ID:

dvi_20146

Coordinate:

scaffold_13049:15993704-15993854 -

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_11728:3]; CDS [Dvir\GJ11709-cds]; intron [Dvir\GJ11709-in]

No Repeatable elements found

Sense Strand Reads

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TCAGCCAGGCATGCCACCGGCTCATCCGCAACCTGGCATGGGGCCAGCAGGTAAGTTTTACTATTGCTTTCTTAATAAGACATGGGCTTCTATGCTGCAACTACTAATGAAAACCACATCGATAAAAACGCGTATGTACACGTATATATTTGGGGGCGCCATGCCAACATTGAAAACAAGTGCAAGATCACAATCAGAATTCTCTGAAACAATTGAGACAAAAGAAATCATTCAATAGCCGATCTTCCACA ************************************************....(((((....(((.((((.........((((((((((((............................((((...(((.((....)).)))...))))))))))).)))))........)))).)))....))))).............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M028 head	M047 female body	SRR060686 Argx9_0-2h_embryos_total	V053 head	V116 male body	SRR060667 160_females_carcasses_total	SRR060668 160x9_males_carcasses_total	SRR060687 9_0-2h_embryos_total	M027 male body	M061 embryo	SRR060661 160x9_0-2h_embryos_total	SRR060679 140x9_testes_total	SRR060682 9x140_0-2h_embryos_total
..................................GGCATGGGGCCAGCAGGC.......................................................................................................................................................................................................	18	1	1	1.00	1	0	1	0	0	0	0	0	0	0	0	0	0	0
..................................................................CTTTCTTAATAGGACATGGGCT...................................................................................................................................................................	22	1	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0	0	0
.........................CCGCAACCTGGCATGGGGC...............................................................................................................................................................................................................	19	0	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0	0	0
.................CGGCTCATCGGTAATCTGGC......................................................................................................................................................................................................................	20	3	7	0.71	5	0	0	0	5	0	0	0	0	0	0	0	0	0
....................................................................................................................................................................................................................................CATTCAATAACTGATCTTCCG..	21	3	2	0.50	1	0	0	0	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................................AAGTGCGACATCACAATGAGA.....................................................	21	3	3	0.33	1	0	0	0	0	0	1	0	0	0	0	0	0	0
..................CGCTCAACCGCTACCTGGCA.....................................................................................................................................................................................................................	20	3	5	0.20	1	0	0	0	0	0	0	1	0	0	0	0	0	0
............................................CAGCAGGTAAGTTTCACG.............................................................................................................................................................................................	18	2	7	0.14	1	0	0	0	0	0	0	0	1	0	0	0	0	0
............................................................................................................GAATGCCACGTCGATAAAAA...........................................................................................................................	20	3	20	0.10	2	0	0	0	0	0	0	0	1	0	0	0	1	0
..................................................................................TGGGATTGTAGGCTGCAACT.....................................................................................................................................................	20	3	10	0.10	1	0	0	0	0	0	0	0	0	0	1	0	0	0
..................................................................................................................................................................................................................................GTCATTCAGTAGGCGATCT......	19	3	13	0.08	1	0	0	0	0	0	0	0	0	1	0	0	0	0
...................................................................................CGGTTTCTATGCTCCAACT.....................................................................................................................................................	19	3	17	0.06	1	0	0	0	0	0	0	0	0	0	0	1	0	0
..................................................................................TCGGATTGTATGCTGCAACT.....................................................................................................................................................	20	3	20	0.05	1	0	0	0	0	0	0	0	0	1	0	0	0	0
.............................................................................AGACATGGGCTTCGTTGAT...........................................................................................................................................................	19	3	20	0.05	1	0	0	0	0	0	0	0	0	0	0	0	0	1

Anti-sense strand reads

AGTCGGTCCGTACGGTGGCCGAGTAGGCGTTGGACCGTACCCCGGTCGTCCATTCAAAATGATAACGAAAGAATTATTCTGTACCCGAAGATACGACGTTGATGATTACTTTTGGTGTAGCTATTTTTGCGCATACATGTGCATATATAAACCCCCGCGGTACGGTTGTAACTTTTGTTCACGTTCTAGTGTTAGTCTTAAGAGACTTTGTTAACTCTGTTTTCTTTAGTAAGTTATCGGCTAGAAGGTGT ************************************************....(((((....(((.((((.........((((((((((((............................((((...(((.((....)).)))...))))))))))).)))))........)))).)))....))))).............************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	SRR060672 9x160_females_carcasses_total	SRR060664 9_males_carcasses_total	SRR060666 160_males_carcasses_total	SRR060669 160x9_females_carcasses_total	SRR060679 140x9_testes_total	SRR060687 9_0-2h_embryos_total	SRR060656 9x160_ovaries_total
AGTTTGTCCGTACGGGGGCC.......................................................................................................................................................................................................................................	20	3	1	1.00	1	1	0	0	0	0	0	0	0
AGTTTGTCCGTACGGGGGC........................................................................................................................................................................................................................................	19	3	8	0.63	5	0	1	0	1	1	1	1	0
AGTCTGTCCGTACGGGGG.........................................................................................................................................................................................................................................	18	2	5	0.20	1	0	0	1	0	0	0	0	0
AGTTTGTCCGTACGGTGG.........................................................................................................................................................................................................................................	18	2	6	0.17	1	0	1	0	0	0	0	0	0
......................................................................................................................................................ACCTCCAAGGTACGGTTGT..................................................................................	19	3	18	0.06	1	0	0	0	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_13049:15993654-15993904 -	dvi_20146	TCAGCCAGGCATGCC------ACCGGCTCATCCGCAACCTGGCATGGGGC------------CAGCAGGTAAGTTTTACTATTGCTTTCTTAATAAGACATGGGCTTC---------------TATGCTGCAACTACTAATGAAAACCAC--ATCGA--------TAAAAACGCGTATGTACACGTATATATTTGGG---------GGCGCCATGCCAACAT-TGAAAACAAGTGCAAGATCACAATCAGAATTCTCTGAA-ACAATTGAGA------CAAAAGAAATCATTCA---ATAGCCGATCTTCCACA
droMoj3	scaffold_6680:20789877-20790126 +		CCAGCCAGGCATGCC------ACCAGCTCAGCCCCATCCAGGCATGGGAC---CGGGAGGACCAGCAGGTAAGTTGCACC---------------------------AGTTGCTAGTAAA--------CA--TAAGGGATCGCACTTTAC--TTCAATCTACAGACGCATG--TACATGT-GGTGTATTTA------TAGGTGTGGGGCACAGCTCGAACAGCTCTGAACGAGTGCGATAGCACAATAGGAATGGACTGAAGTCAATTAAGA------CAAGGGAACGCATTCAGACATAGCCCAGTT-TTACA
droGri2	scaffold_15110:12666130-12666321 +		ACAGCCTCGTATGCCTGGACCGCCCGCC---------------ATGGGCGGCGTAGCTGGTCCAGCTGGTGAGTTGTGCT------------TCTGA-TG-TATTTTTTATATAGACA--CACACTGCTGCAATTGCAGATGT-----------------------------------------------------------------------TGGCAGCA-TTTTAACAATCACAATTCCGCA-TCGGCATCAAATAAAATCAATTGAAACAGACGCAGACGAGAGCGTTGA------------------GC
droWil2	scf2_1100000004837:447036-447079 +		ACAGCCAGGAGTACC------CCAGCCTCAG---CAGCCAGGGATGGGTG------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG
dp5	XR_group6:8610488-8610532 -		ACAGCCAGGAATGCC------GCCCGCTCAGCCGCAGCCGGGCATGGGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C
droPer2	scaffold_27:1050593-1050637 -		GCAGCCAGGAATGCC------GCCCGCTCAGCCGCAGCCGGGCATGGGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C
droAna3	scaffold_13034:1964122-1964179 +		GTTTTTCTGTT------------------------------------------------------------------------ATTTATTTAATAAATTATTATTTTT---------------TATGCTACAACCCGGA-TAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA
droBip1	scf7180000396789:43593-43696 +		AATAATATAAA----------GTATTTTAAGCTGTAAGAATA------------------------------------------------------------------------------------------------TATATAAATAAC--ATATA--------TGAATATATATATATATATATATATATATATACAAA---------------------------ATGAACACAAGAACAAA-------------------------------------------------------------------AT
droKik1	scf7180000302810:56686-56743 +		AGCTGCAAA-----------------------------------------------------------------------------------------------------------------------------------TGAAAAACAA--GCAAA--------CAAATAAATATAAGCACAGATATATATTTTGG-------------------------------------------------------------------------------------------------------------------GG
droFic1	scf7180000453841:845669-845699 +		TTCGGCGGATAT-CC------ACCGGGACAGCCGCAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000490970:451784-451894 -		TGTTGTTTTCTT---------------------------------------------------------------CTC------------CAAAAAA-TT-TAATTTTTATGTTCACA--------------ATTATTATCAAAAAATGTTTATTTA--------TCAAAAAATGTTTGTATATGCCCGTATATATCTAGG-----GCTGT----------------------CA-----------------------------------------------------------------------------TG
droRho1	scf7180000767329:332-375 +		AATGAAAAGCAAA-------------------------------------------------------------------------------------------------------------------------------------GTGC--TTAAA-------------TCATATATGTACATATATATA--------------------------------------------------------------------------------------------------------------------------T
droBia1	scf7180000302087:321746-321854 +		AGAATATGT----------------------------------------------------------------------------------------------TCG-TCTTGCTTGGA--------------AATACTATTAAAGAATAC--ATAAA--------TATGTGAATGTATGTACATATATACATTTGTGTGAA-----G---TCATTCTGATTA-TGTTAATAAATAC-----------------------------------------------------------------------------A
droTak1	scf7180000415878:400105-400154 +		CCTCGAAACAACGG--------------------CGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATAGAAGGCATTGC---ACTGCTTGCACTCCCCG
droEre2	scaffold_4784:10205820-10205872 -		GCAGCCGGGAATGAG---ACCGCGGATTCCA---TCACGGGGC---GGAA------------CAGCGGGCAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

TCAGCCAGGCATGCC------ACCGGCTCATCCGCAACCTGGCATGGGGC------------CAGCAGGTAAGTTTTACTATTGCTTTCTTAATAAGACATGGGCTTC---------------TATGCTGCAACTACTAATGAAAACCAC--ATCGA--------TAAAAACGCGTATGTACACGTATATATTTGGG---------GGCGCCATGCCAACAT-TGAAAACAAGTGCAAGATCACAATCAGAATTCTCTGAA-ACAATTGAGA------CAAAAGAAATCATTCA---ATAGCCGATCTTCCACA	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
........................................GGCATGGGGC------------CAGCAGGC....................................................................................................................................................................................................................................................	18	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
...............................CCGCAACCTGGCATGGGGC------------............................................................................................................................................................................................................................................................	19	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	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

droMoj3

CCAGCCAGGCATGCC------ACCAGCTCAGCCCCATCCAGGCATGGGAC---CGGGAGGACCAGCAGGTAAGTTGCACC---------------------------AGTTGCTAGTAAA--------CA--TAAGGGATCGCACTTTAC--TTCAATCTACAGACGCATG--TACATGT-GGTGTATTTA------TAGGTGTGGGGCACAGCTCGAACAGCTCTGAACGAGTGCGATAGCACAATAGGAATGGACTGAAGTCAATTAAGA------CAAGGGAACGCATTCAGACATAGCCCAGTT-TTACA	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
..............................................................................................................................................................................................................................................................................GA------CAAGGGAACGCATTCAGACATAGC............	26	1	1.00	1	0	0	0	1	0	0
...........................................ATGGGAC---CGGGAGGACCAGC........................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	0	0	0	1
...................................ATCCAGGCATGGGAC---CGGGA................................................................................................................................................................................................................................................................	20	1	1.00	1	0	0	1	0	0	0

droGri2

ACAGCCTCGTATGCCTGGACCGCCCGCC---------------ATGGGCGGCGTAGCTGGTCCAGCTGGTGAGTTGTGCT------------TCTGA-TG-TATTTTTTATATAGACA--CACACTGCTGCAATTGCAGATGT-----------------------------------------------------------------------TGGCAGCA-TTTTAACAATCACAATTCCGCA-TCGGCATCAAATAAAATCAATTGAAACAGACGCAGACGAGAGCGTTGA------------------GC	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
.......CGTATGCCTGGACCGCCCGCC---------------...............................................................................................................................................................................................................................................................................	21	1	2.00	2	2	0
.CAGCCTCGTATGCCTGGACC.....................................................................................................................................................................................................................................................................................................	20	1	1.00	1	1	0
..........................CC---------------ATGGGCGGCGTAGCTGGTCCAGCTGGC....................................................................................................................................................................................................................................................	29	1	1.00	1	0	1
..AGCCTCGTATGCCTGGACCGC...................................................................................................................................................................................................................................................................................................	21	1	1.00	1	1	0
.........................................................................................................................................................................................................................................................................ATTGAAACAGACGCAGAC...............................	18	1	1.00	1	1	0

droWil2

ACAGCCAGGAGTACC------CCAGCCTCAG---CAGCCAGGGATGGGTG------------C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
......................CAGCCTCAG---CAGCCAGGGATGGGT.........................................................................................................................................................................................................................................................................	24	2	0.50	1	0	0	1	0	0

dp5

ACAGCCAGGAATGCC------GCCCGCTCAGCCGCAGCCGGGCATGGGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C	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
..AGCCAGGAATGCC------GCCCGCTC.............................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
..AGCCAGGAATGCC------GCCCGCTCAGCC.........................................................................................................................................................................................................................................................................................	25	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.........................GCTCAGCCGCAGCCGGGCATGGGA.........................................................................................................................................................................................................................................................................	24	1	1.00	1	0	1	0	0	0	0	0	0	0	0
......AGGAATGCC------GCCCGCTCAGC..........................................................................................................................................................................................................................................................................................	20	1	1.00	1	0	1	0	0	0	0	0	0	0	0
....CCAGGAATGCC------GCCCGCTC.............................................................................................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0

droPer2

GCAGCCAGGAATGCC------GCCCGCTCAGCCGCAGCCGGGCATGGGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C	Size	Hit Count	Total Norm	Total	M021 Embryo	M042 Female-body	V042 Embryo	V050 Head	V057 Head	V111 Male-body
No Reads

droAna3

GTTTTTCTGTT------------------------------------------------------------------------ATTTATTTAATAAATTATTATTTTT---------------TATGCTACAACCCGGA-TAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

AATAATATAAA----------GTATTTTAAGCTGTAAGAATA------------------------------------------------------------------------------------------------TATATAAATAAC--ATATA--------TGAATATATATATATATATATATATATATATACAAA---------------------------ATGAACACAAGAACAAA-------------------------------------------------------------------AT	Size	Hit Count	Total Norm	Total
No Reads

droKik1

AGCTGCAAA-----------------------------------------------------------------------------------------------------------------------------------TGAAAAACAA--GCAAA--------CAAATAAATATAAGCACAGATATATATTTTGG-------------------------------------------------------------------------------------------------------------------GG	Size	Hit Count	Total Norm	Total
No Reads

droFic1

TTCGGCGGATAT-CC------ACCGGGACAGCCGCAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

droEle1

TGTTGTTTTCTT---------------------------------------------------------------CTC------------CAAAAAA-TT-TAATTTTTATGTTCACA--------------ATTATTATCAAAAAATGTTTATTTA--------TCAAAAAATGTTTGTATATGCCCGTATATATCTAGG-----GCTGT----------------------CA-----------------------------------------------------------------------------TG	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AATGAAAAGCAAA-------------------------------------------------------------------------------------------------------------------------------------GTGC--TTAAA-------------TCATATATGTACATATATATA--------------------------------------------------------------------------------------------------------------------------T	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AGAATATGT----------------------------------------------------------------------------------------------TCG-TCTTGCTTGGA--------------AATACTATTAAAGAATAC--ATAAA--------TATGTGAATGTATGTACATATATACATTTGTGTGAA-----G---TCATTCTGATTA-TGTTAATAAATAC-----------------------------------------------------------------------------A	Size	Hit Count	Total Norm	Total
No Reads

droTak1

CCTCGAAACAACGG--------------------CGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATAGAAGGCATTGC---ACTGCTTGCACTCCCCG	Size	Hit Count	Total Norm	Total
No Reads

droEre2

GCAGCCGGGAATGAG---ACCGCGGATTCCA---TCACGGGGC---GGAA------------CAGCGGGCAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT	Size	Hit Count	Total Norm	Total	M055 Female-body	M057 Embryo	V060 Head	V040 Embryo	V107 Male-body	V108 Head	GSM1528801 follicle cells
........................GATTCCA---TCACGGGGC---GGAA------------CAGCGGGA....................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	0	0	1	0	0
..........................TTCCA---TCACGGGGC---GGAA------------CAGC........................................................................................................................................................................................................................................................	22	1	1.00	1	1	0	0	0	0	0	0

Generated: 05/16/2015 at 08:40 PM