ID:

dsi_222

 Coordinate:

2R:11376756-11376802 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-17.8 -17.8 -17.5

Flybase annnotation

intron [Dsim\GD25516-in]

No Repeatable elements found

Sense Strand Reads

GCGGCCAGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCCGTTGCCATGACCGAAATCATCAGCAAGGCCGGCAACAGCAGCAAGCAGAGGGATTTGAACCAAACCATCTTACAAACCAAAAGCAACTGAAG
***********************************.....(((((((...(((..((((((....((..............))..)))))).)))....)).)))))....************************************ 		Read size # Mismatch Hit Count Total Norm Total O001
Testis
 O002
Head
 M053
Female-body
.............................................................................GCAAGGCCGGCAACAGCAG................................................... 19 0 1 12.00 12 9 3 0
.............................................................................GCAAGGCCGGCAACAGCAGCA................................................. 21 0 1 1.00 1 1 0 0
...............................................................................................GCAAGCAGAGGGATTTGAACCAAAC........................... 25 0 1 1.00 1 0 0 1
......................................GATCCTCGTCGATGCCCGTTGC....................................................................................... 22 0 1 1.00 1 1 0 0
............................................................................AGCAAGGCCGGCAACAGCAG................................................... 20 0 1 1.00 1 1 0 0
..................................................TGCCCGTTGCCATGACCGAAA............................................................................ 21 0 1 1.00 1 1 0 0
............................................................................................................TTTGAACCAAACGTTATTACAAA................ 23 3 2 1.00 2 0 0 0
.......................................................GCTGCCATGACCGAA............................................................................. 15 1 4 0.50 2 0 0 0
....................................GTGATCCTCGTCGATGCCG............................................................................................ 19 2 4 0.25 1 0 0 0
..................CAAATCATGGTTAAGGAT............................................................................................................... 18 2 5 0.20 1 0 0 0
................................................GATTCCCGTTGCCTTGACTG............................................................................... 20 3 7 0.14 1 0 0 0
.........................................................TGCCATGTCCGAAAT........................................................................... 15 1 10 0.10 1 0 0 0
.........................................................................................ACAGAAGCAAGCAGA........................................... 15 1 20 0.05 1 0 0 0

Anti-sense strand reads

CTTCAGTTGCTTTTGGTTTGTAAGATGGTTTGGTTCAAATCCCTCTGCTTGCTGCTGTTGCCGGCCTTGCTGATGATTTCGGTCATGGCAACGGGCATCGACGAGGATCATATCCTGAACCATGATGTGGACCCGGATCCTGGCCGC
************************************....(((((.((....(((.((((((..((..............))....))))))..)))...))))))).....*********************************** 		Read size # Mismatch Hit Count Total Norm Total M024
male body
.........................................................................................................................ATGATGTAGACCCGAAACCT...... 20 3 1 8.00 8 1
........................................................................................................................CATGATGTAGACCCGAAACCT...... 21 3 1 7.00 7 5
........................................................................................................................CATGATGTAGACCCGAAACC....... 20 3 1 5.00 5 3
................................................................................................ATCGACGAGGATCATATCCTGAACC.......................... 25 0 1 2.00 2 2
................................................................................................................TCCGGAACCAGGATGTGGA................ 19 2 3 1.67 5 0
...................................................................TGCTGATGATTTCGGTCAT............................................................. 19 0 1 1.00 1 1
................................................................................................ATCGACGAGGATCATATCCTGAAC........................... 24 0 1 1.00 1 1
...............................GGTTCAAATCCCTCCGCTCGT............................................................................................... 21 3 1 1.00 1 0
................................GTTCAAATCCCTCCGCT.................................................................................................. 17 1 1 1.00 1 0
.................................................................................................................CCGGAACCAGGATGTGGA................ 18 2 8 0.88 7 0
....................................................TGCTGTTGCCGGCCTTGTCGGT......................................................................... 22 3 3 0.67 2 0
.................................................................................................................CCGGAACCAGGATGTGGATCC............. 21 3 3 0.67 2 0
.........................................................................................................................ATGATGTAGACCCGAAACC....... 19 3 9 0.56 5 2
........................................................................................................................CATGATGTAGACCCGAAAC........ 19 3 10 0.50 5 3
..........................................................................................................................TGATGTAGACCCGAAACCT...... 19 3 8 0.38 3 2
.................................TTCAAATCCCTCTGCTCGT............................................................................................... 19 2 3 0.33 1 0
....................................................................................................................GTATCATGATGTAGACCCG............ 19 3 6 0.33 2 2
................................GTTCGAATCCCTCTGC................................................................................................... 16 1 4 0.25 1 0
................................GTTCGAATCCCTTCGCTTGCT.............................................................................................. 21 3 4 0.25 1 0
................................GTTCAAATCCCTCCGCTCGT............................................................................................... 20 3 4 0.25 1 0
..............................................................................................................................GTTGACCCGGTTCCCGGCC.. 19 3 17 0.12 2 0
................................................................................................................TCCGGAACCAGGATGTG.................. 17 2 19 0.11 2 0
.................................................................................................................CCTGAACCAGGACGTGGA................ 18 2 13 0.08 1 0
.................TTGTGAGATAGTTTGGTT................................................................................................................ 18 2 13 0.08 1 0
..................................................................................................................CGGAACCATGATGTGGATT.............. 19 3 16 0.06 1 0
....................................................................................................................GAACCAGGATGTGGATCCT............ 19 3 17 0.06 1 0
................................................................................................................TCCGGAACCAGAATGTGGA................ 19 3 17 0.06 1 0
................................GTTCAAATCCTTCCGCTCG................................................................................................ 19 3 20 0.05 1 0
...............................GGTTCAAATCCGTCCGCC.................................................................................................. 18 3 20 0.05 1 1
......................................................................................................................ATCATGATGTAGACCCGAA.......... 19 3 20 0.05 1 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droSim3 2R:11376706-11376852 - dsi_222 GCGGCC-AGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCCGTTGCCATGACCGAAATCATCAGCAAGGCCGGCAACAGCAGCA------AGCAGAGGGATTTGA---ACCAAACCATCTTACAAACCAAAAGCAACTGAAG-----
droSec2 scaffold_1:10147455-10147601 - GCGGCC-GGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCCGTTGCCATGAGCGAATTCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGGGATTTGA---ACCAAACCATCCTACAAACCAAAAGCAACTGAAG-----
dm3 chr2R:12641988-12642134 - GCGGCC-CGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCAGTTGTCATGACCGAATCCATCAGCAAGGCCGGCAGCAGCAGAA------AGCAGAGGGAATTGA---ACCAAACCATCATGCAAAACAAAAGCAACTGAAG-----
droEre2 scaffold_4845:13209605-13209748 + GCGACC-CGGATCCGGGTCCACATCATGGTTAACGACATGATCCTCGTC---GTCAGTTGACGTGACCGAATTCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGAGATTTTA---ACCGAGCCATCCTACAAATCAAAAGCAACTGAAG-----
droYak3 2R:16335835-16335978 + GCGTCC-CGGATCCGGGTCCACATCATGGTCTAGGATATGATCCTCGTC---GTCAGTTGACGTGACCGAAATCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGTGATTTAA---ACCAAACCATCCTACAAATCAAAAGCAACTGAAG-----
droEug1 scf7180000409672:2505304-2505456 + GCGACC-CGGATCCGGGTCCACTTCATGGTTTATAACTGTTTGCTCAGGAATGCCAGTTGCCCGAACCGAAATCATTAATAAAGCCGGCAGCAGCAGCAGCAGCCAACAGAGAGACTTTA---ACTTAATCATCCTAAGAATCAAAAGCAACTGAAG-----
droBia1 scf7180000301506:2039974-2040120 - CCGACC-CGGATCCGGGTCTTCATAATGGTTCAGTACCGTTTCCTCTGCAAAGCCAGTTGACATAGCCGAATTTATAAATAAAACTGGTAGTACCAGCC------AAGAAAGAGACTTGA---TCCAAACCATCCTATAAGCCAAACGCAACTGAAG-----
droTak1 scf7180000414504:27279-27425 - ACGACT-CGGATCCGGGTCCACTTCGTGGTTAAGAACAGTTTCCTCCGCAAAGCCAGTTGTCATCACGGAATTCACAAATAATGCCGGCAGCAGCAGCA------AAAAAAGAGACTTTA---ACCAAATCATCCTGCAAACCAGAGGCAACTGAAA-----
droEle1 scf7180000491214:1741711-1741854 + ACGATC-CGGATCCGGGTCCACCTCATGGTTGATAATGTAATTTC---CAAAGCCAGTTGACATCACTGTTCTTATTAAAAACGCTGGCAACAGCAGCA------AACAGAGAAGCTTAA---ACCAAATCATTCTTAAAGCCAAATGCAACTGAGG-----
droRho1 scf7180000780084:710438-710584 + GCGACT-CGGATCCGGGTCCACCTCATGGTGGAGAACTTGTTCCTCTGCAAAGCCTGTTGCCATCACCGATTTCAACAATAACGCCGGCAGCAGCAGCA------AACAGAGCGACGTTA---ACCAAAACATCCTAAAAACCTGAAGCAACTGAGG-----
droFic1 scf7180000453851:855598-855744 - GCGACC-CGGATCCGGGTCACCTTCATGGCTCAAAATGTGTTCCTCTGCAAAGCCAGTTGTCATCAAAGAAATCATGAATACAGCTGGCAGCAGCAGCA------AATAGAGAAACTTCA---ACTCGATCATCGTACGAACAAAAGGCAACTGAAG-----
droKik1 scf7180000302470:1050093-1050239 - ACGATC-CGGATCCGGGTCCACCTTATGGTGTAGAACAGTCTCAT---CAAAGCTAGTAACCATCACCATTTTCATGAACAAAGCTGCTGGCAGAAGCA------AAGAAAGGGAGAATAGCAACCGAGCCATTATAGAAACCAAAAGCAACTGGAG-----
droAna3 scaffold_13266:13949661-13949804 + CCGAGT-CGGATCCGGGTTTTTATCGTGGCCCAAAATTGTTTCCAAAGGCAAGCTTTCGGCCATCAATGCTGGAAAGTATATAGCTGGCAGCAGCAGGA-------GC--AGAAAGCTGG---AGCACATCATCCTCCAAGTCGGTGCAAACTCAAA-----
droBip1 scf7180000396759:2187713-2187861 - CCGATT-CGGATCCGGGTCTAGTTTGTGGCTCAAAACCGTTTCCGATGACCAGCTGACGGACATCAGTGTTGGGATGTATATAGCTGGCAGCAGCAGGA-------GCA--GAAAACTGG---AGCACATCATCCTCCAAGTTGGATCAAGCTCAAACTAAT
dp5 3:19069459-19069581 + GCGATC-CGGGTCCGGGATTGCGTCATGAACCAACACATCGCTC------------ATTT------CCATGACCACAACGAGAGCTGGCAGCAGCAAAA-------ACA-----GACTCA---ACCGAATCATTCGGCGTTTCGTGACTAACTGAAA-----
droPer2 scaffold_37:72247-72369 + GCGATC-CGGGTCCGGGATTGCGTCATGAACCAACACATCGCTC------------ATTT------CCATGACCACAACGAGAGCTGGCAGCAGCAGAA-------ACA-----GACTCA---ACCGAATCATTCGGCGTTTCGTGACTAACTGAAA-----
droWil2 scf2_1100000004382:576178-576223 + GCCTTTGCGGGTCAGGATCTGTTAGATGATGTATAATGTGATCTTC--------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12875:2678655-2678686 + GCGATC-CGGTTCCGGATCATCATGATGCATCA---------------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15112:3492067-3492158 - GCGCTC-CGGGTTGGGATTGGTATAGTCATCCAGCACCACATTGG------CGCCATATGCCCAAAGTTGATTATAGGCCAAGAGCCAGAACAGCAGCA---------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droSim3
GCGGCC-AGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCCGTTGCCATGACCGAAATCATCAGCAAGGCCGGCAACAGCAGCA------AGCAGAGGGATTTGA---ACCAAACCATCTTACAAACCAAAAGCAACTGAAG-----SizeHit CountTotal NormTotalV044
Embryo		M023
Head		M024
Male-body		M025
Embryo		O001
Testis		O002
Head		M053
Female-body		SRR553485
Ovary		SRR553486
Ovary		SRR553487
Ovary		SRR553488
Ovary		SRR618934
Ovary
..............................................................................GCAAGGCCGGCAACAGCAG.................................................................19112.0012000093000000
..............................................................................GCAAGGCCGGCAACAGCAGCA------.........................................................2111.001000010000000
................................................................................................GCA------AGCAGAGGGATTTGA---ACCAAAC................................2511.001000000100000
.......................................GATCCTCGTCGATGCCCGTTGC.....................................................................................................2211.001000010000000
.............................................................................AGCAAGGCCGGCAACAGCAG.................................................................2011.001000010000000
...................................................TGCCCGTTGCCATGACCGAAA..........................................................................................2111.001000010000000
droSec2
GCGGCC-GGGATCCGGGTCCACATCATGGTTCAGGATATGATCCTCGTCGATGCCCGTTGCCATGAGCGAATTCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGGGATTTGA---ACCAAACCATCCTACAAACCAAAAGCAACTGAAG-----SizeHit CountTotal NormTotalV113
Male-body		V114
Embryo		V115
Head		M054
Female-body
No Reads
droEre2
GCGACC-CGGATCCGGGTCCACATCATGGTTAACGACATGATCCTCGTC---GTCAGTTGACGTGACCGAATTCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGAGATTTTA---ACCGAGCCATCCTACAAATCAAAAGCAACTGAAG-----SizeHit CountTotal NormTotalV040
Embryo		V060
Head		V107
Male-body		V108
Head		M055
Female-body		M057
Embryo
No Reads
droYak3
GCGTCC-CGGATCCGGGTCCACATCATGGTCTAGGATATGATCCTCGTC---GTCAGTTGACGTGACCGAAATCATCAGTAAGGCCGGCAGCAGCAGCA------AGCAGAGTGATTTAA---ACCAAACCATCCTACAAATCAAAAGCAACTGAAG-----SizeHit CountTotal NormTotalV046
Embryo		V052
Head		V120
Male-body		V058
Head		M026
Head		M043
Female-body		M056
Embryo
No Reads
droEug1
GCGACC-CGGATCCGGGTCCACTTCATGGTTTATAACTGTTTGCTCAGGAATGCCAGTTGCCCGAACCGAAATCATTAATAAAGCCGGCAGCAGCAGCAGCAGCCAACAGAGAGACTTTA---ACTTAATCATCCTAAGAATCAAAAGCAACTGAAG-----SizeHit CountTotal NormTotal
No Reads
droBia1
CCGACC-CGGATCCGGGTCTTCATAATGGTTCAGTACCGTTTCCTCTGCAAAGCCAGTTGACATAGCCGAATTTATAAATAAAACTGGTAGTACCAGCC------AAGAAAGAGACTTGA---TCCAAACCATCCTATAAGCCAAACGCAACTGAAG-----SizeHit CountTotal NormTotal
No Reads
droTak1
ACGACT-CGGATCCGGGTCCACTTCGTGGTTAAGAACAGTTTCCTCCGCAAAGCCAGTTGTCATCACGGAATTCACAAATAATGCCGGCAGCAGCAGCA------AAAAAAGAGACTTTA---ACCAAATCATCCTGCAAACCAGAGGCAACTGAAA-----SizeHit CountTotal NormTotal
No Reads
droEle1
ACGATC-CGGATCCGGGTCCACCTCATGGTTGATAATGTAATTTC---CAAAGCCAGTTGACATCACTGTTCTTATTAAAAACGCTGGCAACAGCAGCA------AACAGAGAAGCTTAA---ACCAAATCATTCTTAAAGCCAAATGCAACTGAGG-----SizeHit CountTotal NormTotal
No Reads
droRho1
GCGACT-CGGATCCGGGTCCACCTCATGGTGGAGAACTTGTTCCTCTGCAAAGCCTGTTGCCATCACCGATTTCAACAATAACGCCGGCAGCAGCAGCA------AACAGAGCGACGTTA---ACCAAAACATCCTAAAAACCTGAAGCAACTGAGG-----SizeHit CountTotal NormTotal
No Reads
droFic1
GCGACC-CGGATCCGGGTCACCTTCATGGCTCAAAATGTGTTCCTCTGCAAAGCCAGTTGTCATCAAAGAAATCATGAATACAGCTGGCAGCAGCAGCA------AATAGAGAAACTTCA---ACTCGATCATCGTACGAACAAAAGGCAACTGAAG-----SizeHit CountTotal NormTotal
No Reads
droKik1
ACGATC-CGGATCCGGGTCCACCTTATGGTGTAGAACAGTCTCAT---CAAAGCTAGTAACCATCACCATTTTCATGAACAAAGCTGCTGGCAGAAGCA------AAGAAAGGGAGAATAGCAACCGAGCCATTATAGAAACCAAAAGCAACTGGAG-----SizeHit CountTotal NormTotal
No Reads
droAna3
CCGAGT-CGGATCCGGGTTTTTATCGTGGCCCAAAATTGTTTCCAAAGGCAAGCTTTCGGCCATCAATGCTGGAAAGTATATAGCTGGCAGCAGCAGGA-------GC--AGAAAGCTGG---AGCACATCATCCTCCAAGTCGGTGCAAACTCAAA-----SizeHit CountTotal NormTotalV105
Male-body		V106
Head		V055
Head		V039
Embryo		M044
Female-body		M058
Embryo
No Reads
droBip1
CCGATT-CGGATCCGGGTCTAGTTTGTGGCTCAAAACCGTTTCCGATGACCAGCTGACGGACATCAGTGTTGGGATGTATATAGCTGGCAGCAGCAGGA-------GCA--GAAAACTGG---AGCACATCATCCTCCAAGTTGGATCAAGCTCAAACTAATSizeHit CountTotal NormTotal
No Reads
dp5
GCGATC-CGGGTCCGGGATTGCGTCATGAACCAACACATCGCTC------------ATTT------CCATGACCACAACGAGAGCTGGCAGCAGCAAAA-------ACA-----GACTCA---ACCGAATCATTCGGCGTTTCGTGACTAACTGAAA-----SizeHit CountTotal NormTotalV112
Male-body		V043
Embryo		V051
Head		M022
Male-body		M040
Female-body		M059
Embryo		M062
Head
.........................................................TTT------CCATGACCACAACGAG................................................................................1911.0010000100
droPer2
GCGATC-CGGGTCCGGGATTGCGTCATGAACCAACACATCGCTC------------ATTT------CCATGACCACAACGAGAGCTGGCAGCAGCAGAA-------ACA-----GACTCA---ACCGAATCATTCGGCGTTTCGTGACTAACTGAAA-----SizeHit CountTotal NormTotalV111
Male-body		V042
Embryo		V050
Head		V057
Head		M021
Embryo		M042
Female-body
No Reads
droWil2
GCCTTTGCGGGTCAGGATCTGTTAGATGATGTATAATGTGATCTTC--------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalV117
Male-body		V118
Embryo		V119
Head		M020
Head		M045
Female-body
No Reads
droVir3
GCGATC-CGGTTCCGGATCATCATGATGCATCA---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalV116
Male-body		V053
Head		V047
Embryo		M027
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
No Reads
droGri2
GCGCTC-CGGGTTGGGATTGGTATAGTCATCCAGCACCACATTGG------CGCCATATGCCCAAAGTTGATTATAGGCCAAGAGCCAGAACAGCAGCA---------------------------------------------------------------SizeHit CountTotal NormTotalV109
Male-body		M041
Female-body
No Reads

Generated: 12/06/2013 at 02:35 PM