ID:

dvi_13246

 Coordinate:

scaffold_12970:5666586-5666736 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-29.2 -28.8

Flybase annnotation

exon [dvir_GLEANR_3690:2]; CDS [Dvir\GJ18872-cds]; intron [Dvir\GJ18872-in]

No Repeatable elements found

mature
  1. scaffold_12815:226058-226074 +
  2. scaffold_12875:5199698-5199714 +
  3. scaffold_12875:14992082-14992098 +
  4. scaffold_12875:15244164-15244180 -
  5. scaffold_12875:19223464-19223480 +
  6. scaffold_12928:4838464-4838480 +
  7. dvi_13246  scaffold_12970:5666591-5666607 -
  8. scaffold_13323:1412-1428 +
star

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
TCTCCATGATTTCTCTATGAAGAGAAAAATCGTTTGAAAAACTAGATAAACTTTAAAAAGTTTGTCAGGTATTCAAGATATCTTTCTGGATATCTTGAATATAGGATTAATATATCGCATATATCTATCTATAAGGGTATTAAATCTCTCCTGTTATTTCATAAGGCTTATTTCTTTTTCTTTTTTTTTTTTCGTTTTCAGTATGCAGATTATTGGTATTTTAAGCTTCCAGTTCTTAAGCTGGATCGCTT
**************************************************(((((..((((....((((((((((((((((((....))))))))))))))..((((..((((((...))))))..))))...((((........))))))))..))))..)))))...................................************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060678
9x140_testes_total
 SRR060680
 9xArg_testes_total
 SRR060681
Argx9_testes_total
 M027
male body		 SRR060670
9_testes_total
 GSM1528803
follicle cells		 SRR060686
Argx9_0-2h_embryos_total
 SRR060666
160_males_carcasses_total
 V047
embryo
..........................................................................................................................................................................................................ATGCAGATTATTGGTATTTTAAGCT........................ 25 0 1 1.00 1 0 1 0 0 0 0 0 0 0
..TCCATGATTTCTCTATGAAGAGAAAAA.............................................................................................................................................................................................................................. 27 0 1 1.00 1 1 0 0 0 0 0 0 0 0
..............................................................TGTCAGGTATTCAAGATATTTTTCTG................................................................................................................................................................... 26 1 1 1.00 1 0 0 1 0 0 0 0 0 0
....CACGATTTCGGTATGAAGAG................................................................................................................................................................................................................................... 20 3 6 0.33 2 0 0 0 2 0 0 0 0 0
......................................................................................................................................................................................TTTTTTTCTCCGTTTTAAGTATG.............................................. 23 3 4 0.25 1 0 0 0 0 1 0 0 0 0
...................................................................................................................................................................................CTTTTTTTTTTTTCGTT....................................................... 17 0 8 0.13 1 0 0 0 0 0 1 0 0 0
........................................................AAGGATTGTCAGGTGTTCAA............................................................................................................................................................................... 20 3 9 0.11 1 0 0 0 0 0 0 1 0 0
....................................................................................................................................................................GTCTTATTGCTTTTTCTTTTTAT................................................................ 23 3 20 0.05 1 0 0 0 0 0 0 0 0 1
....CACGATTTCGGTATGAAGA.................................................................................................................................................................................................................................... 19 3 20 0.05 1 0 0 0 0 0 0 0 1 0

Anti-sense strand reads

AGAGGTACTAAAGAGATACTTCTCTTTTTAGCAAACTTTTTGATCTATTTGAAATTTTTCAAACAGTCCATAAGTTCTATAGAAAGACCTATAGAACTTATATCCTAATTATATAGCGTATATAGATAGATATTCCCATAATTTAGAGAGGACAATAAAGTATTCCGAATAAAGAAAAAGAAAAAAAAAAAAGCAAAAGTCATACGTCTAATAACCATAAAATTCGAAGGTCAAGAATTCGACCTAGCGAA
**************************************************(((((..((((....((((((((((((((((((....))))))))))))))..((((..((((((...))))))..))))...((((........))))))))..))))..)))))...................................************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR060677
Argx9_ovaries_total
 M061
embryo
 V053
head
 SRR060672
9x160_females_carcasses_total
 SRR060668
160x9_males_carcasses_total
 SRR060663
160_0-2h_embryos_total
 SRR060664
9_males_carcasses_total
 SRR060671
9x160_males_carcasses_total
 V047
embryo
...........................................................................................................................................................................................AAAAAGCAAAAGTCATTCGT............................................ 20 1 1 2.00 2 2 0 0 0 0 0 0 0 0
...............................................................CAGTCCATAAGTTCTATAGAAAGACC.................................................................................................................................................................. 26 0 1 1.00 1 0 1 0 0 0 0 0 0 0
...........................................................................TCTATAAAAGGACCTACAGAAC.......................................................................................................................................................... 22 3 3 0.33 1 0 0 1 0 0 0 0 0 0
ACAGGTACCAAAGAGATA......................................................................................................................................................................................................................................... 18 2 4 0.25 1 0 0 0 1 0 0 0 0 0
................................AAACTTTTGGATCTATTTT........................................................................................................................................................................................................ 19 2 8 0.13 1 0 0 0 0 1 0 0 0 0
AGAGGTACTGAAGTGATAG........................................................................................................................................................................................................................................ 19 3 17 0.12 2 0 0 0 0 0 2 0 0 0
...............................................................................................................................................................................................................................TCGAAAGTCACGAACTCGAC........ 20 3 20 0.05 1 0 0 0 0 0 0 0 1 0
.......................................................................................................................................................................................AAAAAAAAAGTAGAAGTCATAG.............................................. 22 3 20 0.05 1 0 0 0 0 0 0 1 0 0
..........................................................................................................................................................................AAAGAAAAAGAAAAAAAAAAAA........................................................... 22 0 20 0.05 1 0 0 0 0 0 1 0 0 0
............................................................................................................................................................................AGAAAAAGAAAAAAAAAA............................................................. 18 0 20 0.05 1 0 0 0 0 1 0 0 0 0
.......................CTTTGTAGCACCCTTTTTG................................................................................................................................................................................................................. 19 3 20 0.05 1 0 0 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droVir3 scaffold_12970:5666536-5666786 - dvi_13246 TCTCCATGA---------TTTCTCTATGAAGAGAAAA--------------------------ATCGT-----------TTGAAAAACTAGATAAACTTT-----------------AAAAAGTTTGTCAGGTATTCAAGATATCTTTCTGGATATCTTGAATATAGGATTAATATATCGCATA-----------------------------------------TATCTATCTATAAGGGTATTAAATC-----------------TCTCCTGTTATTTCATAAGGCTTATTTCTTTTTCTTTTTTTTTTTTCGTTTTCAGTATGCAGATTATTGGTATTTTAAGCTTCCAGTTCTTAAGCTGGATCGCTT
droMoj3 scaffold_6473:15990475-15990538 + TTTCTCGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTCAGTACGCAGACTATTGGTACTTCAAGCTGCAAGTGCTGAAGCTGGATCGCCT
droGri2 scaffold_15252:15168769-15168973 + TCTTAATTA---------CCACGATATCCAGGACCAAA-CTGGCTAGATGA-TGCTTAAAATGAAATCTAA--GGAATTGTCAATAATGGACTACTCTTTACTACAC-----TGTCT--------------------------------TAAGTC----------------------TCCCATAGCTCT--------------------------------------TCTATCGGTAAGGGTATTGAAATTTCGGCGGGTCTAAGTTTCTTCTGTTCCTTCTTTGGTTTTGCTTCTTTTATTATTATTTTT---------------------------------------------------------TGCG
droWil2 scf2_1100000004762:4175653-4175783 - TCTCAATAA---------CTTCGTTATTTTCTGAGCT--------------------------ATTGT-----------CGTGAAATTT-----AATATT-----------------AGTGAGTTTATAATACATATAAACGACTATGCCGAATTTGATAAATATCGGGTTACTATTATATAT-------------------------------------------------------------------------------------------------------------------------------TATATTATATA----------------------------------------------TAGCT
droKik1 scf7180000302517:1153404-1153613 - TTTCAACGTATTTTTATCTACTCTA-----AGATATAAGCTTTTTTTATTATTTTAGAATT---------------------------------------------T-----TGGTA--------------------------------TAAATTTCATAAAAATCGGACAACTATATCATATTGTGTGTGTTTTCAGCATTATAATTAATAATATAAATATCAAAACCAATCTGCAAGGGTATACAAACTTCGGCAAGCCGAAGT----------------------TAGCTTCCTTTCTTGTTTTTTTTTCTGTT-----------------------------------------------------TT
droFic1 scf7180000454078:136840-136944 + TTTTTTTA---------------------------TAGG-----------------------GAATGTTTT--ATAATTATTATTATTGAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTATTTATTAATAGTACTCCAACTACTGGTGCTTTAAGTTGGCCTATCTGAAAATTGAGCAAGT
droEle1 scf7180000490779:1368-1556 - TTTTTTTTG---------TTCTTTG-----ACATATAGT-----------------------AATTGTTAA--ATATTTCAGAATAACGGTTTAAATTTCAGAATAA-----CGGTT--------------------------------TAAATTTCAGCGAAATCGGACGACTATATCATATAGCTCA--------------------------------------TATATATAT----A-----------------------------TTTTTTTGTTCATTTGTTTTGTTCCACCAATTG----------------------T---------CATCCATTCATTTCTTCATCCTT-----AGATTTCAG
droRho1 scf7180000771752:635-690 + TTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGTATTCAAACTACTGGTGCTTCAAGCTGCCCTATCTCAAGATCGAGCGGAC
droBia1 scf7180000302292:1332930-1333021 + TTTATATAA---------CCTTCTAAGCTTGGAAATAA-CATTTTTAAATAGTTCAGAATT---------------------------------------------T-----CGAAA--------------------------------TAAATTTTATCAAAATCGGACGACTATATCATATA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droTak1 scf7180000415145:14863-15036 - TCTTATGG----------CTCCCATAGGAATA----------------------------------ATCAAAAAAATAATAGAAAAACCATTGTAACTTTGAAGAAAGTAGGCGTTT--------------------------------TAATTTTTGGCAATGTAAAAACAACATTTTAAGTA-----------------------------------------GGCATACCTGCAAGGGTATATAAACTTCGGCTGGCCGAAGT----------------------TAACTTCCTTTCTTGTTTTT-----------------------------------------------------------TTATT
droEug1 scf7180000404992:215850-215910 - TTCTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATAGTACTCAGTTTACTGGTGCTTCAAGCTGTCCTACATTAAAATCGAACGCCT
droSim2 2l:15779671-15779741 + TTTAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTATTTTACAGTACTCAAACTTCTGGTGCTTCAAGCTTTCCTTTCTCAGAATGGAACGCGT
droSec2 scaffold_5:4935103-4935173 + TTTAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTATTTTACAGTACTCAAACTTCTGGTGCTTCAAGCTTTCCTTTCTCAGAATGGAACGCGT
droYak3 2L:19120619-19120688 - TTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTCTTTTACAGTACTCAAACTACTGGTGCTTTAAGCTGTCGTACCTCAGAATAGAACGCGT
droEre2 scaffold_4929:7910003-7910083 + TTTATACTT---------ATT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCT---------------------------------GTATTTTCTTTCACAGTACTCAAGCTACTGGTGCTTTAAGCTGTCCTACCTCAGAATAGAACGCGT

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droVir3
TCTCCATGA---------TTTCTCTATGAAGAGAAAA--------------------------ATCGT-----------TTGAAAAACTAGATAAACTTT-----------------AAAAAGTTTGTCAGGTATTCAAGATATCTTTCTGGATATCTTGAATATAGGATTAATATATCGCATA-----------------------------------------TATCTATCTATAAGGGTATTAAATC-----------------TCTCCTGTTATTTCATAAGGCTTATTTCTTTTTCTTTTTTTTTTTTCGTTTTCAGTATGCAGATTATTGGTATTTTAAGCTTCCAGTTCTTAAGCTGGATCGCTTSizeHit 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
...................................................................................................................................................................................................................................................................................................................................ATGCAGATTATTGGTATTTTAAGCT........................2511.001000000000000000000000000000000100000000000000000000000000000000
..TCCATGA---------TTTCTCTATGAAGAGAAAA--------------------------A....................................................................................................................................................................................................................................................................................................................2711.001000000000000000000000000000010000000000000000000000000000000000
............................................................................................................................................................................................................................................................................................................CTTTTTTTTTTTTCGTT.......................................................1780.131000000000000000000000000000000000000000000000000000000000000001
droMoj3
TTTCTCGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTCAGTACGCAGACTATTGGTACTTCAAGCTGCAAGTGCTGAAGCTGGATCGCCTSizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads
droGri2
TCTTAATTA---------CCACGATATCCAGGACCAAA-CTGGCTAGATGA-TGCTTAAAATGAAATCTAA--GGAATTGTCAATAATGGACTACTCTTTACTACAC-----TGTCT--------------------------------TAAGTC----------------------TCCCATAGCTCT--------------------------------------TCTATCGGTAAGGGTATTGAAATTTCGGCGGGTCTAAGTTTCTTCTGTTCCTTCTTTGGTTTTGCTTCTTTTATTATTATTTTT---------------------------------------------------------TGCGSizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
No Reads
droWil2
TCTCAATAA---------CTTCGTTATTTTCTGAGCT--------------------------ATTGT-----------CGTGAAATTT-----AATATT-----------------AGTGAGTTTATAATACATATAAACGACTATGCCGAATTTGATAAATATCGGGTTACTATTATATAT-------------------------------------------------------------------------------------------------------------------------------TATATTATATA----------------------------------------------TAGCTSizeHit CountTotal NormTotalM020
Head		M045
Female-body		V117
Male-body		V118
Embryo		V119
Head
............................TTCTGAGCT--------------------------ATTGT-----------CGTGAAATTT-----A.....................................................................................................................................................................................................................................................................................25200.05101000
droKik1
TTTCAACGTATTTTTATCTACTCTA-----AGATATAAGCTTTTTTTATTATTTTAGAATT---------------------------------------------T-----TGGTA--------------------------------TAAATTTCATAAAAATCGGACAACTATATCATATTGTGTGTGTTTTCAGCATTATAATTAATAATATAAATATCAAAACCAATCTGCAAGGGTATACAAACTTCGGCAAGCCGAAGT----------------------TAGCTTCCTTTCTTGTTTTTTTTTCTGTT-----------------------------------------------------TTSizeHit CountTotal NormTotal
No Reads
droFic1
TTTTTTTA---------------------------TAGG-----------------------GAATGTTTT--ATAATTATTATTATTGAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTATTTATTAATAGTACTCCAACTACTGGTGCTTTAAGTTGGCCTATCTGAAAATTGAGCAAGTSizeHit CountTotal NormTotal
No Reads
droEle1
TTTTTTTTG---------TTCTTTG-----ACATATAGT-----------------------AATTGTTAA--ATATTTCAGAATAACGGTTTAAATTTCAGAATAA-----CGGTT--------------------------------TAAATTTCAGCGAAATCGGACGACTATATCATATAGCTCA--------------------------------------TATATATAT----A-----------------------------TTTTTTTGTTCATTTGTTTTGTTCCACCAATTG----------------------T---------CATCCATTCATTTCTTCATCCTT-----AGATTTCAGSizeHit CountTotal NormTotal
No Reads
droRho1
TTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGTATTCAAACTACTGGTGCTTCAAGCTGCCCTATCTCAAGATCGAGCGGACSizeHit CountTotal NormTotal
No Reads
droBia1
TTTATATAA---------CCTTCTAAGCTTGGAAATAA-CATTTTTAAATAGTTCAGAATT---------------------------------------------T-----CGAAA--------------------------------TAAATTTTATCAAAATCGGACGACTATATCATATA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
TCTTATGG----------CTCCCATAGGAATA----------------------------------ATCAAAAAAATAATAGAAAAACCATTGTAACTTTGAAGAAAGTAGGCGTTT--------------------------------TAATTTTTGGCAATGTAAAAACAACATTTTAAGTA-----------------------------------------GGCATACCTGCAAGGGTATATAAACTTCGGCTGGCCGAAGT----------------------TAACTTCCTTTCTTGTTTTT-----------------------------------------------------------TTATTSizeHit CountTotal NormTotal
No Reads
droEug1
TTCTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATAGTACTCAGTTTACTGGTGCTTCAAGCTGTCCTACATTAAAATCGAACGCCTSizeHit CountTotal NormTotal
No Reads
droSim2
TTTAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTATTTTACAGTACTCAAACTTCTGGTGCTTCAAGCTTTCCTTTCTCAGAATGGAACGCGTSizeHit CountTotal NormTotalM023
Head		M024
Male-body		M025
Embryo		M053
Female-body		O001
Testis		O002
Head		SRR553485
Ovary		SRR553486
Ovary		SRR553487
Ovary		SRR553488
Ovary		SRR618934
Ovary		V044
Embryo		SRR902008
Ovary		SRR902009
Testis		SRR1275487
Male larvae		SRR1275485
Male prepupae		SRR1275483
Male prepupae
No Reads
droSec2
TTTAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTATTTTACAGTACTCAAACTTCTGGTGCTTCAAGCTTTCCTTTCTCAGAATGGAACGCGTSizeHit CountTotal NormTotalM054
Female-body		V113
Male-body		V114
Embryo		V115
Head
No Reads
droYak3
TTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTTTCTTTTACAGTACTCAAACTACTGGTGCTTTAAGCTGTCGTACCTCAGAATAGAACGCGTSizeHit 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
TTTATACTT---------ATT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCT---------------------------------GTATTTTCTTTCACAGTACTCAAGCTACTGGTGCTTTAAGCTGTCCTACCTCAGAATAGAACGCGTSizeHit CountTotal NormTotalM055
Female-body		M057
Embryo		V060
Head		V040
Embryo		V107
Male-body		V108
Head		GSM1528801
follicle cells
No Reads

Generated: 05/16/2015 at 10:03 PM