ID:

dvi_11448

Coordinate:

scaffold_12963:12202723-12202873 +

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_2001:5]; CDS [Dvir\GJ17405-cds]; intron [Dvir\GJ17405-in]

No Repeatable elements found

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################-------------------------------- TTATTTGTTGAAAATATTATCTCTCAATTTACTTTGTGAATTAATATGGACTTGCATAGATGTAATTTTGATTACTCAAAATTACTTTTGATATATATTGGCTTGCATACCCTTTCCTAGCTTCAAGGATTATTTATCTTACGTCAAATTTTTTAAATCAATTCTGAAATGATGTTTATATATTTATGATTTTTTTTTTAGAATATCTTCGTGCTATAAAAAAAAAACAGCTTTTCTCAACACATTTGACA ************************************************......((((.((((((((((....)))))))))).)))).......(((((............((((.......)))).............)))))................((((((.((...(((((....)))))...)).))))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	SRR060673 9_ovaries_total	SRR060675 140x9_ovaries_total	SRR060665 9_females_carcasses_total	SRR060656 9x160_ovaries_total	SRR060666 160_males_carcasses_total	SRR060674 9x140_ovaries_total
..................................................................................................................................................................................................................................ACAGCTTTTCTCAACACATTT....	21	0	1	1.00	1	1	0	0	0	0	0	0
..........................................................................................................................TCAAGGATTATTTATCTTACGCCAAA.......................................................................................................	26	1	1	1.00	1	0	1	0	0	0	0	0
.............................................................................................................................................................................................................TCGTCGTGTTATAAAAAAAAAA........................	22	2	3	0.33	1	0	0	1	0	0	0	0
.....................................................................................................................................................TTCTGAAATCAATTCTGAGAT.................................................................................	21	3	7	0.14	1	0	0	0	1	0	0	0
...............................................................................................................................................................................................................TTCGTGGTGTAAAAAAAAA.........................	19	2	14	0.07	1	0	0	0	0	1	0	0
............................................................................................................................................................................................................CACTTCGTGGTATAAAAAAAAA.........................	22	3	16	0.06	1	0	0	0	0	0	1	0
........................................................................................................................CTTCAAGGATTATTTATCTGACGCCC.........................................................................................................	26	3	20	0.05	1	1	0	0	0	0	0	0
.............................................................................................................................................................................................................TCGTCGTGATATATAAAAAAAA........................	22	3	20	0.05	1	0	0	0	0	0	0	1

Anti-sense strand reads

AATAAACAACTTTTATAATAGAGAGTTAAATGAAACACTTAATTATACCTGAACGTATCTACATTAAAACTAATGAGTTTTAATGAAAACTATATATAACCGAACGTATGGGAAAGGATCGAAGTTCCTAATAAATAGAATGCAGTTTAAAAAATTTAGTTAAGACTTTACTACAAATATATAAATACTAAAAAAAAAATCTTATAGAAGCACGATATTTTTTTTTTGTCGAAAAGAGTTGTGTAAACTGT ************************************************......((((.((((((((((....)))))))))).)))).......(((((............((((.......)))).............)))))................((((((.((...(((((....)))))...)).))))))************************************************	Read size	# Mismatch	Hit Count	Total Norm	Total	M047 female body	V047 embryo	SRR060666 160_males_carcasses_total	M027 male body	SRR060665 9_females_carcasses_total
..........................................................................................................................................AATATGGTTTAAAAAATTTAGTTA.........................................................................................	24	3	4	0.50	2	2	0	0	0	0
...............................................................................................................................................TGTTTAAAAAATTTAGTTA.........................................................................................	19	1	3	0.33	1	0	1	0	0	0
.................................................................................................................................................................................................................................TAGTCGTAAAGAGTTGTGT.......	19	2	6	0.17	1	0	0	1	0	0
................................................................................................................................................................................................AAAAAAGTCTTATAGCTGCA.......................................	20	3	13	0.08	1	0	0	0	1	0
..........................................................................................................................................................TTTAGTTAAGACTCTATTAGA............................................................................	21	3	14	0.07	1	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
droVir3	scaffold_12963:12202673-12202923 +	dvi_11448	TTATTTGTTGAA----AAT--ATTAT-----CTCT-CAATTTACTTTGTGAAT------TAATATGGACTTGCATAGATGTAA------------------TTT------------------TGATTACTCAAAATTACTTTTGATATATATTGGCTTGCATACCCTTTCCTAGCTTCAAGGATTATTTATCTTACGTCAAATTT--------------------TTTAAATCAATTCTGAAATGATGTTTAT----------------------------------------------------------------AT-ATTTATGATTTTTTT--------TTTAGAATATCTTCGTGCTATAAAAAAAAAACAGCT--TTTCTCAAC--------ACATTTG------------ACA
droBip1	scf7180000393158:1444-1560 -		ATTTTTTGT-----------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAATGACGTATTTTTTCTAAATTTATTCAACAATGTCTTTTAT----------------------------------------------------------------TT-AAATCTGAATTTTA-----------------AACTTGGCACTACGAAAA---AATGTTTTTTTTCGAAAA--------TCATTTG------------ACA
droKik1	scf7180000302351:1072451-1072524 +		ATATTTATATAAA----TA--TATTT-----ATAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATAGAATATATTTAAATTATA-------TATAGGTAGTTTCAGAAC--------ACATTAA------------ACA
droEle1	scf7180000490141:502976-503197 -		CTAAATATTAAA----GAG--AGTAT-----ATATGAAATTTAAAAAGTTAAC------TAAAATAAGTTTG---------------------AAGTGTCCATT------------------TTATAA--AGAAATTCCTTATGAAATAT---------GTAACTAT---------------------------------------------------------------------------------------------------TTACTTTTAAAGA--TTATTATTAAGT--AAATATTTGTTTTTTTATTAATAT-ATATATGAGTTTTTCTCTATGTGTAG--CTGCTAC-------------------CAGCT--ATTTCTTCAGCTTCGTTC---TTTCTATTCTATTTGAT-
droRho1	scf7180000777191:11991-12107 -		TCGACATTTTTAA----CA--CGATT-----AAAA--------------------------------------------------------------------------------------------------------ATATGATGT---------TGTCTG---------------------------------------------TTCACTGACA---------------------------------------------------------------------------------------------------AT-ATTTATAAATATTTT--------TCACAGATGTCATAG--CAAAC-------AAAAGAA--ATAAATAAAGGATCGAGA---CAT------------TTG
droBia1	scf7180000299365:5469-5735 +		TTAATTTATTAATTTAAAC--ATTGT-----ATAG-GAACTCACTTTGTGAATGCGAAGTGAAAGGCATCTGCACGAGTGAAA------------------GTTAAAGTTAAAATTCAAATGAAACTTTTTGAAGTCACTTTGGATTTCACTTGTTTCTTAAACCCATTTTTG--------TATAAACTGTCACCTGACAAGTTCCAA-----------------GTGAAATCAGTTTGGAAATATTGCATTTTTCCAACGAGTTTTCACTTTTGAAAATATTGAATTTAAGT--AAAAACTTATT-------------------------------------------------------------------------------TGTTT--------ACATTTT------------AC-
droTak1	scf7180000415769:1857998-1858259 +		TTACTTGCTATG----AAAATAGTTTATTTATTTC-CAATGTGTTTTTTTTAT------TAAAATATACATACATTTACGGAAATATTTTTCAAAATATTTTTC------------------GTACTA--TGACTATAGTCATAAAAT---------TTCAAACTCCTTACTAATTT-GTGT-----------------------------------------------------------------------------------------TTTATTAA--TCAATATGTTTTAAAATTATATATTCTTATATCACAATGTTATATGTATTTTTATACCCTTGTAG--AGGGTATTATAATTTCA-------GTCAGAT--GTTTGCAACGCAGTGAAG---GAG------------ACG

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

droVir3

TTATTTGTTGAA----AAT--ATTAT-----CTCT-CAATTTACTTTGTGAAT------TAATATGGACTTGCATAGATGTAA------------------TTT------------------TGATTACTCAAAATTACTTTTGATATATATTGGCTTGCATACCCTTTCCTAGCTTCAAGGATTATTTATCTTACGTCAAATTT--------------------TTTAAATCAATTCTGAAATGATGTTTAT----------------------------------------------------------------AT-ATTTATGATTTTTTT--------TTTAGAATATCTTCGTGCTATAAAAAAAAAACAGCT--TTTCTCAAC--------ACATTTG------------ACA	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
.....................................................................................................................................................................................................................................................................................................................................................................................ACAGCT--TTTCTCAAC--------ACATTT................	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

droBip1

ATTTTTTGT-----------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAATGACGTATTTTTTCTAAATTTATTCAACAATGTCTTTTAT----------------------------------------------------------------TT-AAATCTGAATTTTA-----------------AACTTGGCACTACGAAAA---AATGTTTTTTTTCGAAAA--------TCATTTG------------ACA	Size	Hit Count	Total Norm	Total
No Reads

droKik1

ATATTTATATAAA----TA--TATTT-----ATAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATAGAATATATTTAAATTATA-------TATAGGTAGTTTCAGAAC--------ACATTAA------------ACA	Size	Hit Count	Total Norm	Total
No Reads

droEle1

CTAAATATTAAA----GAG--AGTAT-----ATATGAAATTTAAAAAGTTAAC------TAAAATAAGTTTG---------------------AAGTGTCCATT------------------TTATAA--AGAAATTCCTTATGAAATAT---------GTAACTAT---------------------------------------------------------------------------------------------------TTACTTTTAAAGA--TTATTATTAAGT--AAATATTTGTTTTTTTATTAATAT-ATATATGAGTTTTTCTCTATGTGTAG--CTGCTAC-------------------CAGCT--ATTTCTTCAGCTTCGTTC---TTTCTATTCTATTTGAT-	Size	Hit Count	Total Norm	Total
No Reads

droRho1

TCGACATTTTTAA----CA--CGATT-----AAAA--------------------------------------------------------------------------------------------------------ATATGATGT---------TGTCTG---------------------------------------------TTCACTGACA---------------------------------------------------------------------------------------------------AT-ATTTATAAATATTTT--------TCACAGATGTCATAG--CAAAC-------AAAAGAA--ATAAATAAAGGATCGAGA---CAT------------TTG	Size	Hit Count	Total Norm	Total
No Reads

droBia1

TTAATTTATTAATTTAAAC--ATTGT-----ATAG-GAACTCACTTTGTGAATGCGAAGTGAAAGGCATCTGCACGAGTGAAA------------------GTTAAAGTTAAAATTCAAATGAAACTTTTTGAAGTCACTTTGGATTTCACTTGTTTCTTAAACCCATTTTTG--------TATAAACTGTCACCTGACAAGTTCCAA-----------------GTGAAATCAGTTTGGAAATATTGCATTTTTCCAACGAGTTTTCACTTTTGAAAATATTGAATTTAAGT--AAAAACTTATT-------------------------------------------------------------------------------TGTTT--------ACATTTT------------AC-	Size	Hit Count	Total Norm	Total
No Reads

droTak1

TTACTTGCTATG----AAAATAGTTTATTTATTTC-CAATGTGTTTTTTTTAT------TAAAATATACATACATTTACGGAAATATTTTTCAAAATATTTTTC------------------GTACTA--TGACTATAGTCATAAAAT---------TTCAAACTCCTTACTAATTT-GTGT-----------------------------------------------------------------------------------------TTTATTAA--TCAATATGTTTTAAAATTATATATTCTTATATCACAATGTTATATGTATTTTTATACCCTTGTAG--AGGGTATTATAATTTCA-------GTCAGAT--GTTTGCAACGCAGTGAAG---GAG------------ACG	Size	Hit Count	Total Norm	Total
No Reads

Generated: 05/17/2015 at 04:24 AM