ID:

dvi_1650

Coordinate:

scaffold_12723:4293536-4293686 -

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\GJ17908-cds]; exon [dvir_GLEANR_2479:1]; intron [Dvir\GJ17908-in]

No Repeatable elements found

Sense Strand Reads

##################################################--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CTCTTCCACGTCCACCCTAAAAGAAGGCAACAAACAGAACTCTGGAGAAAGTGAGGACTCCATTGCATCAGACGACATATCAACTAAAACGGATTCCTTAAATACGCCAGCTTCGGTAGATGACATAGAGAACACCAAAAATGAAGAAAAACCAGAAACTACAAAAGACTCTTCTAAATCGAAAGACCCCACAATCTCGATCGAAGAATCAAACAAAGAGCTTTCGGGGAATTTAAAATTTAAAAAGCAAG ************************************************.((((((.(((.............................))).)))))).....(((......))).........................(((((......................)))))...(((((..((........)))))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR060678 9x140_testes_total	SRR060659 Argentina_testes_total	SRR060668 160x9_males_carcasses_total	SRR060679 140x9_testes_total	SRR060682 9x140_0-2h_embryos_total	SRR060686 Argx9_0-2h_embryos_total	SRR060689 160x9_testes_total	M047 female body
................................................................................................................................................................ATAGAAGACTCTTCGAAATCGAA....................................................................	23	3	1	1.00	1	1	0	0	0	0	0	0	0
..............................................................................................................................................................................................................AATCAAACAAAGAGCTTTCGGGGAAT...................	26	0	1	1.00	1	0	0	1	0	0	0	0	0
....................................GAACTCTGGGGAAAGTGAGGA..................................................................................................................................................................................................	21	1	1	1.00	1	0	0	0	1	0	0	0	0
...........................CAACAAACAGAACTCTGGGGAAAGT.......................................................................................................................................................................................................	25	1	1	1.00	1	0	1	0	0	0	0	0	0
........................................ACTGGAGAAAGTGAGCACTT...............................................................................................................................................................................................	20	3	6	0.50	3	3	0	0	0	0	0	0	0
.............................................................................................................................................................ACTATAGAAGACTCTTCGAAA.........................................................................	21	3	2	0.50	1	1	0	0	0	0	0	0	0
........................................................................................................................TGACATAGAGAACACCACC................................................................................................................	19	2	2	0.50	1	0	1	0	0	0	0	0	0
.......................................................................................................................................................................ACTCTGCGAAGTCGAAAGAC................................................................	20	3	11	0.36	4	0	0	0	0	3	0	1	0
.........................................CTGGGGAAAGTGAGGAGT................................................................................................................................................................................................	18	2	5	0.20	1	0	1	0	0	0	0	0	0
.......................................................................................................................................................................ACTCTGCTAACTCGAAAGAG................................................................	20	3	7	0.14	1	0	0	0	0	0	1	0	0
......................................................................................................................................................................................................................GAAGGGCTTTCTGGGAATT..................	19	3	20	0.05	1	0	0	0	0	0	0	0	1

Anti-sense strand reads

GAGAAGGTGCAGGTGGGATTTTCTTCCGTTGTTTGTCTTGAGACCTCTTTCACTCCTGAGGTAACGTAGTCTGCTGTATAGTTGATTTTGCCTAAGGAATTTATGCGGTCGAAGCCATCTACTGTATCTCTTGTGGTTTTTACTTCTTTTTGGTCTTTGATGTTTTCTGAGAAGATTTAGCTTTCTGGGGTGTTAGAGCTAGCTTCTTAGTTTGTTTCTCGAAAGCCCCTTAAATTTTAAATTTTTCGTTC ************************************************.((((((.(((.............................))).)))))).....(((......))).........................(((((......................)))))...(((((..((........)))))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	GSM1528803 follicle cells	M027 male body	V116 male body	M028 head	M047 female body	SRR060687 9_0-2h_embryos_total	V053 head	SRR060684 140x9_0-2h_embryos_total	SRR060686 Argx9_0-2h_embryos_total	SRR060658 140_ovaries_total	SRR1106730 embryo_16-30h
.......................................................................................................................................................................................................TAGCTTCTTAGTTTTT....................................	16	1	20	2.95	59	58	0	0	0	0	0	0	0	0	0	1
.......................................................................................................................................................................................................TAGCTTCTTAGTTTT.....................................	15	1	20	1.25	25	25	0	0	0	0	0	0	0	0	0	0
......................................................................................................................................................................................................CTAGCTTCTTAGTTTTT....................................	17	1	1	1.00	1	1	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................TCTGCGGTGTTAGAGCTA..................................................	18	1	2	1.00	2	0	2	0	0	0	0	0	0	0	0	0
GAGAAGGTGAAGGTCGGAT........................................................................................................................................................................................................................................	19	2	5	0.60	3	0	0	2	0	0	1	0	0	0	0	0
GAGAAGGTGAAGGTCGGA.........................................................................................................................................................................................................................................	18	2	10	0.30	3	0	0	1	0	0	0	0	1	1	0	0
......................................................................................................................................................................................................CTAGCTTCTTAGTTTCTA...................................	18	2	5	0.20	1	1	0	0	0	0	0	0	0	0	0	0
........................................................................................................................................................................................................AGCTTAGTAGTTCGTTTCTCGA.............................	22	3	5	0.20	1	0	0	0	0	1	0	0	0	0	0	0
.....................................................................................................................................TGGTTTTTACTTCTT.......................................................................................................	15	0	6	0.17	1	1	0	0	0	0	0	0	0	0	0	0
.........................................................................................................CTGTCGGAGCCATATACTG...............................................................................................................................	19	3	7	0.14	1	0	0	0	1	0	0	0	0	0	0	0
...............................................................................................................................CTCTTGTAGTTTCTACTTGTT.......................................................................................................	21	3	7	0.14	1	0	0	0	0	0	0	1	0	0	0	0
.............................................................TAACGTAGTCTGCGGTG.............................................................................................................................................................................	17	2	20	0.10	2	2	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................................................................................................TAGCTTCTTAGTTTA.....................................	15	1	20	0.10	2	2	0	0	0	0	0	0	0	0	0	0
...........................................................................................................GTCGGAGCCATATACTGTG.............................................................................................................................	19	3	11	0.09	1	0	0	0	1	0	0	0	0	0	0	0
......GTTTAGGTGGGATTTTATTC.................................................................................................................................................................................................................................	20	3	16	0.06	1	0	0	1	0	0	0	0	0	0	0	0
..........................................................................................................AGTCGAAGCCAATTACTGTA.............................................................................................................................	20	3	17	0.06	1	0	0	1	0	0	0	0	0	0	0	0
.................................................................................................................................................................................TAGTTCTCTGGGGTGTTGG.......................................................	19	3	20	0.05	1	0	0	1	0	0	0	0	0	0	0	0
.....................................................................................................................................................................................................TGTAGCTTCTTAGTTTGT....................................	18	2	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12723:4293486-4293736 -	dvi_1650	CTCTTC-----CACGTCCACCCTAAAAGAAG-----------------------------------------GCAACAAACAGAACTC-------------------------------------------------------------TGGAGAAAGTGAGGACTCCATTGCATCAGACGACATATCAACTAAAACGGAT------------------------------------TCCTTAAATACGCCAGC-----TTCGGTAGATGACATAGAGAACACCAAAAATGAAGAAAAACCAGAAACTACA---------------------AAAGACTCTT---------------CTAAATCGAAAGACCCCACAATCTCGATCGAAGAATCAAACAAAGAGCTTTCGGGG---------------AA-T-------------------------------TTAAAATTTAAAAAGCAAG
droMoj3	scaffold_6500:14375191-14375455 +		CTCATC-----TACGACCACCTTGAAGGAAA-----------------------------------------CTAAGAGTGAGAGCTCTGACGAGGACAGTAAAGAGGATAGAACTGTAGAAA----------------ATGAAAA------------------------------------------AGTTAAAGCAGATAAGTCTA-TAGA-----------------------GTTTTCC------TCAAC-----TTCGGTAAACGCAGTGAAAACTGACGA----------TTCTTCGT--CATCAGTAAGTACAAAGAAACCAGAAGGCGATTCCT---------------CCACATCGGTAAATGCA-CA---------------------------------GAA---------------GATTACGGGATACGCAACAGAAACTCCAGTGGTGTCCGAAGA--AGAAAAATCG
droGri2	scaffold_15252:3387407-3387591 +		TTCAAG-----TACGTCCACCTTAAGAGAAG-----------------------------------------GTGAGACACAGGAAAATAATCAGTTCTAT-------------------------------------------------AA---------------------ATTAGTCAGAACTTCGATTGAAACAGATAAGCCAGATACAGCCAGAAGTTCCACAAATTCA-----------------------------------------------------------------------------------------------------------------------------------------------------ATTAAACTATTCTACGAAGCTGTTATACCAGAGCCAATAAAACATCA-T-------------------------------TGGCAAGTTAATGAATAAT
droWil2	scf2_1100000004952:576165-576217 -		TAGAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTTAAAAGATCAAAAAGTCCAAGAAATAAAA---------------------AAAAATTCTT---------------TCA------------------------------------------------------------------------------------------------------------------------AA
droAna3	scaffold_12943:3465031-3465133 +		TTTTTTAAATGTACATACATCGGAAAAAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCA-TA-----------------------TATTTTTTG------AG---------------------------AGTTTCGAAAAAAAACCAATACTACAAATTAGA---------------------AAAAACTCTT---------------CTGATTT---------------------------------------------------------------------------------------------------------------TAAGTAC
droBip1	scf7180000396737:1081434-1081518 -		CTTCAGAA--------GGACATGAAGAA--------------------------------------------------CACAAAGGA-----------------------------------AAAACAAAAGTCATAAACCAAAAAGTCTGAAG----------------------------------------------------------A--GCAAAGCCCGAA--------------------------------------------------------------------------------------------------------------------------------------------A----------------------AAC----------------------------------------------------------------------------------CAAACAA
droKik1	scf7180000302318:18471-18534 +		ATGGAA------------------------------------------------------------------TAAAAGAAA----------------------------------------------------------CCAAAAAGTATGAAGTA---------------------------------------------------------AACGAAAGTACGAAAGACTTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATAAAACAAA
droFic1	scf7180000453832:30830-30895 -		ACCCCA------------------------------------------------------------------CCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTAATAGACGATCTTATTGAAAAACTTTCCGAA---------------AA-A-------------------------------GTAATTTTTACCAAGTAAG
droEle1	scf7180000490579:4883-4944 +		AAAATG------------------------------------------------------------------ACA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAAACCGAAAACGGTA---------------------GCAGGTTTTT---------------AGAAAT--------------------------------------------------------------------A-------------------------------GAAAATGTGACCCTTTAAT
droRho1	scf7180000774181:1167-1318 -		AAGAAT------------------------------------------------------------------ATAATAAATCG----------------------------------------------------------ATCCATTCTGTAACA---------------------------------------------------------AAAGAAAGCCCCATAAATA--TATTTTTTAGAAGCACAATCTCCAGTTCAGTAGAAGACATAGAAAAAATCGAGAAGA----------------AAGA---------------------AGAAGAA*CTCCAAAACTCTCTTGCCTAACCTGGAA--------------------------------------------------------------------------------------------------------------GACC
droBia1	scf7180000302267:8939-9056 +		AACGGTGAAACAACAG--------AATC---AACAAGTTCAAAGCAAGACAGTCCAAATACACAGAAAACGATCATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGAACGAA-CGTACAAAAGGGCAACTGGA---------------AATT-------------------------------GAAAATTTT-GAAACAGAA
droTak1	scf7180000415357:68226-68320 -		TTCCA--------CATCCACTCTAAAAGCTA-----------------------------------------GCAATGAACAG------------CTCTCG-------------------------------------------------AA-TTCAAGGAGCACTCTAAA------------------------------------------GGCGGAGGAACGACACTCCGA-----------------------------------------------------------------------ACCAAA---------------------A----------------------------------------------------------------------------------------------------------------------------------------------CAGATCC
droEug1	scf7180000409528:319742-319779 +		GAAAAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAAATGCAA--------------------------------------------------------------------AAATCTCGAAAACT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAAAG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

CTCTTC-----CACGTCCACCCTAAAAGAAG-----------------------------------------GCAACAAACAGAACTC-------------------------------------------------------------TGGAGAAAGTGAGGACTCCATTGCATCAGACGACATATCAACTAAAACGGAT------------------------------------TCCTTAAATACGCCAGC-----TTCGGTAGATGACATAGAGAACACCAAAAATGAAGAAAAACCAGAAACTACA---------------------AAAGACTCTT---------------CTAAATCGAAAGACCCCACAATCTCGATCGAAGAATCAAACAAAGAGCTTTCGGGG---------------AA-T-------------------------------TTAAAATTTAAAAAGCAAG	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
......................................................................................................................................................................................................................................................................................................................................................................................................AATCAAACAAAGAGCTTTCGGGG---------------AA-T-------------------------------...................	26	1	1.00	1	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	0	0	0	0	0	0	0	0
............................................................................................................................................................................................................................................................................TGACATAGAGAACACCACC...................................................................................................................................................................................................	19	2	0.50	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

droMoj3

CTCATC-----TACGACCACCTTGAAGGAAA-----------------------------------------CTAAGAGTGAGAGCTCTGACGAGGACAGTAAAGAGGATAGAACTGTAGAAA----------------ATGAAAA------------------------------------------AGTTAAAGCAGATAAGTCTA-TAGA-----------------------GTTTTCC------TCAAC-----TTCGGTAAACGCAGTGAAAACTGACGA----------TTCTTCGT--CATCAGTAAGTACAAAGAAACCAGAAGGCGATTCCT---------------CCACATCGGTAAATGCA-CA---------------------------------GAA---------------GATTACGGGATACGCAACAGAAACTCCAGTGGTGTCCGAAGA--AGAAAAATCG	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

TTCAAG-----TACGTCCACCTTAAGAGAAG-----------------------------------------GTGAGACACAGGAAAATAATCAGTTCTAT-------------------------------------------------AA---------------------ATTAGTCAGAACTTCGATTGAAACAGATAAGCCAGATACAGCCAGAAGTTCCACAAATTCA-----------------------------------------------------------------------------------------------------------------------------------------------------ATTAAACTATTCTACGAAGCTGTTATACCAGAGCCAATAAAACATCA-T-------------------------------TGGCAAGTTAATGAATAAT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
No Reads

droWil2

TAGAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTTAAAAGATCAAAAAGTCCAAGAAATAAAA---------------------AAAAATTCTT---------------TCA------------------------------------------------------------------------------------------------------------------------AA	Size	Hit Count	Total Norm	Total	M020 Head	M045 Female-body	V117 Male-body	V118 Embryo	V119 Head
.AGAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTTAAAAGATCAAAAAG.........................................................................................................................................................................................	23	7	0.29	2	0	2	0	0	0
...AG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTTAAAAGATCAAAAAGTCCAAGA..................................................................................................................................................................................	28	5	0.20	1	0	1	0	0	0

droAna3

TTTTTTAAATGTACATACATCGGAAAAAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCA-TA-----------------------TATTTTTTG------AG---------------------------AGTTTCGAAAAAAAACCAATACTACAAATTAGA---------------------AAAAACTCTT---------------CTGATTT---------------------------------------------------------------------------------------------------------------TAAGTAC	Size	Hit Count	Total Norm	Total	M044 Female-body	M058 Embryo	V039 Embryo	V055 Head	V105 Male-body	V106 Head
No Reads

droBip1

CTTCAGAA--------GGACATGAAGAA--------------------------------------------------CACAAAGGA-----------------------------------AAAACAAAAGTCATAAACCAAAAAGTCTGAAG----------------------------------------------------------A--GCAAAGCCCGAA--------------------------------------------------------------------------------------------------------------------------------------------A----------------------AAC----------------------------------------------------------------------------------CAAACAA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ATGGAA------------------------------------------------------------------TAAAAGAAA----------------------------------------------------------CCAAAAAGTATGAAGTA---------------------------------------------------------AACGAAAGTACGAAAGACTTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATAAAACAAA	Size	Hit Count	Total Norm	Total
No Reads

droFic1

ACCCCA------------------------------------------------------------------CCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTAATAGACGATCTTATTGAAAAACTTTCCGAA---------------AA-A-------------------------------GTAATTTTTACCAAGTAAG	Size	Hit Count	Total Norm	Total
No Reads

droEle1

AAAATG------------------------------------------------------------------ACA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAAACCGAAAACGGTA---------------------GCAGGTTTTT---------------AGAAAT--------------------------------------------------------------------A-------------------------------GAAAATGTGACCCTTTAAT	Size	Hit Count	Total Norm	Total
No Reads

droRho1

AAGAAT------------------------------------------------------------------ATAATAAATCG----------------------------------------------------------ATCCATTCTGTAACA---------------------------------------------------------AAAGAAAGCCCCATAAATA--TATTTTTTAGAAGCACAATCTCCAGTTCAGTAGAAGACATAGAAAAAATCGAGAAGA----------------AAGA---------------------AGAAGAA*CTCCAAAACTCTCTTGCCTAACCTGGAA--------------------------------------------------------------------------------------------------------------GACC	Size	Hit Count	Total Norm	Total
No Reads

droBia1

AACGGTGAAACAACAG--------AATC---AACAAGTTCAAAGCAAGACAGTCCAAATACACAGAAAACGATCATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGAACGAA-CGTACAAAAGGGCAACTGGA---------------AATT-------------------------------GAAAATTTT-GAAACAGAA	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTCCA--------CATCCACTCTAAAAGCTA-----------------------------------------GCAATGAACAG------------CTCTCG-------------------------------------------------AA-TTCAAGGAGCACTCTAAA------------------------------------------GGCGGAGGAACGACACTCCGA-----------------------------------------------------------------------ACCAAA---------------------A----------------------------------------------------------------------------------------------------------------------------------------------CAGATCC	Size	Hit Count	Total Norm	Total
No Reads

droEug1

GAAAAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAAATGCAA--------------------------------------------------------------------AAATCTCGAAAACT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAAAG	Size	Hit Count	Total Norm	Total
No Reads

Generated: 05/19/2015 at 11:25 AM