ID:

dvi_19947

 Coordinate:

scaffold_13049:14532942-14533092 +

 Confidence:

Candidate

 Type:

Unknown

 [View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

-16.8 -16.6 -16.6 -16.4

Flybase annnotation

exon [dvir_GLEANR_13448:1]; CDS [Dvir\GJ13565-cds]; intron [Dvir\GJ13565-in]

Repeatable elements

NameClassFamilyStrand
AT_richLow_complexityLow_complexity+
mature
star
  1. scaffold_13047:15042643-15042660 +
  2. dvi_19947  scaffold_13049:14532986-14533003 +

Sense Strand Reads

----------------------------######################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
AGCTGTAAATTATTACAGAACAGACAACATGATGTCAAAGAGATTATTGGGTGAGTGCAAATGTTGCCTTATAATATATATAAATAATAACATTGTGTAGATACAAGCATGATTGTGTTTATCACAGTTTACGTTTAAAGAATTTGTAATTAAAAAAAGAAAAACGCAAAGTGTGGACTCTTAATTGCTTTACCACCCGCAAGAGGAAAACAACAATGTTTGCGACGAATAAATTTTGATTATCTTAAATT
**********************************************************************************************..........(((...(((((......(((((.(((.(((((......((((....)))).......))))).))).))))).....))))).)))************************************************************* 		Read size # Mismatch Hit Count Total Norm Total V053
head
 M047
female body
 V116
male body		 M027
male body		 SRR060659
Argentina_testes_total
 SRR060660
Argentina_ovaries_total
 SRR060665
9_females_carcasses_total
 SRR060683
160_testes_total
 SRR060687
9_0-2h_embryos_total
 SRR060676
9xArg_ovaries_total
 SRR060667
160_females_carcasses_total
 SRR060668
160x9_males_carcasses_total
......AACTTATTACAGAACAGACAACATGAT.......................................................................................................................................................................................................................... 27 1 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0
................AGAACAGACAACATGATGTC....................................................................................................................................................................................................................... 20 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0
.................................GTCAAAGAGATTATTGGCTCAGA................................................................................................................................................................................................... 23 3 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0
........................................................................................................................................................................AAGTGTGGACTCTTAATTGCTT............................................................. 22 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0
...............................................TGGGTGAGTGGTAATGTTGCC....................................................................................................................................................................................... 21 2 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0
................AGAACAGACAACATGATGT........................................................................................................................................................................................................................ 19 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0
......................................AGGGATTATTGGGTGAGTGCA................................................................................................................................................................................................ 21 1 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0
.....................................AGGAGATTGTTGGGTGAGTGC................................................................................................................................................................................................. 21 2 1 1.00 1 0 0 0 0 0 1 0 0 0 0 0 0
.........TTGTTACAGAACAGACAACA.............................................................................................................................................................................................................................. 20 1 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0
...........ATTACAGAACAGACAACATGATGT........................................................................................................................................................................................................................ 24 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTGTGTGCAAAGGTTGCC....................................................................................................................................................................................... 21 2 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0
.....................................................................................................................................................................GCAAAGTGTGGACTCTTAATTGC............................................................... 23 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0
........................CAACATGATGTCAAAGAG................................................................................................................................................................................................................. 18 0 1 1.00 1 0 0 0 0 0 0 0 0 1 0 0 0
...............................................CGGGTGAGTGGTAATGTTGCC....................................................................................................................................................................................... 21 3 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGAGAGTGTTAATGTTGCC....................................................................................................................................................................................... 21 3 2 1.00 2 2 0 0 0 0 0 0 0 0 0 0 0
..........................ACATGATGTCATAGAGAGAATT........................................................................................................................................................................................................... 22 3 2 0.50 1 0 0 1 0 0 0 0 0 0 0 0 0
..............................................................................................GTGTAGATACAAGCATGA........................................................................................................................................... 18 0 2 0.50 1 0 0 0 0 0 0 0 0 0 1 0 0
...............................................TGGGAGAGTGGTAATGTTGCC....................................................................................................................................................................................... 21 3 2 0.50 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTGAGTGGTTATGTTGCC....................................................................................................................................................................................... 21 3 4 0.25 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................CGGGTGAGTGTTAATGTTGCC....................................................................................................................................................................................... 21 3 11 0.18 2 2 0 0 0 0 0 0 0 0 0 0 0
.......................................................................................................................................TAAAGAATTTGTAACAAAAAAAAAAAA......................................................................................... 27 3 6 0.17 1 0 0 0 0 0 0 0 0 0 0 1 0
...............................................TGGGTGAGTGGTAAGGTTGC........................................................................................................................................................................................ 20 3 6 0.17 1 1 0 0 0 0 0 0 0 0 0 0 0
................................................GGGTGAGCGTGAATGTTGCC....................................................................................................................................................................................... 20 3 7 0.14 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTGAGCGCCGATGTTGC........................................................................................................................................................................................ 20 3 7 0.14 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTCAGTGGTAATGTTGC........................................................................................................................................................................................ 20 3 8 0.13 1 1 0 0 0 0 0 0 0 0 0 0 0
...................................................................................................GATACAGGCGTGATCGTGT..................................................................................................................................... 19 3 9 0.11 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGAGAGTGTTAATGTTGC........................................................................................................................................................................................ 20 3 12 0.08 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTGAGTGGTGATGTTGC........................................................................................................................................................................................ 20 3 12 0.08 1 1 0 0 0 0 0 0 0 0 0 0 0
...............................................TGGGTGATTGGTAATGTTGC........................................................................................................................................................................................ 20 3 17 0.06 1 1 0 0 0 0 0 0 0 0 0 0 0
................................................................................................ATAGATACAAGGAGGATTG........................................................................................................................................ 19 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 1

Anti-sense strand reads

TCGACATTTAATAATGTCTTGTCTGTTGTACTACAGTTTCTCTAATAACCCACTCACGTTTACAACGGAATATTATATATATTTATTATTGTAACACATCTATGTTCGTACTAACACAAATAGTGTCAAATGCAAATTTCTTAAACATTAATTTTTTTCTTTTTGCGTTTCACACCTGAGAATTAACGAAATGGTGGGCGTTCTCCTTTTGTTGTTACAAACGCTGCTTATTTAAAACTAATAGAATTTAA
*************************************************************..........(((...(((((......(((((.(((.(((((......((((....)))).......))))).))).))))).....))))).)))********************************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total V116
male body		 SRR060654
160x9_ovaries_total
 SRR060668
160x9_males_carcasses_total
 SRR060683
160_testes_total
 M047
female body
 SRR060679
140x9_testes_total
 SRR060676
9xArg_ovaries_total
 SRR060680
 9xArg_testes_total
 V047
embryo
 SRR060678
9x140_testes_total
 SRR060689
160x9_testes_total
 SRR060661
160x9_0-2h_embryos_total
 SRR060663
160_0-2h_embryos_total
 SRR060682
9x140_0-2h_embryos_total
 SRR060687
9_0-2h_embryos_total
.............................................................................................................................................................TCTTTTTGCGTTTCACACCT.......................................................................... 20 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................TGTACTACAGTTTCTCTAATA............................................................................................................................................................................................................ 21 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.....................................................................................................................................................................CGTTTCACACCTGAGAATTAA................................................................. 21 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................................................................................................................................ACTGAGAATTAACGAAAT........................................................... 18 1 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
..................................................................................................................................................ATTTATTTTTTTCTTTTGGCGTCT................................................................................. 24 3 5 0.60 3 0 0 0 0 0 2 0 1 0 0 0 0 0 0 0
......................................................................................................................................................................................GTAAGGAAATGGTGGGCGT.................................................. 19 2 3 0.33 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
..........AGAAAGTCTTGACTGTTGTA............................................................................................................................................................................................................................. 20 3 20 0.30 6 3 0 0 0 0 0 0 0 0 0 0 1 0 1 1
......................................................................................................................................................................................GTAAGGAAATGGTGGGCG................................................... 18 2 4 0.25 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
..............................................................................................................CTAACACAAATAGTGACGAGT........................................................................................................................ 21 3 5 0.20 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
...............................................................................................................................................................................................................TTTTTTTTTACAAACGCTGATTA..................... 23 3 7 0.14 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
..................................................................................................................................................ATTTATTTTTTTCTTTTGGCGT................................................................................... 22 2 8 0.13 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
...............................................................................................................................................................................ATGATAATTAACGAAATGGTA....................................................... 21 3 12 0.08 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
........TAAGAATGTTTAGTCTGTTG............................................................................................................................................................................................................................... 20 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_13049:14532892-14533142 + dvi_19947 AGCTGTAAATTATTACAGAACAGA--CAACATGATGTCAAAGAGATTATTGGGTGAGTGCAAATGTTGCCTTATAATATATATAAATAATAACATTGTGTAGA--------------------TACAAGCATGATTGTGTTTATCACAGTT----TACGTTTAAAGAATT------------------------TGTA-------------------------ATTAAAAAAAGAAAAACGCAAAGTGTGGACTCTTAATTGCTTTACCACCCGCAAGAGGAAAACAACAATGTTTGCGACGAATAAATTTTGATTATCTTAAATT
droMoj3 scaffold_6680:12766668-12766727 - AACTAGAAATT---ATAGAATATATTTAATATGATGTCGAAGAGATTATTAGGTAAGTGCAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15110:15699845-15700107 - GACTTAAA-----------ACAAT--CAATATGATGTCAAAGAAATTGTTTGGTGAGTGAATATGCTTTCTAATA-------CAAATTATTTTTATATATAGATTTCTATAATTTTTTTTATATTTATA-----------------CATTTGTTGTTTGCTCAAAGAAGAAGAAAATGAAACAGCATTTTTATATGTAAATATATATTTTGAAGGAAAACAAGACAATAAAAAGATAAACAG-AAATGCGAATTAT-------TTCGCTAT-----ATATTAAAACA-------------AGTACATATTTTGATTAGTTCCAAAA

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
AGCTGTAAATTATTACAGAACAGA--CAACATGATGTCAAAGAGATTATTGGGTGAGTGCAAATGTTGCCTTATAATATATATAAATAATAACATTGTGTAGA--------------------TACAAGCATGATTGTGTTTATCACAGTT----TACGTTTAAAGAATT------------------------TGTA-------------------------ATTAAAAAAAGAAAAACGCAAAGTGTGGACTCTTAATTGCTTTACCACCCGCAAGAGGAAAACAACAATGTTTGCGACGAATAAATTTTGATTATCTTAAATTSizeHit CountTotal NormTotalM027
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
................AGAACAGA--CAACATGATGTC................................................................................................................................................................................................................................................................................................2011.001000000000000000100000000000000000000000000000000000000000000000
...................................................................................................................................................................................................................................................AAGTGTGGACTCTTAATTGCTT.............................................................2211.001100000000000000000000000000000000000000000000000000000000000000
................AGAACAGA--CAACATGATGT.................................................................................................................................................................................................................................................................................................1911.001001000000000000000000000000000000000000000000000000000000000000
...........ATTACAGAACAGA--CAACATGATGT.................................................................................................................................................................................................................................................................................................2411.001001000000000000000000000000000000000000000000000000000000000000
................................................................................................................................................................................................................................................GCAAAGTGTGGACTCTTAATTGC...............................................................2311.001000000000000000000000000000000000000000000000000000000000000010
..........................CAACATGATGTCAAAGAG..........................................................................................................................................................................................................................................................................................1811.001000000000000000000000000000000000000010000000000000000000000000
................................................................................................GTGTAGA--------------------TACAAGCATGA................................................................................................................................................................................................1820.501000000000000000000000000001000000000000000000000000000000000000
droMoj3
AACTAGAAATT---ATAGAATATATTTAATATGATGTCGAAGAGATTATTAGGTAAGTGCAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
.....................ATATTTAATATGATGTCGAAGAGA.........................................................................................................................................................................................................................................................................................2411.001000001
droGri2
GACTTAAA-----------ACAAT--CAATATGATGTCAAAGAAATTGTTTGGTGAGTGAATATGCTTTCTAATA-------CAAATTATTTTTATATATAGATTTCTATAATTTTTTTTATATTTATA-----------------CATTTGTTGTTTGCTCAAAGAAGAAGAAAATGAAACAGCATTTTTATATGTAAATATATATTTTGAAGGAAAACAAGACAATAAAAAGATAAACAG-AAATGCGAATTAT-------TTCGCTAT-----ATATTAAAACA-------------AGTACATATTTTGATTAGTTCCAAAASizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
No Reads

Generated: 05/17/2015 at 05:10 AM