ID:

dvi_5113

 Coordinate:

scaffold_12875:3319061-3319211 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-7.3 -7.3 -6.9

Flybase annnotation

CDS [Dvir\GJ20955-cds]; exon [dvir_GLEANR_6356:3]; intron [Dvir\GJ20955-in]

No Repeatable elements found

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
CCGTCCATGATGTCTAGGCGAACAGAATCATGGAGATTGGGCTCACAGATCTATAGTTATAGCGATGCCGAAGAATATTATGGTTTAATCAAAAATGTGGAGGAAAAGTTTAAAGAGGACTTTCCCGACAGCTATGTATTGTAGGTATTTTTGCATGTGTTTATGGAATAAGAGAAAATTTTCATCCTTTGGCAACTATAGAGAAAAATACGTTTATCGTGGTATGGTGACTATTGTAATACCCGACAACG
***********************************************************************************************************..............((((.((((..((((((.............))))))))))...)))).............********************************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060682
9x140_0-2h_embryos_total
 SRR060684
140x9_0-2h_embryos_total
 SRR060679
140x9_testes_total
 SRR060689
160x9_testes_total
 SRR060687
9_0-2h_embryos_total
 SRR060686
Argx9_0-2h_embryos_total
 SRR060681
Argx9_testes_total
 V116
male body		 M047
female body
 SRR060685
9xArg_0-2h_embryos_total
 SRR060661
160x9_0-2h_embryos_total
 SRR060665
9_females_carcasses_total
 V053
head
 SRR060668
160x9_males_carcasses_total
 SRR060662
9x160_0-2h_embryos_total
.......................................................................................................................................................................................ATCCTTTGACCACTCTAGAGA............................................... 21 3 1 6.00 6 4 1 0 0 1 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................CATCCTTTGACCACTCTAGAG................................................ 21 3 3 2.33 7 2 1 0 1 1 1 0 0 0 1 0 0 0 0 0
.......................................................................................................................................................................................ATCCTTTGACCACTCTAGAG................................................ 20 3 5 2.20 11 3 3 0 2 0 3 0 0 0 0 0 0 0 0 0
..........................ATCATGGAGATTGGGCTCAC............................................................................................................................................................................................................. 20 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
........GATGTCTAGGCGAACAGAATCATGGA......................................................................................................................................................................................................................... 26 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
..........................................TCACAGATCTATAGTTATAGCGATG........................................................................................................................................................................................ 25 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................GTTTAAAGAGGACTTTCCCGAC.......................................................................................................................... 22 0 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................CATCCTTTGACCACTCTAGAGA............................................... 22 3 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................................................TGTGTTTATGGAATAAGAGAAAATTT...................................................................... 26 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
.......................................................................................................................................................................................ATCCTTTGACCACTCTAGA................................................. 19 3 18 0.61 11 1 1 0 0 2 4 0 0 0 2 0 0 0 1 0
......................................................................................................................................................................................CATCCTTTGACCACTCTAGA................................................. 20 3 6 0.50 3 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0
................................................................................................GCGGAAGAAAAGTTTAAAG........................................................................................................................................ 19 2 2 0.50 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
...TCCACGATGTCCAGGCGAA..................................................................................................................................................................................................................................... 19 2 2 0.50 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
..................................................................................................................................................................................................................CCTTTATGGTGGTATGGT....................... 18 2 4 0.25 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
.....................................................................................TAATCAAAGATGTGGACGA................................................................................................................................................... 19 2 5 0.20 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
......................................................................................................................................................................................CATCCTTTGACCACTCTAG.................................................. 19 3 13 0.15 2 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0
......................................................................................................................................TGGATTGTAGGTAATTTT................................................................................................... 18 2 15 0.07 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
.......................AGAATCATGGAGGTAGAGC................................................................................................................................................................................................................. 19 3 19 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................................................CACCGTGGTATGGGGACT................... 18 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

Anti-sense strand reads

GGCAGGTACTACAGATCCGCTTGTCTTAGTACCTCTAACCCGAGTGTCTAGATATCAATATCGCTACGGCTTCTTATAATACCAAATTAGTTTTTACACCTCCTTTTCAAATTTCTCCTGAAAGGGCTGTCGATACATAACATCCATAAAAACGTACACAAATACCTTATTCTCTTTTAAAAGTAGGAAACCGTTGATATCTCTTTTTATGCAAATAGCACCATACCACTGATAACATTATGGGCTGTTGC
**********************************************************************..............((((.((((..((((((.............))))))))))...)))).............*********************************************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060677
Argx9_ovaries_total
 SRR060676
9xArg_ovaries_total
 SRR060655
9x160_testes_total
 SRR060674
9x140_ovaries_total
 SRR060673
9_ovaries_total
 SRR060675
140x9_ovaries_total
 SRR060678
9x140_testes_total
 SRR1106720
embryo_8-10h
 V047
embryo
 SRR060659
Argentina_testes_total
 SRR060667
160_females_carcasses_total
 M028
head
 M027
male body		 V053
head
........................................................................................................TTTCAAATTTCTCCTGAAAGGGCTGT......................................................................................................................... 26 0 1 2.00 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0
......................................................TCAATATCGCTACGGCTTCTTATAAT........................................................................................................................................................................... 26 0 1 2.00 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................................TGTCGATACATAACATCCATAAAAACG................................................................................................. 27 0 1 1.00 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
...........................................................................................................CAAATTTCTCCTGAAAGGGCTGTCGAT..................................................................................................................... 27 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................GTCTAGATATCAATATCGCTACGGCTT................................................................................................................................................................................... 27 0 1 1.00 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
.......................................................................................................................................................................TATTCTCTTTTAAAAGTAGGAAACCGT......................................................... 27 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................................AGTTGTTATACCTCCTTTTCTA............................................................................................................................................. 22 3 1 1.00 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
.............................................................................................................................................................................................................................CATACCACTGATAACATTATGGGCTGT... 27 0 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.......................................................................................................................GAAAGGGCTGTCGATACATAACATCCA......................................................................................................... 27 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
................................................................................................................TTCTCCTGAAAGGGCTGTCGATACATA................................................................................................................ 27 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................TTTCTCCTGAAAGGGCTGTCGATACAT................................................................................................................. 27 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................................................................................TTTAAAAGTAGGAAACCGTTGATATC.................................................. 26 0 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................CTAGATATCAATATCGCTACGGCTTCT................................................................................................................................................................................. 27 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
.........................................................................................................TTCAAATTTCTCCTGAAAGGGCTGT......................................................................................................................... 25 0 1 1.00 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
........................................................................................AGTTTGTACACCTCATTTTCGA............................................................................................................................................. 22 3 2 0.50 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
...................................................................................................CTCCTTTTCAAATTGATCC..................................................................................................................................... 19 2 4 0.25 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
....................................................................................................................................................................................................................................CTGATAAGATTATAGGCT..... 18 2 6 0.17 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
........................................................................................AGTTTTGAGACCTCCTTTGCA.............................................................................................................................................. 21 3 6 0.17 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0
....................................................................................................................CCTAAAGGGGCTGTCGTTA.................................................................................................................... 19 3 15 0.13 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0
..........TCAGATCGGCTTGTCATAG.............................................................................................................................................................................................................................. 19 3 9 0.11 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
.GCACGTACTATAGATCAGC....................................................................................................................................................................................................................................... 19 3 14 0.07 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_12875:3319011-3319261 - dvi_5113 CCGTCCATGA-TGTCTAGGCGAACAGAATCATGGA--------GATTGGGCTCACAGATCTATAGTTAT-AGCGATGCCGAAGAATATTATGGTTTAATCAAAAATGTGGAGGAAAAGTTTAAAGAGGACTTTCCCGACAGCTATGTATTGTAGGTA--------------TTTTTGCATGTGTTTATGGAATAAGAGAAAATTTTC-----ATCCTTTGGCAACT----ATAGAGAAAAATACGTTTATCGTGGTATGGTGACTATTGTAATACCCGACAACG
droMoj3 scaffold_6496:21823380-21823626 + TCCTT---AT-TTTCGAGGAG---------CTGGG--------CATATGATTCGCACATCAG----TACGAATGAGTTTACTGACTATGTTGAATTGATCCGAAATGTCGAAGCAAAATTCAAGGCTGATTTTCCCGACTGCTATATCATGTAAGAGCTGTACTCTATATACATTT--------ATATAACTTTCTTGCCAACCATCGTCTAATCCCTTACTAATT----TTAGAGAGAGTTACTCGTATCGTGGCTACGTGGTTATCGTAATACCCGACAAAG
droGri2 scaffold_15112:2824676-2824916 + CCAACCTCAACCATTTCAGC------------AGGGATAAAGGTTTTAGATT-------CTGAAGTTATGAATGATGTGACCGAATATGATGTACTCATCCAAAATGTGGAAAAGCAATTTCAAATCGATTTTCCAAGCAGTTACATCTTGTATGTA--------------T----GCA-ACACAGATGAGTTGAGCACCATTTACCATCTAAT-----CCCAACCCTTGTCAGAGAGAAGAACACGTCTCATGGCTTGGTCACCATAGCAATAGCCGACTTCG
droBip1 scf7180000396427:1589570-1589621 - ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGAAAGGTTTACCTACCGCGGAATAATCATCTTTAGCATTCCAAAGGGGG
droKik1 scf7180000302228:69933-70080 - GAGAT---AT-TT---------------------------------------------------------------------------TAAAATTAAAACAAAAAT--GAATTAATAGTTCAAAAA--ACCTTCACGGCTC--TCCTTT---------TGTAATTTAT-------------------------ATGTATTATTTTTC-----AT--------TTCC----ACAGTGAAAAGTTCTCCTTTCGAGGAATGATTACCTTTGTCATACCCAAGGAAA
droBia1 scf7180000302291:3160589-3160640 - ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGCGAAGTACCCCTACCGAGGCATGATTACCTTCTGCATTCCGAACGGGA

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
CCGTCCATGA-TGTCTAGGCGAACAGAATCATGGA--------GATTGGGCTCACAGATCTATAGTTAT-AGCGATGCCGAAGAATATTATGGTTTAATCAAAAATGTGGAGGAAAAGTTTAAAGAGGACTTTCCCGACAGCTATGTATTGTAGGTA--------------TTTTTGCATGTGTTTATGGAATAAGAGAAAATTTTC-----ATCCTTTGGCAACT----ATAGAGAAAAATACGTTTATCGTGGTATGGTGACTATTGTAATACCCGACAACGSizeHit 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
...........................ATCATGGA--------GATTGGGCTCAC.....................................................................................................................................................................................................................................2011.001000000000000000000000000000000010000000000000000000000000000000
........GA-TGTCTAGGCGAACAGAATCATGGA--------.................................................................................................................................................................................................................................................2611.001000000000000000000000000000001000000000000000000000000000000000
...................................................TCACAGATCTATAGTTAT-AGCGATG...............................................................................................................................................................................................................2511.001000000000000000000000000000001000000000000000000000000000000000
.....................................................................................................................GTTTAAAGAGGACTTTCCCGAC.................................................................................................................................................2211.001000000000000000000000000000001000000000000000000000000000000000
...................................................................................................................................................................................TGTGTTTATGGAATAAGAGAAAATTT...............................................................................2611.001000000000000000000000000000000000000000100000000000000000000000
droMoj3
TCCTT---AT-TTTCGAGGAG---------CTGGG--------CATATGATTCGCACATCAG----TACGAATGAGTTTACTGACTATGTTGAATTGATCCGAAATGTCGAAGCAAAATTCAAGGCTGATTTTCCCGACTGCTATATCATGTAAGAGCTGTACTCTATATACATTT--------ATATAACTTTCTTGCCAACCATCGTCTAATCCCTTACTAATT----TTAGAGAGAGTTACTCGTATCGTGGCTACGTGGTTATCGTAATACCCGACAAAGSizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads
droGri2
CCAACCTCAACCATTTCAGC------------AGGGATAAAGGTTTTAGATT-------CTGAAGTTATGAATGATGTGACCGAATATGATGTACTCATCCAAAATGTGGAAAAGCAATTTCAAATCGATTTTCCAAGCAGTTACATCTTGTATGTA--------------T----GCA-ACACAGATGAGTTGAGCACCATTTACCATCTAAT-----CCCAACCCTTGTCAGAGAGAAGAACACGTCTCATGGCTTGGTCACCATAGCAATAGCCGACTTCGSizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
No Reads
droBip1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGAAAGGTTTACCTACCGCGGAATAATCATCTTTAGCATTCCAAAGGGGGSizeHit CountTotal NormTotal
No Reads
droKik1
GAGAT---AT-TT---------------------------------------------------------------------------TAAAATTAAAACAAAAAT--GAATTAATAGTTCAAAAA--ACCTTCACGGCTC--TCCTTT---------TGTAATTTAT-------------------------ATGTATTATTTTTC-----AT--------TTCC----ACAGTGAAAAGTTCTCCTTTCGAGGAATGATTACCTTTGTCATACCCAAGGAAASizeHit CountTotal NormTotal
No Reads
droBia1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGCGAAGTACCCCTACCGAGGCATGATTACCTTCTGCATTCCGAACGGGASizeHit CountTotal NormTotal
No Reads

Generated: 05/16/2015 at 07:56 PM