ID:

dvi_4245

 Coordinate:

scaffold_12855:6925343-6925408 -

 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_10141:5]; CDS [Dvir\GJ10201-cds]; CDS [Dvir\GJ10201-cds]; exon [dvir_GLEANR_10141:4]; intron [Dvir\GJ10201-in]

No Repeatable elements found

Sense Strand Reads

##################################################------------------------------------------------------------------##################################################
CGAGACGCTGCCGTCGGATGGGACTGAAGACGAAGCTGATGCCAACACAAGTAAGCACAAGTACTTTATGAATAAAAGCAATTACTAATGTATTTTCTACTCGCTCTCTGTCATAGCCGGAGTGCGTCGCTCCAGACGCGGCCAGGTGCAGCTGTGCAACACTTGG
**************************************************...............((((((.....(((((.(((....))).)).......))).....))))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060673
9_ovaries_total
 SRR1106728
larvae
 V116
male body		 SRR060681
Argx9_testes_total
 SRR060670
9_testes_total
 SRR060672
9x160_females_carcasses_total
 SRR060687
9_0-2h_embryos_total
......GCTGCCGTCGGATGGGACTGAAG......................................................................................................................................... 23 0 1 1.00 1 1 0 0 0 0 0 0
................GATGGGACTGAGGAC....................................................................................................................................... 15 1 2 0.50 1 0 1 0 0 0 0 0
................GATGGGATTGAAGACAAGGC.................................................................................................................................. 20 3 5 0.20 1 0 0 1 0 0 0 0
................GATGCCATTGAAGACGAAGCT................................................................................................................................. 21 3 6 0.17 1 0 0 0 1 0 0 0
.....................................................................................TAATGTATGTTCTCCTCGGT............................................................. 20 3 7 0.14 1 0 0 0 0 1 0 0
.......................................................................................ATGTGGTTGCTACTCGCTCT........................................................... 20 3 9 0.11 1 0 0 0 0 0 1 0
.......................CTGAAGACGAAGCTAACGAC........................................................................................................................... 20 3 17 0.06 1 0 0 0 0 0 0 1
............GCCAGATGGGACTGAGGAC....................................................................................................................................... 19 3 20 0.05 1 0 0 0 0 0 0 1

Anti-sense strand reads

GCTCTGCGACGGCAGCCTACCCTGACTTCTGCTTCGACTACGGTTGTGTTCATTCGTGTTCATGAAATACTTATTTTCGTTAATGATTACATAAAAGATGAGCGAGAGACAGTATCGGCCTCACGCAGCGAGGTCTGCGCCGGTCCACGTCGACACGTTGTGAACC
**************************************************...............((((((.....(((((.(((....))).)).......))).....))))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total GSM1528803
follicle cells		 SRR060662
9x160_0-2h_embryos_total
 SRR060672
9x160_females_carcasses_total
 V053
head
 SRR060686
Argx9_0-2h_embryos_total
 M047
female body
 M061
embryo
........................................................................................................................................GCGCCGGTCCATGTCGAAA........... 19 2 1 1.00 1 1 0 0 0 0 0 0
..............................................................................................AAGATGAGGGAGACACAG...................................................... 18 2 6 0.17 1 0 1 0 0 0 0 0
..............................................................................................AAGATGAGGGAGATACAG...................................................... 18 2 6 0.17 1 0 0 1 0 0 0 0
............................................................................................ATAAGATGAGGGAGATACAG...................................................... 20 3 9 0.11 1 0 0 0 1 0 0 0
...........................................................................................TAAAGGATGAACGAGAGA......................................................... 18 2 12 0.08 1 0 0 0 0 1 0 0
................................................................................................................................CGCGGGCTGCGACGGTCCA................... 19 3 20 0.05 1 0 0 0 0 0 1 0
.............................................................................................TAAGATGAGGGAGATACAG...................................................... 19 3 20 0.05 1 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_12855:6925293-6925458 - dvi_4245 CGAGA-CGC--------------TGCCGTCGGATG------GGA-----------CTGAAG---------ACGAAGCTGATGCCAACACAAGT----AAGCACAAGTA-CT-T---TATGAATAAAAGCAATTACTAATGTATTTTCTACTCGCT-C-TCTG--T-C-ATAGCCGGAGTGCGTCGCTCCAGACGCGGCCAGGTGCAGCTGTGCAACACTTGG
droMoj3 scaffold_6540:25687169-25687322 + TGCCA-CTC--------------TTCCGCCGGATGAGCGAGATGACG-----------ATGC---CA------------------ACACGAGT----AAGTAAACTGCTGGCAAATGAC---TAGGCCAATCCACTAATGCATACTCAATTT--------------CATCAGCTGGCGTTCGTCGTTCCAGACGTGGTCAGGTGCCGCTGTGCAATACCTGG
droGri2 scaffold_15074:4867214-4867379 - CGAGA-CGC--------------TGCCGCCGGAGG------AGA-----------ATGAAGCACGCAATGCCCACGATG------AGACAAGT----AAGAAAATGTA-TT-T---CAATTGCTA----TCAACGAATTA--TGTTTATATTTTT-CC-ATGCAA-AACCAGGTGGCGTGCGCAGATCGAGACGTGGTCAAGTGCCGTTGCGCAACACTTGG
droWil2 scf2_1100000004909:7015507-7015568 - CAATGAT---------------A------------AGGATGATAGTG-----------ATAAGAATAATGATGATGATGATGCCAACAATAAT----AAACA----------------------------------------------------------------------------------------------------------------------CA
dp5 2:17288268-17288427 - AAGGAACTCCGTCATACATAATGAA------GTGGAAGTGGATT--------------TCAA---TGAA------------------TCTTGT----AAGTAGTACCA-----AACGATATGTTA----TTGCAATATTT-TCATTCAATTTT-TTCG---G--T-TATTAGCAGCCATTCGGCGGTCTCGGCGTGGTCAGGTACCATTAAAGAACACTTGG
droPer2 scaffold_0:11133061-11133219 - AGGGA-CTCCGTGATATATAATGAA------GTGGAAGTGGATT--------------TCAA---TGAA------------------TCTTGT----AAGTAGTACCA-----AACGATATGATA----TTGCAATATTT-TCATTCAATTTT-TTCG---G--T-TATTCGCAGCCCTTCGGCGGTCCCGGCGTGGTCAGGTACCATTTAAGAACACTTGG
droFic1 scf7180000454106:2761283-2761444 - ATTGAAGCTTTCCAAAATTCCAGTG------GAGACGGAGGATCAGG-----------ACCA---CGAT------------------ACCTGT----GAGTATATTTT-----AACAACGACTTA----ATTAAAACTTA-ATATTAACATTA-TTTC---G--T-T-GTAGCCGGCATTCGGCGCTCGAAGCGAGGCCAAAAACCACTCCAAATGAGTTGG
droEle1 scf7180000491212:1416165-1416310 - TGGA-----------------------------AATGGATGAAAACG-----------ACCA---CAAC------------------ACCTGTGAGTAACTAAAAAAA-----AACTATGATTTC----TTGAAATATTT-TATTTAT-ATTATT-TT-ATTG-T-TCTTAGCCGGCATTCGGCGTTCGAAGCGAGGCCATGTGCCACTCCAGAATACCTGG
droRho1 scf7180000780121:12713-12862 + TCCGG------------------TG------GTAATGGATGAAGGCG-----------ACCA---CAAT------------------ACCTGT----GAGTATATTTTGAAATAACGTT---TTAACCTTCCATTAAACC--TATTTTTGTTT-----TCTGT-T-ACTCAGCCGGCATTCGGCGTTCAAAACGAGGCCAAGTGCCAATCCAGATGACTTTT
droTak1 scf7180000414445:283583-283601 + CGAGGTT---------------A---------------------ACG-----------ATGT---CA------------------TC---------------------------------------------------------------------------------------------------------------------------------------
droYak3 2R:12081074-12081121 + ACATGGT---------------G---------------------GGGTGGCCGCCCTGAAG-----------------------------------------------------------------------------------------------------------------------CAGCAACTGCTGCAAAAGCAGGT-------------------
droEre2 scaffold_4770:17181684-17181824 - AATTC-CGG--------------TGGAATCAGAGG------AA-----------------CT---AAAT------------------ACAAGT----AAGTATATTTTATATTAGGTGC---TTTA-------TTTTTTA--TATTATTATTT-----TCTGT-TTCTTCAGCTGGTATTCGGCGATCGAAGCGAGGTCAAGTTCCACTCCAGATGAGTTGG

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
CGAGA-CGC--------------TGCCGTCGGATG------GGA-----------CTGAAG---------ACGAAGCTGATGCCAACACAAGT----AAGCACAAGTA-CT-T---TATGAATAAAAGCAATTACTAATGTATTTTCTACTCGCT-C-TCTG--T-C-ATAGCCGGAGTGCGTCGCTCCAGACGCGGCCAGGTGCAGCTGTGCAACACTTGGSizeHit 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
.......GC--------------TGCCGTCGGATG------GGA-----------CTGAAG---------........................................................................................................................................................2311.001000000000000000000000001000000000000000000000000000000000000000
droMoj3
TGCCA-CTC--------------TTCCGCCGGATGAGCGAGATGACG-----------ATGC---CA------------------ACACGAGT----AAGTAAACTGCTGGCAAATGAC---TAGGCCAATCCACTAATGCATACTCAATTT--------------CATCAGCTGGCGTTCGTCGTTCCAGACGTGGTCAGGTGCCGCTGTGCAATACCTGGSizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads
droGri2
CGAGA-CGC--------------TGCCGCCGGAGG------AGA-----------ATGAAGCACGCAATGCCCACGATG------AGACAAGT----AAGAAAATGTA-TT-T---CAATTGCTA----TCAACGAATTA--TGTTTATATTTTT-CC-ATGCAA-AACCAGGTGGCGTGCGCAGATCGAGACGTGGTCAAGTGCCGTTGCGCAACACTTGGSizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
No Reads
droWil2
CAATGAT---------------A------------AGGATGATAGTG-----------ATAAGAATAATGATGATGATGATGCCAACAATAAT----AAACA----------------------------------------------------------------------------------------------------------------------CASizeHit CountTotal NormTotalM020
Head		M045
Female-body		V117
Male-body		V118
Embryo		V119
Head
.........................................ATAGTG-----------ATAAGAATAATT........................................................................................................................................................1811.00101000
dp5
AAGGAACTCCGTCATACATAATGAA------GTGGAAGTGGATT--------------TCAA---TGAA------------------TCTTGT----AAGTAGTACCA-----AACGATATGTTA----TTGCAATATTT-TCATTCAATTTT-TTCG---G--T-TATTAGCAGCCATTCGGCGGTCTCGGCGTGGTCAGGTACCATTAAAGAACACTTGGSizeHit CountTotal NormTotalM022
Male-body		M040
Female-body		M059
Embryo		M062
Head		V043
Embryo		V051
Head		V112
Male-body		SRR902010
Ovary		SRR902011
Testis		SRR902012
CNS imaginal disc
No Reads
droPer2
AGGGA-CTCCGTGATATATAATGAA------GTGGAAGTGGATT--------------TCAA---TGAA------------------TCTTGT----AAGTAGTACCA-----AACGATATGATA----TTGCAATATTT-TCATTCAATTTT-TTCG---G--T-TATTCGCAGCCCTTCGGCGGTCCCGGCGTGGTCAGGTACCATTTAAGAACACTTGGSizeHit CountTotal NormTotalM021
Embryo		M042
Female-body		V042
Embryo		V050
Head		V057
Head		V111
Male-body
No Reads
droFic1
ATTGAAGCTTTCCAAAATTCCAGTG------GAGACGGAGGATCAGG-----------ACCA---CGAT------------------ACCTGT----GAGTATATTTT-----AACAACGACTTA----ATTAAAACTTA-ATATTAACATTA-TTTC---G--T-T-GTAGCCGGCATTCGGCGCTCGAAGCGAGGCCAAAAACCACTCCAAATGAGTTGGSizeHit CountTotal NormTotal
No Reads
droEle1
TGGA-----------------------------AATGGATGAAAACG-----------ACCA---CAAC------------------ACCTGTGAGTAACTAAAAAAA-----AACTATGATTTC----TTGAAATATTT-TATTTAT-ATTATT-TT-ATTG-T-TCTTAGCCGGCATTCGGCGTTCGAAGCGAGGCCATGTGCCACTCCAGAATACCTGGSizeHit CountTotal NormTotal
No Reads
droRho1
TCCGG------------------TG------GTAATGGATGAAGGCG-----------ACCA---CAAT------------------ACCTGT----GAGTATATTTTGAAATAACGTT---TTAACCTTCCATTAAACC--TATTTTTGTTT-----TCTGT-T-ACTCAGCCGGCATTCGGCGTTCAAAACGAGGCCAAGTGCCAATCCAGATGACTTTTSizeHit CountTotal NormTotal
No Reads
droTak1
CGAGGTT---------------A---------------------ACG-----------ATGT---CA------------------TC---------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droYak3
ACATGGT---------------G---------------------GGGTGGCCGCCCTGAAG-----------------------------------------------------------------------------------------------------------------------CAGCAACTGCTGCAAAAGCAGGT-------------------SizeHit CountTotal NormTotalM026
Head		M043
Female-body		M056
Embryo		V046
Embryo		V052
Head		V058
Head		V120
Male-body		SRR1275488
Male larvae		SRR1275486
Male prepupae		SRR1275484
Male prepupae		GSM1528802
follicle cells
No Reads
droEre2
AATTC-CGG--------------TGGAATCAGAGG------AA-----------------CT---AAAT------------------ACAAGT----AAGTATATTTTATATTAGGTGC---TTTA-------TTTTTTA--TATTATTATTT-----TCTGT-TTCTTCAGCTGGTATTCGGCGATCGAAGCGAGGTCAAGTTCCACTCCAGATGAGTTGGSizeHit CountTotal NormTotalM055
Female-body		M057
Embryo		V060
Head		V040
Embryo		V107
Male-body		V108
Head		GSM1528801
follicle cells
...TC-CGG--------------TGGAATCAGAGG------AA-----------------CT---.............................................................................................................................................................2111.0011000000

Generated: 05/16/2015 at 08:35 PM