ID:

dvi_9266

Coordinate:

scaffold_12928:7413221-7413371 +

Confidence:

Candidate

Type:

Unknown

[View on UCSC Genome Browser {Cornell Mirror}]

Legend:

mature

star

mismatch in alignment

mismatch in read

Predicted structure

Flybase annnotation

CDS [Dvir\GJ17060-cds]; exon [dvir_GLEANR_17561:1]; intron [Dvir\GJ17060-in]

No Repeatable elements found

Sense Strand Reads

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GAATTTCCTGCGCCAAACATTCAACGTTACGAAACAATTGACGGCACAAGGTAAGTTTTAACAAAAATCCCTATTTAAAACATTGCGTTGCGGCTATTTATTCAACTTCGAGTCCCGTGTTCTATATACATACGCGCCCACGCGCCTAATTGCCAACCATGTGAGGCAGCCGGTAGCCGCTTGCGCACATCCATTTCCAATTGGTGACTGTGCGCATTTTGTGTTTATCCAAGGATCCTGCGTTCCATTGT ************************************************....(((((((.............)))))))..(((((.(((((((((.((((......))))...((((.....))))....((((....))))....(((((..........)))))..)))))))))..)))))..............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V053 head	M047 female body	SRR060663 160_0-2h_embryos_total	SRR060687 9_0-2h_embryos_total	V047 embryo	SRR060674 9x140_ovaries_total	SRR060671 9x160_males_carcasses_total	SRR060686 Argx9_0-2h_embryos_total	M028 head	SRR060668 160x9_males_carcasses_total	SRR060679 140x9_testes_total	SRR060684 140x9_0-2h_embryos_total	SRR060672 9x160_females_carcasses_total	SRR060666 160_males_carcasses_total	SRR060664 9_males_carcasses_total	V116 male body
...............AACATTCAACGTTACGAAACA.......................................................................................................................................................................................................................	21	0	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................CGAGGCAGCCGGTACCCGCCT.....................................................................	21	3	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.................................................................................................................................................................................................................................TAGCCAAGGATCCTGCATT.......	19	2	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
......................................................................CTAATTAAAACATAGCGTTGC................................................................................................................................................................	21	2	1	1.00	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
............................ACGAAACAATTGACGGCACAAGC........................................................................................................................................................................................................	23	1	1	1.00	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
..........................................................................TTAAAACATAGCATTGCG...............................................................................................................................................................	18	2	18	0.72	13	0	1	0	0	0	0	3	3	0	0	2	2	0	0	1	1
................................................................................................................................................................................................AGTGCCAATTGGTGACTGT........................................	19	2	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
.........................................CGACACAAGGTAAATTTTA...............................................................................................................................................................................................	19	2	2	0.50	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
...............................................................................................ATTTATTCAGGTTCGACTCC........................................................................................................................................	20	3	13	0.15	2	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0
........................................................................ATTTAAAACATAGCATTGC................................................................................................................................................................	19	2	8	0.13	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
......................................................................CTACTTAAAACATAGCATTGC................................................................................................................................................................	21	3	10	0.10	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
.......................................GAAGGCACAAGGGAAGTCT.................................................................................................................................................................................................	19	3	16	0.06	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
.......CTGCGCCGAAGATGCAACG.................................................................................................................................................................................................................................	19	3	20	0.05	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

Anti-sense strand reads

CTTAAAGGACGCGGTTTGTAAGTTGCAATGCTTTGTTAACTGCCGTGTTCCATTCAAAATTGTTTTTAGGGATAAATTTTGTAACGCAACGCCGATAAATAAGTTGAAGCTCAGGGCACAAGATATATGTATGCGCGGGTGCGCGGATTAACGGTTGGTACACTCCGTCGGCCATCGGCGAACGCGTGTAGGTAAAGGTTAACCACTGACACGCGTAAAACACAAATAGGTTCCTAGGACGCAAGGTAACA ************************************************....(((((((.............)))))))..(((((.(((((((((.((((......))))...((((.....))))....((((....))))....(((((..........)))))..)))))))))..)))))..............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V116 male body	SRR060662 9x160_0-2h_embryos_total	M047 female body	SRR060687 9_0-2h_embryos_total	SRR060659 Argentina_testes_total	SRR060669 160x9_females_carcasses_total
....................................................................................................................................................................................AACGCGTGGTGGTAAAGGTT...................................................	20	2	1	1.00	1	1	0	0	0	0	0
.................................................................................................................................................................................GCGAACTCGCGTAGGTAAA.......................................................	19	2	4	0.25	1	1	0	0	0	0	0
.........................................................................................................................................................................................GTGTAGGAAAAGGTGAACC...............................................	19	2	5	0.20	1	0	1	0	0	0	0
.................................................................................................................................................................ACCGCGTCGGCCATCGGGGA......................................................................	20	3	8	0.13	1	0	0	1	0	0	0
...............................................................................................................................................................................GTGCGAACTCGTGTAGGTAAA.......................................................	21	3	8	0.13	1	0	1	0	0	0	0
........................................................................................................................AGATATATGAGTGAGCGGGT...............................................................................................................	20	3	9	0.11	1	0	0	0	1	0	0
.................................................................................................................................................................ACCGCGTCGGCCATCGGC........................................................................	18	2	12	0.08	1	0	0	1	0	0	0
...................................................................................................................................................................................GAACTCGCGTAGGTAAAAGT....................................................	20	3	20	0.05	1	0	0	0	0	1	0
..................................................GATGTAAAATTGTTTTTAGGG....................................................................................................................................................................................	21	3	20	0.05	1	0	0	0	0	0	1
.........................................................................................................................................................................................GTGTAGGGAAAGGTGAATC...............................................	19	3	20	0.05	1	1	0	0	0	0	0
................................................................................................................................................................................TGCGAACTCGCGTAGGTAAA.......................................................	20	3	20	0.05	1	1	0	0	0	0	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12928:7413171-7413421 +	dvi_9266	GAATTTCCTGCGCCAAACATTCAACGTTACGAAACAATTGACGGCACAAGGTAAGTTTTA-ACAAAAATCCCTATTT--AAA-----ACATTGCGTTGCGGCTATTTATTCAACTTCG-------------------------------------AGTCCCGTGTTCTATATACATACGCGCCCACGCGCCTAATTGCCAACCATGTGAGGCAGCCGGTAGCCGCTT--------GCGCACATCCATTTCCAATT-GGTGACTGTGCGCATTT-T---------------------GTGTTTATCCAAGGATCCTGCGTTCCATTGT------
droMoj3	scaffold_6473:2636797-2637042 -		GAATTTCCTGCGCCAAACATTCAACGTTACGAAACAGTTGACGACCCAGGGTAAGTTCGGCCCGC-AAGCTTAAT-C-GAAACTTATATA---TGTTCCGG-TATTTGTCCATATTGCAG------------------------------------------TTGTCTAAGCACCGCCACGTCCATGCTCCCTTT-------TATTTGACTAGGCCTGCAGTCGCCAATCAACGGGTCCTCTTCCCTGT-----CAAGTGACTGTGCGCATTTTCT--------------------CTATTTATCCAACGATCCTGCTTTTCATTGT------
droGri2	scaffold_15081:3294868-3294940 -		GAACTTCTTGCGTCAAACATTCAACGTTACGAAACAATTGACGGCCCAAGGTAAACG-------AAAAATCCAAT-T-AGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp5	XL_group1a:3513714-3513938 -		GAACTTCCTGCGGCAAACATTCAGCATTACGAAACAATTGACGGCGCAGGGTAAGTTTG-CCTGC-AAGTTGGC--CAAAAACT-----G-TC--------C----TATCTATTTTGCAGAGGGTCCCTTCAGACAGCCCCTTCAAGATCGGTCTGGTCTGGTCTTCTGTT---------------------------------------------------------------------------TTTACAATC-AATGACTGTGCGCATTT-CTCCCCCTCGCCGTCTGTGCAAGTATTTATCCAGCGATCCT---------TGTCGCGTC
droPer2	scaffold_11:55156-55385 -		GAACTTCCTGCGGCAAACATTCAGCATTACGAAACAATTGACGGCGCAGGGTAAGTTTG-CCTGC-AAGTTGGC--CAAAAACTTGACTG-TC--------C----TATCTATTTTGCAGAGGGTCCCTCCAGACAGCCCCTTCAGGATCGGTCTGGTCTGGTCTTCTGTT---------------------------------------------------------------------------TTTACAATC-AATGACTGTGCGCATTT-CTCCCCCTCGACGTCTGTGCAAGTATTTATCCAGCGATCCT---------TGTCGCGTC
droKik1	scf7180000302258:468812-468872 -		GAACTTCTTGCGGCAAACTTTCGGCATTACGAAACAATTGACGACGCTGGGTGAGTTTTA-A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000453927:135125-135185 -		GAATTTCCTGCGGCAAACTTTCGGCATTACGAAACACCTGACTTCGCTTGGTAAGTTCGA-A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000491011:644760-644816 -		GAATTTCCTGCGGCAAACTTTTGGCATTACGAAACAACTGACTTCGCAGGGTGAGTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000779506:436905-436997 -		GAATTTCCTGCGGCAAACTTTGGGCATTACGAAACAGTTGACTTCACAAGGTGAGTTCA-CCTA--AAATAAGT--TTAAAACTAAAGTAGTGCTTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1	scf7180000415151:473167-473260 +		GAATTTCCTGCGGCAAACCTTGGGCATTACGAAACAGTTGACTTCGCAGGGTAAGTTTAG-ACTA-AAACAAAT--TAAAAGCTCATATATTGCGTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEug1	scf7180000409277:19333-19389 -		GAATTTCCTGCGGCAAACTTTCGGCATTACGAAACAGTTGACATCCCGGGGTAAGTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

GAATTTCCTGCGCCAAACATTCAACGTTACGAAACAATTGACGGCACAAGGTAAGTTTTA-ACAAAAATCCCTATTT--AAA-----ACATTGCGTTGCGGCTATTTATTCAACTTCG-------------------------------------AGTCCCGTGTTCTATATACATACGCGCCCACGCGCCTAATTGCCAACCATGTGAGGCAGCCGGTAGCCGCTT--------GCGCACATCCATTTCCAATT-GGTGACTGTGCGCATTT-T---------------------GTGTTTATCCAAGGATCCTGCGTTCCATTGT------	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
...............AACATTCAACGTTACGAAACA.........................................................................................................................................................................................................................................................................................................	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
............................ACGAAACAATTGACGGCACAAGC..........................................................................................................................................................................................................................................................................................	23	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	1	0	0	0

droMoj3

GAATTTCCTGCGCCAAACATTCAACGTTACGAAACAGTTGACGACCCAGGGTAAGTTCGGCCCGC-AAGCTTAAT-C-GAAACTTATATA---TGTTCCGG-TATTTGTCCATATTGCAG------------------------------------------TTGTCTAAGCACCGCCACGTCCATGCTCCCTTT-------TATTTGACTAGGCCTGCAGTCGCCAATCAACGGGTCCTCTTCCCTGT-----CAAGTGACTGTGCGCATTTTCT--------------------CTATTTATCCAACGATCCTGCTTTTCATTGT------	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

GAACTTCTTGCGTCAAACATTCAACGTTACGAAACAATTGACGGCCCAAGGTAAACG-------AAAAATCCAAT-T-AGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

dp5

GAACTTCCTGCGGCAAACATTCAGCATTACGAAACAATTGACGGCGCAGGGTAAGTTTG-CCTGC-AAGTTGGC--CAAAAACT-----G-TC--------C----TATCTATTTTGCAGAGGGTCCCTTCAGACAGCCCCTTCAAGATCGGTCTGGTCTGGTCTTCTGTT---------------------------------------------------------------------------TTTACAATC-AATGACTGTGCGCATTT-CTCCCCCTCGCCGTCTGTGCAAGTATTTATCCAGCGATCCT---------TGTCGCGTC	Size	Hit Count	Total Norm	Total	M022 Male-body	M040 Female-body	M059 Embryo	M062 Head	V043 Embryo	V051 Head	V112 Male-body	SRR902010 Ovary	SRR902011 Testis	SRR902012 CNS imaginal disc
...................TTCAGCATTACGAAACAATTGACGGC................................................................................................................................................................................................................................................................................................	26	1	2.00	2	0	0	0	0	0	0	0	0	2	0
...........................TACGAAACAATTGACGGCGCAGGC..........................................................................................................................................................................................................................................................................................	24	1	2.00	2	0	2	0	0	0	0	0	0	0	0
..........................TTACGAAACAATTGACGGCGCAG............................................................................................................................................................................................................................................................................................	23	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.AACTTCCTGCGGCAAACATTCAGC....................................................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...................TTCAGCATTACGAAACAATTGACGG.................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.....TCCTGCGGCAAACATTCAGCATTAC...............................................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	0	0	0	0	0	0	1	0	0
....................TCAGCATTACGAAACAATTGACGGCG...............................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................TTACGAAACAATTGACGGCGCAGGC..........................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..........................TTACGAAACAATTGACGGCGCAGG...........................................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
...CTTCCTGCGGCAAACATTCAGCATTAC...............................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....................TCAGCATTACGAAACAATTGACGGCGC..............................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droPer2

GAACTTCCTGCGGCAAACATTCAGCATTACGAAACAATTGACGGCGCAGGGTAAGTTTG-CCTGC-AAGTTGGC--CAAAAACTTGACTG-TC--------C----TATCTATTTTGCAGAGGGTCCCTCCAGACAGCCCCTTCAGGATCGGTCTGGTCTGGTCTTCTGTT---------------------------------------------------------------------------TTTACAATC-AATGACTGTGCGCATTT-CTCCCCCTCGACGTCTGTGCAAGTATTTATCCAGCGATCCT---------TGTCGCGTC	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
GAACTTCCTGCGGCAAACATTCAGCA...................................................................................................................................................................................................................................................................................................................	26	1	1.00	1	0	1	0	0	0	0
......................................................................................................................................................GGTCTGGTCTGGTCTTCTGA...................................................................................................................................................................	20	3	0.67	2	0	0	0	0	0	2
......................................................................................................................................................GGTCTGGTCTGGTCTTCTGT...................................................................................................................................................................	20	2	0.50	1	0	1	0	0	0	0

droKik1

GAACTTCTTGCGGCAAACTTTCGGCATTACGAAACAATTGACGACGCTGGGTGAGTTTTA-A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droFic1

GAATTTCCTGCGGCAAACTTTCGGCATTACGAAACACCTGACTTCGCTTGGTAAGTTCGA-A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

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

droRho1

GAATTTCCTGCGGCAAACTTTGGGCATTACGAAACAGTTGACTTCACAAGGTGAGTTCA-CCTA--AAATAAGT--TTAAAACTAAAGTAGTGCTTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droTak1

GAATTTCCTGCGGCAAACCTTGGGCATTACGAAACAGTTGACTTCGCAGGGTAAGTTTAG-ACTA-AAACAAAT--TAAAAGCTCATATATTGCGTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEug1

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

Generated: 05/16/2015 at 09:38 PM