ID:

dvi_12788

Coordinate:

scaffold_12970:1224985-1225135 -

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_3869:2]; CDS [Dvir\GJ19055-cds]; intron [Dvir\GJ19055-in]

Repeatable elements

Name	Class	Family	Strand
AT_rich	Low_complexity	Low_complexity	+

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------###########--------------------------------------- GTAACAGCGCTTATTTATGTAAGCACACACACAGTGGATAGCTTTGCATGTGTGCGTGTGCGCTACCTCAACATTTCAATAAACTGCGATCTGCAATTTCTTTCATGTTTTTTTTTTTATTATATTTTCAATTTTTTTTGTTGTCTTCTGAGCTTGTCGCTCATTCAACTCCATAAATTTGTCATTCATTTTAATTTCCAGCTTATCGCTAAATTGTTGCGATAACAGCGTGCAGTTCTTACATTACGCAT ************************************************.((((....))))......(((((......(((.(((.....))).))).....)))))...................(((.(((....((((.....(((((.....)))))..)))).....))).)))....................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M061 embryo	SRR060670 9_testes_total	GSM1528803 follicle cells	M047 female body	SRR060676 9xArg_ovaries_total	SRR060668 160x9_males_carcasses_total
.....................................ATAGCTTTGCATGTGTGCGTGTGCGC............................................................................................................................................................................................	26	0	1	1.00	1	1	0	0	0	0	0
...............................................................................TAAACTGAGATCTGCCGTTTCTT.....................................................................................................................................................	23	3	1	1.00	1	0	1	0	0	0	0
........................................GCCTTGCATGTGTGCGTGT................................................................................................................................................................................................	19	1	7	0.14	1	0	0	0	1	0	0
....................................................................................................................................................................................GTCATTCATTTTAGATCCCA...................................................	20	3	20	0.10	2	0	0	2	0	0	0
.....................................................................................................................................................................................................................................CTGCAGTTCTTACAAAACGC..	20	3	11	0.09	1	0	0	0	0	1	0
................................................................................................................TTATTTATTATATTTTCAAT.......................................................................................................................	20	1	12	0.08	1	0	0	1	0	0	0
...................................................................................................................................................................TTCAACTCCATAAAATTGTTT...................................................................	21	3	20	0.05	1	0	0	0	0	0	1

Anti-sense strand reads

CATTGTCGCGAATAAATACATTCGTGTGTGTGTCACCTATCGAAACGTACACACGCACACGCGATGGAGTTGTAAAGTTATTTGACGCTAGACGTTAAAGAAAGTACAAAAAAAAAAATAATATAAAAGTTAAAAAAAACAACAGAAGACTCGAACAGCGAGTAAGTTGAGGTATTTAAACAGTAAGTAAAATTAAAGGTCGAATAGCGATTTAACAACGCTATTGTCGCACGTCAAGAATGTAATGCGTA ************************************************.((((....))))......(((((......(((.(((.....))).))).....)))))...................(((.(((....((((.....(((((.....)))))..)))).....))).)))....................************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	V116 male body	SRR060678 9x140_testes_total	V053 head	SRR060687 9_0-2h_embryos_total	SRR1106729 mixed whole adult body	SRR060682 9x140_0-2h_embryos_total	SRR060685 9xArg_0-2h_embryos_total	SRR060670 9_testes_total	SRR060666 160_males_carcasses_total	SRR060667 160_females_carcasses_total
.......................................................................................................................................................................................................................................CGTGAAGACTGTAATGCGTA	20	2	2	0.50	1	1	0	0	0	0	0	0	0	0	0
...............................GTCACCTAGCGTAACGTACCCA......................................................................................................................................................................................................	22	3	2	0.50	1	0	1	0	0	0	0	0	0	0	0
......................................................GCACCGGCGATAGAGTTGTA.................................................................................................................................................................................	20	3	3	0.33	1	0	0	1	0	0	0	0	0	0	0
.....................TCGTGGGTGTGGTACCTATC..................................................................................................................................................................................................................	20	3	7	0.14	1	0	0	0	1	0	0	0	0	0	0
.........................GTGTTTGTCACCTCTCGATAC.............................................................................................................................................................................................................	21	3	7	0.14	1	0	0	0	0	1	0	0	0	0	0
..............................................................................................TTACAGAAAGTACCAAAAA..........................................................................................................................................	19	2	18	0.11	2	0	0	1	0	0	0	0	1	0	0
...................................................................................................................................................................................................TAGGTCGAATAGCAATTT......................................	18	2	12	0.08	1	0	0	0	0	0	1	0	0	0	0
.................................................................................................................................................................................................TGTAGGTCGAATAGCAATTT......................................	20	3	14	0.07	1	0	0	0	0	0	0	1	0	0	0
...........................................................................................AAGTTCAAGAAAGTACCAAA............................................................................................................................................	20	3	20	0.05	1	0	0	0	0	0	1	0	0	0	0
...........................................................................................................................................................................................................................GTTATTGTCGATCGTCAAGA............	20	3	20	0.05	1	1	0	0	0	0	0	0	0	0	0
..........................................................................AAGTTATTTGACTGTAGA...............................................................................................................................................................	18	2	20	0.05	1	0	0	0	0	0	0	0	0	0	1
................................................................................................................................................................................................TTAAAGGTCGAATACAGA.........................................	18	2	20	0.05	1	0	0	0	0	0	0	0	0	1	0

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12970:1224935-1225185 -	dvi_12788	GTAACAGCGCTT---A--T---------------------------TTATGTAAGCACACACACA-GTGGATAGCTTTGCATGTGTGCGTG-----------------TGCGCTACCTCAACA-TTTC--------------------AATAAACTGC------GAT-----CTGCAATTTCTTTCATGTTTTTTTTTTTATTATATTTTCAATTTTTTTTGTTGTC-TTCTGAGCTTGTCGCTCATTCAACTC----------------------------------CATAAATTTGTCATTCATTTT--AATTTCCAGCTTATCGCTAAATT-----------------GTTGCGATAACAGCGTGCAGTTCTTACATTACGCAT
droMoj3	scaffold_6308:1169792-1170037 +		GTTTG-------------CTG-----------------------------TTATGCGCACACTCA----------------------TGCACTG--------------TTAGCTACCTCAACA-TTTC-TACTCTGCCCATCTGCTGCTGCTGTTATC------GCT-----TTAATCTTTTTGTT---------------------GTTCTTTTTTTTTTGT-GAC-TTTTGAACGTGTTGCCCATTCAACCCGCTGTTGTTCATGGCTGAAATTATTATTTATTTGCATATATTTGTCATACGCTCTGCCATTGCAAACTTATCGCCAAATT-----------------GTTGCGATAAG----------TCTTATATTACGCAT
droGri2	scaffold_15081:1811134-1811368 -		GTACGAATGT-----ATGT-----------------------------ATGTATGTCCATATGTATGTATGTATGTATGCATGTGTGTGCATTGTACGTTTATTCTTTTTCACTACCTCAACA-TTTGTGGCTCTTTCTGCCTGCTTTATCTGCGCTC------GTCTCTTGTCAGTCTT-------------------------------------------------------CTTGTCGCCCATTCAACTT-----------------------------------------TTGTCATTCA-------------GGTTTGTCACTCAATTTTAATGAAAACTTTAAAGCTGCGATAAGATCAGACATTTCTT--ATTACGCAT
dp5	XL_group1a:2179065-2179225 +		CCAAGATCGGTT---G--TCGTTCAGCGCAATTTTTACAACAGATTTGCTTTTT--TTGCTTGCTTGT------------GTGTGTGTGTGTTTCGG--------TTTTT--------CGCTG-CT--------------------GTAGTAATTCTC------GGT-----TTTGGCGTTTTTTGGTTTTTTTTTGTTTTTTGTATTTTTTGTTTTTTTCGTTGTT-T--------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000453912:1460862-1461005 +		CTGCTGATGCTGCAGATGT---------------------------TGCTGTTG--CCACATGCCTTGAGCTGT---------------TGCGTCAG--------TTGCT--------CGCTAACG--------------------ATGACAATTCCATAAACATGT-----TTTCGGTTTCCTTCCTGTTTCGTTTGTTCTTCAACTTTCCTCTTTCTTTTTGGTTTT--------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

GTAACAGCGCTT---A--T---------------------------TTATGTAAGCACACACACA-GTGGATAGCTTTGCATGTGTGCGTG-----------------TGCGCTACCTCAACA-TTTC--------------------AATAAACTGC------GAT-----CTGCAATTTCTTTCATGTTTTTTTTTTTATTATATTTTCAATTTTTTTTGTTGTC-TTCTGAGCTTGTCGCTCATTCAACTC----------------------------------CATAAATTTGTCATTCATTTT--AATTTCCAGCTTATCGCTAAATT-----------------GTTGCGATAACAGCGTGCAGTTCTTACATTACGCAT	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
......................................................................ATAGCTTTGCATGTGTGCGTG-----------------TGCGC..................................................................................................................................................................................................................................................................................	26	1	1.00	1	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	0	0	0	0	0	0

droMoj3

GTTTG-------------CTG-----------------------------TTATGCGCACACTCA----------------------TGCACTG--------------TTAGCTACCTCAACA-TTTC-TACTCTGCCCATCTGCTGCTGCTGTTATC------GCT-----TTAATCTTTTTGTT---------------------GTTCTTTTTTTTTTGT-GAC-TTTTGAACGTGTTGCCCATTCAACCCGCTGTTGTTCATGGCTGAAATTATTATTTATTTGCATATATTTGTCATACGCTCTGCCATTGCAAACTTATCGCCAAATT-----------------GTTGCGATAAG----------TCTTATATTACGCAT	Size	Hit Count	Total Norm	Total	M046 Female-body	V041 Embryo	V049 Head	V056 Head	M060 Embryo	V110 Male-body
No Reads

droGri2

GTACGAATGT-----ATGT-----------------------------ATGTATGTCCATATGTATGTATGTATGTATGCATGTGTGTGCATTGTACGTTTATTCTTTTTCACTACCTCAACA-TTTGTGGCTCTTTCTGCCTGCTTTATCTGCGCTC------GTCTCTTGTCAGTCTT-------------------------------------------------------CTTGTCGCCCATTCAACTT-----------------------------------------TTGTCATTCA-------------GGTTTGTCACTCAATTTTAATGAAAACTTTAAAGCTGCGATAAGATCAGACATTTCTT--ATTACGCAT	Size	Hit Count	Total Norm	Total	M041 Female-body	V109 Male-body
...............................................................................................................................GTGGCTCTTTCTGCCTGCTTT...............................................................................................................................................................................................................................................	21	1	1.00	1	1	0

dp5

CCAAGATCGGTT---G--TCGTTCAGCGCAATTTTTACAACAGATTTGCTTTTT--TTGCTTGCTTGT------------GTGTGTGTGTGTTTCGG--------TTTTT--------CGCTG-CT--------------------GTAGTAATTCTC------GGT-----TTTGGCGTTTTTTGGTTTTTTTTTGTTTTTTGTATTTTTTGTTTTTTTCGTTGTT-T--------------------------------------------------------------------------------------------------------------------------------------------------------------	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
............................................................................................................................................................................................................TATTTTTTGTTTTTTTCGTTG..................................................................................................................................................................	21	1	1.00	1	0	0	0	0	0	0	0	1	0	0
..................TCGTTCAGCGCAATTTTTACAACAGAT......................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	1	0	0	1	0	0	0	0	0	0	0
..........................................................................................................TTTT--------CGCTG-CT--------------------GTAGTAATTCTC------...............................................................................................................................................................................................................................	23	1	1.00	1	0	0	0	0	0	0	1	0	0	0
.......................................................................................................................GCTG-CT--------------------GTAGTAATTCTC------G..............................................................................................................................................................................................................................	19	1	1.00	1	0	1	0	0	0	0	0	0	0	0
........................................................................................GTGTTTCGG--------TTTTT--------CGCTG-CT--------------------.................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
CCAAGATCGGTT---G--TCGTTCAGCGCAATT..................................................................................................................................................................................................................................................................................................................................................................	28	1	1.00	1	0	0	1	0	0	0	0	0	0	0
..............................................TGCTTTTT--TTGCTTGCTTGT------------G..................................................................................................................................................................................................................................................................................................................	21	1	1.00	1	0	1	0	0	0	0	0	0	0	0
.................................................................TGT------------GTGTGTGTGTGTTTCG...................................................................................................................................................................................................................................................................................................	19	20	0.05	1	0	0	0	0	0	0	1	0	0	0

droFic1

CTGCTGATGCTGCAGATGT---------------------------TGCTGTTG--CCACATGCCTTGAGCTGT---------------TGCGTCAG--------TTGCT--------CGCTAACG--------------------ATGACAATTCCATAAACATGT-----TTTCGGTTTCCTTCCTGTTTCGTTTGTTCTTCAACTTTCCTCTTTCTTTTTGGTTTT--------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

Generated: 05/16/2015 at 09:22 PM