTTGGATTCAACCTTAACAACCCTCGTACGCCGAACTGTCCGTCGAGTGACTAATCAACGCAAGTTCCTAAAAGGACCGTAGTTGTTACGCCAAATTATCACACTTTCTAGGACCTTCTACCTTTTAGTTAAGCCGTTAAACAACCGGTAAGAGCGACTTGACGAAAGGGGTACAAAGAACAT ************************************************.......(((((((((.............)))))))))..((((..((((((...(((........)))...))))))))))....(((((((.((.(((....((((.........))))....))))).))))))).............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060666 160_males_carcasses_total	V053 head	V047 embryo
...........................CGAGTTTTTGTGCCCGAT..............................................................................................................................................................................................................	18	1	1	1.00	1	1	0	0
............................................................................................................CGCCCAGTGACTAATCTAC............................................................................................................................	19	3	7	0.14	1	1	0	0
..............................GTTCTTGTGGCTGAGACTAC.........................................................................................................................................................................................................	20	3	11	0.09	1	0	1	0
....................................................................................................................................................................................ATCTTCCACCTTTTACTTAA...................................................	20	3	20	0.05	1	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_13042:2264444-2264694 -	dvi_14400	ACCCAT---ATCCAGT-----GTG------CTGG-----------AGGAGCTGCTCAAAAACACCGGCTATGATGGTAAGTAAGC-------AATTCCTTAAACCTAAGTTGGAATTGTTGGGAGCATGCGGCTTGACAGGCAGCTCACTGATTAGTTGCGTTCAAGGATTTTCCTGGCATCAACAATGCGGTTTAATA------GTGTGAAAGATCCTGGAAGATGG-------------------------------------------------AAAATCAATTCGGCAA---------------TTTGTTGGCCATTCTCGCTGAACT--------------------------------------------GCTTTCCCCATGTTTCTTGTA
droMoj3	scaffold_6328:1296605-1296673 +		GCCCAT---TAGTACA-----GTG------CTAG-----------ACGATCTGCTCAAGACAACTGGCTTTGATGGTAAGTAACA-----GAAATTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT
droGri2	scaffold_15203:6223809-6223811 +		GTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil2	scf2_1100000004909:1184127-1184189 +		TTCTGCAGCTTCCAAA-----GTG------ATTA-----------CCGAACTTCTCCAGTCTACAGGACATGCTGGTAAGTCAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13045:909687-909785 +		AATAGT---------------------------------------AGGGCTTATTAGTGC-----------------------------------------------------------------------------------------------------------------------------------------------CGATT---------TTAGATGTTC--------------------------------------------------GAAGGTAGTTTGACAG---------------TTAGCTGTCCACTCGAATTTTACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA
droBip1	scf7180000395673:7016-7124 +		TTCTTTGC----AAC--------A------GAGT-----------TTGGTTTATTAATGC-----------------------------------------------------------------------------------------------------------------------------------------------TGATT---------TAAAATGTTC--------------------------------------------------AAAGGCGTTTTGACAT---------------TCTGTAGTCCATTCGAATTTTACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA
droKik1	scf7180000298918:1234-1373 -		TCCTTCAGCCAGAAAA-----AGT---------------------ATTATTTTATA-TTT-----------------------------------------------------------------------------------------------------------------------------------------------TGAAA---------TCAAATTTTG--------------------------------------------------GAGGACAATTCGGAAA---------------GCTGTT-----------CTGAATTGGGTTTTCTACGCTTAACAAATCTGCATACTACATTTAGGGCTTTTTATACCCTTGCA--GGGTA
droFic1	scf7180000454072:751121-751159 -		GGA----------------------------------------------GCTGCTCGGACCCACGGGATACAGTGGTAAGTAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000491033:157823-158048 -		ATATCA----AGTAAG-----CTG-----AACAG-----------AGGGTTTATTTAAAAAAACAAGAAAGAAAGCAAACAAAGCAAGCAAGCCG-----------AAGTTC------ATATACCCTTGCAGCT--ACAAGTATTGCAATAATTAAACATTTTTGAA---------AACATTAAAATTATGATTTACTTGCGTATATGTGAAACAACAT------------------------------------------------------------TGTAGCTATGATGATTTGCAGCTCAATAATTAGATA----------------G------------------------------------------TTATTATACCCTTCCAGAGGGTA
droRho1	scf7180000765085:458-627 -		CGGCTTGC----CGAAGTTAGCTTCCGTCCTCGTTGCGTTTATTTTTGATCTGTCG---ACAATCA---AGTTTGAAAACGAAACATTCAGGTCA-----------AAAT--------------------------------------------------------------------------------------------------------------------GTATAATTTCGCCGGTTTTTTTGTAAGTTGAGTATAGATCGCCAATTTTTGGAG------------------------------------------------AACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA
droBia1	scf7180000301398:6534-6536 +		GTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000410408:25722-25817 +		TTTAGTAATGTGA----------------------------------------------AAAATTAAAGTGAATGAAAAAGAAAATATCAGATCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTTTGCATTCTTTAAATTTGTA------------------------------------------TTTTTATACCCTTGTAGAGGGTA
droEug1	scf7180000409522:331602-331674 +		TCCTT----ATCTGTT-----GCG------ATAA-----------CTGATCTGCTTAGACCCACCGGATACAGTGGTGAGTGGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------AACCTATACCT----------TA
droYak3	X:2623807-2623854 +		TGT--------------------G------ATCT-----------TGGGTCTGTTAAAACCCACGGGATACAGTGGTGAGTGAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

ACCCAT---ATCCAGT-----GTG------CTGG-----------AGGAGCTGCTCAAAAACACCGGCTATGATGGTAAGTAAGC-------AATTCCTTAAACCTAAGTTGGAATTGTTGGGAGCATGCGGCTTGACAGGCAGCTCACTGATTAGTTGCGTTCAAGGATTTTCCTGGCATCAACAATGCGGTTTAATA------GTGTGAAAGATCCTGGAAGATGG-------------------------------------------------AAAATCAATTCGGCAA---------------TTTGTTGGCCATTCTCGCTGAACT--------------------------------------------GCTTTCCCCATGTTTCTTGTA	Size	Hit Count	Total Norm	Total	M027 Male-body	M028 Head	M047 Female-body	M061 Embryo	SRR060654 Ovary	SRR060655 Testis	SRR060656 Ovary	SRR060657 Testis	SRR060658 Ovary	SRR060659 Testis	SRR060660 Ovary	SRR060661 Embryo	SRR060662 Embryo	SRR060663 Embryo	SRR060664 Male-body	SRR060665 Female-body	SRR060666 Male-body	SRR060667 Female-body	SRR060668 Male-body	SRR060669 Female-body	SRR060670 Testis	SRR060671 Male-body	SRR060672 Female-body	SRR060673 Ovary	SRR060674 Ovary	SRR060675 Ovary	SRR060676 Ovary	SRR060677 Ovary	SRR060678 Testis	SRR060679 Testis	SRR060680 Testis	SRR060681 Testis	SRR060682 Embryo	SRR060683 Testis	SRR060684 Embryo	SRR060685 Embryo	SRR060686 Embryo	SRR060687 Embryo	SRR060688 Ovary	SRR060689 Testis	SRR1106712 embryo_0-2h	SRR1106713 embryo_0-2h	SRR1106714 embryo_2-4h	SRR1106715 embryo_4-6h	SRR1106716 embryo_4-6h	SRR1106717 embryo_6-8h	SRR1106718 embryo_6-8h	SRR1106719 embryo_8-10h	SRR1106720 embryo_8-10h	SRR1106721 embryo_10-12h	SRR1106722 embryo_10-12h	SRR1106723 embryo_12-14h	SRR1106724 embryo_12-14h	SRR1106725 embryo_14-16h	SRR1106726 embryo_14-16h	SRR1106727 larvae	SRR1106728 larvae	SRR1106729 mixed whole adult body	SRR1106730 embryo_16-30h	V047 Embryo	V053 Head	V116 Male-body	GSM1528803 follicle cells
.................................G-----------AGGAGCTGCTCAAAAACACCGGCTA.......................................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
....AT---ATCCAGT-----GTG------CTGG-----------AGGAGCT.........................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.....................GTG------CTGG-----------AGGAGCTGCTCAAAAACACC............................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
ACCCAT---ATCCAGT-----GTG------CTGG-----------A...............................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
..............................................................................................................................................................................................................................................................................................................................ATTCTCGCTGAACT--------------------------------------------GCTTTCCCCA...........	24	1	1.00	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1

droMoj3

GCCCAT---TAGTACA-----GTG------CTAG-----------ACGATCTGCTCAAGACAACTGGCTTTGATGGTAAGTAACA-----GAAATTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

GTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

TTCTGCAGCTTCCAAA-----GTG------ATTA-----------CCGAACTTCTCCAGTCTACAGGACATGCTGGTAAGTCAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
...............................TTA-----------CCGAACTTCTCCAGTCTACAG...........................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0

droAna3

AATAGT---------------------------------------AGGGCTTATTAGTGC-----------------------------------------------------------------------------------------------------------------------------------------------CGATT---------TTAGATGTTC--------------------------------------------------GAAGGTAGTTTGACAG---------------TTAGCTGTCCACTCGAATTTTACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
.....................................................................................................................................................................................................................................................................................................................................TTTTACA------------------------------------------TTTTTATACCCTTGCAGAGG...	27	6	0.17	1	1	0	0	0	0	0

droBip1

TTCTTTGC----AAC--------A------GAGT-----------TTGGTTTATTAATGC-----------------------------------------------------------------------------------------------------------------------------------------------TGATT---------TAAAATGTTC--------------------------------------------------AAAGGCGTTTTGACAT---------------TCTGTAGTCCATTCGAATTTTACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

TCCTTCAGCCAGAAAA-----AGT---------------------ATTATTTTATA-TTT-----------------------------------------------------------------------------------------------------------------------------------------------TGAAA---------TCAAATTTTG--------------------------------------------------GAGGACAATTCGGAAA---------------GCTGTT-----------CTGAATTGGGTTTTCTACGCTTAACAAATCTGCATACTACATTTAGGGCTTTTTATACCCTTGCA--GGGTA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GGA----------------------------------------------GCTGCTCGGACCCACGGGATACAGTGGTAAGTAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

ATATCA----AGTAAG-----CTG-----AACAG-----------AGGGTTTATTTAAAAAAACAAGAAAGAAAGCAAACAAAGCAAGCAAGCCG-----------AAGTTC------ATATACCCTTGCAGCT--ACAAGTATTGCAATAATTAAACATTTTTGAA---------AACATTAAAATTATGATTTACTTGCGTATATGTGAAACAACAT------------------------------------------------------------TGTAGCTATGATGATTTGCAGCTCAATAATTAGATA----------------G------------------------------------------TTATTATACCCTTCCAGAGGGTA	Size	Hit Count	Total Norm	Total
No Reads

droRho1

CGGCTTGC----CGAAGTTAGCTTCCGTCCTCGTTGCGTTTATTTTTGATCTGTCG---ACAATCA---AGTTTGAAAACGAAACATTCAGGTCA-----------AAAT--------------------------------------------------------------------------------------------------------------------GTATAATTTCGCCGGTTTTTTTGTAAGTTGAGTATAGATCGCCAATTTTTGGAG------------------------------------------------AACA------------------------------------------TTTTTATACCCTTGCAGAGGGTA	Size	Hit Count	Total Norm	Total
No Reads

droBia1

GTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTTAGTAATGTGA----------------------------------------------AAAATTAAAGTGAATGAAAAAGAAAATATCAGATCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTTTGCATTCTTTAAATTTGTA------------------------------------------TTTTTATACCCTTGTAGAGGGTA	Size	Hit Count	Total Norm	Total
No Reads

droEug1

TCCTT----ATCTGTT-----GCG------ATAA-----------CTGATCTGCTTAGACCCACCGGATACAGTGGTGAGTGGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------AACCTATACCT----------TA	Size	Hit Count	Total Norm	Total
No Reads

droYak3

TGT--------------------G------ATCT-----------TGGGTCTGTTAAAACCCACGGGATACAGTGGTGAGTGAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M026 Head	M043 Female-body	M056 Embryo	V046 Embryo	V052 Head	V058 Head	V120 Male-body	SRR1275488 Male larvae	SRR1275486 Male prepupae	SRR1275484 Male prepupae	GSM1528802 follicle cells
...........................................................CCCACGGGATACAGTGGTGAGT............................................................................................................................................................................................................................................................................................................................	22	1	1.00	1	0	0	0	0	0	1	0	0	0	0	0

Generated: 05/17/2015 at 04:18 AM