ID:

dvi_1532

 Coordinate:

scaffold_12723:3629130-3629280 +

 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_2840:2]; CDS [Dvir\GJ18284-cds]; intron [Dvir\GJ18284-in]

Repeatable elements

NameClassFamilyStrand
AT_richLow_complexityLow_complexity+

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
GCTTTTACTATATAATATAGTTCTTGGATATTATATTATAGTTATCCAAATAGACTTAAATCCTTAAAAGCTTTTTTAATATATATATATATTTCTTTATTGGGAATAACATTAGATAGATATCATGAGAATAATTGCTCTTCAAAACCCCAAATAGACTTAACAAATTAATGCTGACAAAACATTTTGAATGCTCTACAGAAAAATTAGTTATTCCAGCGTCCTTCGCAAAGGTGTCCCATGGTAATTCG
**************************************************......................................((((((.((((.((.......)).)))).))))))..(((((......((..(((((((.......(((..((((....))))..)))........))))))).))))).)).************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060679
140x9_testes_total
 SRR060681
Argx9_testes_total
 SRR060678
9x140_testes_total
 M047
female body
 SRR060657
140_testes_total
 SRR060668
160x9_males_carcasses_total
 SRR060680
 9xArg_testes_total
 SRR060677
Argx9_ovaries_total
 SRR060669
160x9_females_carcasses_total
 SRR060671
9x160_males_carcasses_total
 V116
male body		 SRR060666
160_males_carcasses_total
 SRR060667
160_females_carcasses_total
 SRR060662
9x160_0-2h_embryos_total
 SRR060663
160_0-2h_embryos_total
 SRR060687
9_0-2h_embryos_total
 SRR060661
160x9_0-2h_embryos_total
 SRR060684
140x9_0-2h_embryos_total
 SRR060672
9x160_females_carcasses_total
 SRR060665
9_females_carcasses_total
 SRR060682
9x140_0-2h_embryos_total
 V047
embryo
...................................................................................................................................................................................................................................GCAAAGGTGACCCGTGAT...... 18 3 20 2.55 51 1 0 0 3 0 6 0 0 10 8 2 4 1 3 3 3 1 1 2 1 1 1
........................................................................................CAATTTCTTTATTGGGAATACCA............................................................................................................................................ 23 3 2 1.00 2 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................................................................................................................................................................................CGCAAAGGTGTCCCATGGTAA.... 21 0 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
..................................................................................................................................................................................................................................CGCAAAGGTGTCCCATGGT...... 19 0 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAATACCA............................................................................................................................................ 22 2 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
.........................................................................................AATTTCTTTATTGGGAATAA.............................................................................................................................................. 20 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.......................................................................................TCAATTTCTTTATTGGGAATAACA............................................................................................................................................ 24 2 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAATAAA............................................................................................................................................. 21 2 2 0.50 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................................................................................................TGCTCTACTGAGAAATTAGT........................................ 20 2 2 0.50 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................ATTTCTTTATTGGGAATTA.............................................................................................................................................. 19 1 4 0.50 2 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................ATTTCTTTATTGGGAATAC.............................................................................................................................................. 19 1 2 0.50 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAATA............................................................................................................................................... 19 1 2 0.50 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..........................................................................................ATTTCTTTATTGGGAACA............................................................................................................................................... 18 1 4 0.25 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................................................................................CATGGTAATTATTGCTCTTCA........................................................................................................... 21 3 4 0.25 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAATAC.............................................................................................................................................. 20 2 6 0.17 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAATGA.............................................................................................................................................. 20 2 16 0.13 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................................................................................................GCTCTACTGAGAAATTAGTA....................................... 20 3 10 0.10 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAAAA............................................................................................................................................... 19 2 20 0.10 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................................................................................................................................................................................CACTGGTGTCCCATGGTACT... 20 3 10 0.10 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................................................................................................................................................................................CACCGGTGTCCCATGGTACT... 20 3 12 0.08 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
.........................................................................................AATTTCTTTATTGGGAACA............................................................................................................................................... 19 2 16 0.06 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
....................................................................................................................................................................AAATGAATGCTGACAAAAA.................................................................... 19 2 20 0.05 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Anti-sense strand reads

CGAAAATGATATATTATATCAAGAACCTATAATATAATATCAATAGGTTTATCTGAATTTAGGAATTTTCGAAAAAATTATATATATATATAAAGAAATAACCCTTATTGTAATCTATCTATAGTACTCTTATTAACGAGAAGTTTTGGGGTTTATCTGAATTGTTTAATTACGACTGTTTTGTAAAACTTACGAGATGTCTTTTTAATCAATAAGGTCGCAGGAAGCGTTTCCACAGGGTACCATTAAGC
**************************************************......................................((((((.((((.((.......)).)))).))))))..(((((......((..(((((((.......(((..((((....))))..)))........))))))).))))).)).************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060679
140x9_testes_total
 SRR060671
9x160_males_carcasses_total
 SRR060682
9x140_0-2h_embryos_total
 V116
male body
........................................................................................................................................CGAGAAGTTTTGGGGTTTATCTGAAT......................................................................................... 26 0 1 1.00 1 1 0 0 0
.................................................................................................................TCTATCTGTAGTAGTCTTA....................................................................................................................... 19 2 7 0.14 1 0 1 0 0
.........................................................................................................................................................................................................................TCGCAGGAAGTGCTTCAAC............... 19 3 7 0.14 1 0 0 1 0
..................................TAATGTCAATAGGTTCAT....................................................................................................................................................................................................... 18 2 20 0.05 1 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_12723:3629080-3629330 + dvi_1532 GCTTTTAC--TAT--ATAATATAGT-------------------------------------------TCTTGGATATTATATTAT-----------AGTTATCCAAATAGACTTAAATCCTTAAAAGCTTTTTTAATATATATATATATTTCTTTATTG--------GGAATAACATTAGAT----------AGA----------TATCATGAGAATAATTGCTCTT--CAAAACCCCAAATAGACTTAACAAATTAA------------------------TGCTGACAAAAC----------------------------------ATTTTG---AA-TGCTCTACAGAAAAATTAGTTATTCCAGCGTCCTTCGCAAAGGT----------------------GTCCCATGGT-AATTC---G
droMoj3 scaffold_6500:15183030-15183110 - TTTTTAAA--TAA--ATA--------------------------------------------------TGTTATATATTTTACTAT-----------TATTATT-------------GTTTATAAAAAATGTTTCAATATATTTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTTTTAAT------------------------------------------------------T
droGri2 scaffold_15252:4002597-4002925 - ATTCTTGC--TAT--CAAAT-CGATGGAGTCAAAAAGCTTGAAAGTTTTCTTAAATTATCAAACAAAATTTAAACAATTTTCTTAT-----------TACCA---------------------------------------------CATTTTCCCATTC--------GGACAGACAGTAGGAAATTGTACAAAAACCTTTTACCTTCCTATAAATATAACAAAAATACTTAGAGCTAAATGTAAAATCCCAGAAATATATAAACTAATATGAAATATTAAAATGTTGGCAG---ATTAAGTTATAAAAATAATGAAACCAATCACCAAACCCTACCCACTTTACCTCCAGAAAAATTAGTTATTCCACCAACTTATGGGGGCGT----------------------GTCCAAGGGG-AATAC---A
droWil2 scf2_1100000004585:2989441-2989515 - AC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAAAAACTAATTGTACCAGCGACTTACAAATCACTCGATCCCGATAAAGGCACAGCCGGAA--TGGTGAATGC---C
droBip1 scf7180000396568:1498909-1499001 - CTAAC--------------------------------------------------------------------------TTAAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTATT---AA-AATTTTCAAGAGAAACTCGTTATCCCCGGAAATTATCCAAAACCGGA-AACAA--AAAGTGCAGTC----CGTGGT-AACGA---G
droKik1 scf7180000302684:688547-688624 - AATG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCTAGAGAAACTACTGATTCCTGGATCGTATGCAAAACCGGG-AGCAA--GTAGAGCAGTG----CAGGGT-AATCAAACA
droEle1 scf7180000491046:3922655-3922927 + GATTTTATGCTTT--ATAATAAAAA-------------------------------------------T----GACCAAGGAATAT-----------ATACAACTAAATGAACTCTAGTCCAAAAAAACTAAATTTTTG----CACTAATAATTTAATGG--------ATAACAACATCC-----------------TTTTTAATATAATGTGATAATAATAAAAATC--CAAACTAAGAACTAGAAATGCAAAAATAA-------------------------------AAAACATTTTGTTGTGAAATTGT-----CCACTTAAAAGGCATAGTTTAA-CTTCTTCTAGAGAAACTGCTGGTTCCCGAGAGCTATGCAAAACG----------------------GCAAGCAAAC-AATGA---G
droRho1 scf7180000779213:40834-41071 - GCTGTTAG--AAACTTAATT-TGGTGCGATTCT----------------------------------------GACAGTACAATTTAAATAACAATGTGTTAAT-------------TTCAATAAAAGTTTTTTTAACATAGTTTTT-------ACATTTAAGAAAAAGTAATGATGGTATCA----------AAA----------TTTTGAAAGAAAAACGCCATT---------------GCGTGTTAATAAAAATC------------------------GACTTACA-------------------------------------AATTGGG---TA-CATTTTCTAGAGAAATTGTTGGTTCCCGTGACCTATGCAAAGCC----------------------GGAGCAGAAA-AGTGC---G
droBia1 scf7180000302422:4572735-4572791 + T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCAGAGAAACTCTTGATTCCCGCGGCCTATGCTAAACC----------------------GGGGCAGAAG-AGTGA---G

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
GCTTTTAC--TAT--ATAATATAGT-------------------------------------------TCTTGGATATTATATTAT-----------AGTTATCCAAATAGACTTAAATCCTTAAAAGCTTTTTTAATATATATATATATTTCTTTATTG--------GGAATAACATTAGAT----------AGA----------TATCATGAGAATAATTGCTCTT--CAAAACCCCAAATAGACTTAACAAATTAA------------------------TGCTGACAAAAC----------------------------------ATTTTG---AA-TGCTCTACAGAAAAATTAGTTATTCCAGCGTCCTTCGCAAAGGT----------------------GTCCCATGGT-AATTC---GSizeHit 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
........................................................................................................................................................................................................................................................................................................................................................................................CGCAAAGGT----------------------GTCCCATGGT-AA.......2111.001001000000000000000000000000000000000000000000000000000000000000
........................................................................................................................................................................................................................................................................................................................................................................................CGCAAAGGT----------------------GTCCCATGGT-.........1911.001000000010000000000000000000000000000000000000000000000000000000
....................................................................................................................................................ATTTCTTTATTG--------GGAATAC............................................................................................................................................................................................................................................................1920.501000000000000000000000000000000010000000000000000000000000000000
droMoj3
TTTTTAAA--TAA--ATA--------------------------------------------------TGTTATATATTTTACTAT-----------TATTATT-------------GTTTATAAAAAATGTTTCAATATATTTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTTTTAAT------------------------------------------------------TSizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads
droGri2
ATTCTTGC--TAT--CAAAT-CGATGGAGTCAAAAAGCTTGAAAGTTTTCTTAAATTATCAAACAAAATTTAAACAATTTTCTTAT-----------TACCA---------------------------------------------CATTTTCCCATTC--------GGACAGACAGTAGGAAATTGTACAAAAACCTTTTACCTTCCTATAAATATAACAAAAATACTTAGAGCTAAATGTAAAATCCCAGAAATATATAAACTAATATGAAATATTAAAATGTTGGCAG---ATTAAGTTATAAAAATAATGAAACCAATCACCAAACCCTACCCACTTTACCTCCAGAAAAATTAGTTATTCCACCAACTTATGGGGGCGT----------------------GTCCAAGGGG-AATAC---ASizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
No Reads
droWil2
AC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAAAAACTAATTGTACCAGCGACTTACAAATCACTCGATCCCGATAAAGGCACAGCCGGAA--TGGTGAATGC---CSizeHit CountTotal NormTotalM020
Head		M045
Female-body		V117
Male-body		V118
Embryo		V119
Head
No Reads
droBip1
CTAAC--------------------------------------------------------------------------TTAAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTATT---AA-AATTTTCAAGAGAAACTCGTTATCCCCGGAAATTATCCAAAACCGGA-AACAA--AAAGTGCAGTC----CGTGGT-AACGA---GSizeHit CountTotal NormTotal
No Reads
droKik1
AATG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCTAGAGAAACTACTGATTCCTGGATCGTATGCAAAACCGGG-AGCAA--GTAGAGCAGTG----CAGGGT-AATCAAACASizeHit CountTotal NormTotal
No Reads
droEle1
GATTTTATGCTTT--ATAATAAAAA-------------------------------------------T----GACCAAGGAATAT-----------ATACAACTAAATGAACTCTAGTCCAAAAAAACTAAATTTTTG----CACTAATAATTTAATGG--------ATAACAACATCC-----------------TTTTTAATATAATGTGATAATAATAAAAATC--CAAACTAAGAACTAGAAATGCAAAAATAA-------------------------------AAAACATTTTGTTGTGAAATTGT-----CCACTTAAAAGGCATAGTTTAA-CTTCTTCTAGAGAAACTGCTGGTTCCCGAGAGCTATGCAAAACG----------------------GCAAGCAAAC-AATGA---GSizeHit CountTotal NormTotal
No Reads
droRho1
GCTGTTAG--AAACTTAATT-TGGTGCGATTCT----------------------------------------GACAGTACAATTTAAATAACAATGTGTTAAT-------------TTCAATAAAAGTTTTTTTAACATAGTTTTT-------ACATTTAAGAAAAAGTAATGATGGTATCA----------AAA----------TTTTGAAAGAAAAACGCCATT---------------GCGTGTTAATAAAAATC------------------------GACTTACA-------------------------------------AATTGGG---TA-CATTTTCTAGAGAAATTGTTGGTTCCCGTGACCTATGCAAAGCC----------------------GGAGCAGAAA-AGTGC---GSizeHit CountTotal NormTotal
No Reads
droBia1
T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCAGAGAAACTCTTGATTCCCGCGGCCTATGCTAAACC----------------------GGGGCAGAAG-AGTGA---GSizeHit CountTotal NormTotal
No Reads

Generated: 05/17/2015 at 04:12 AM