ID:

dan_2377

 Coordinate:

scaffold_13337:3166077-3166227 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-13.6 -13.0 -12.6

Flybase annnotation

CDS [Dana\GF24704-cds]; exon [dana_GLEANR_9407:1]; intron [Dana\GF24704-in]

Repeatable elements

NameClassFamilyStrand
AT_richLow_complexityLow_complexity+
mature
  1. scaffold_12276:63821-63848 -
  2. scaffold_13082:1052988-1053015 +
  3. scaffold_13250:2314887-2314914 -
  4. scaffold_13258:313219-313246 -
  5. dan_2377  scaffold_13337:3166114-3166141 -
star
  1. scaffold_3892:2464-2489 +
  2. scaffold_10423:16562-16587 +
  3. scaffold_12928:731569-731594 +
  4. scaffold_12943:975959-975984 +
  5. scaffold_12947:1503980-1504005 +
  6. scaffold_12947:1507185-1507210 +
  7. scaffold_13045:976612-976637 +
  8. scaffold_13082:1431282-1431307 +
  9. scaffold_13099:2500792-2500817 +
  10. scaffold_13116:29952-29977 +
  11. scaffold_13228:809266-809291 +
  12. scaffold_13230:763440-763465 +
  13. scaffold_13239:272866-272891 +
  14. scaffold_13239:276489-276514 +
  15. scaffold_13250:2925307-2925332 +
  16. scaffold_13280:1144884-1144909 +
  17. scaffold_13333:420537-420562 +
  18. scaffold_13333:445821-445846 +
  19. scaffold_13339:649819-649844 +
  20. scaffold_13339:1375997-1376022 +
  21. scaffold_1304:374-399 -
  22. scaffold_1701:824-849 -
  23. scaffold_6743:1022-1047 -
  24. scaffold_8772:4370-4395 -
  25. scaffold_9455:1644-1669 -
  26. scaffold_10329:8044-8069 -
  27. scaffold_10423:15318-15343 -
  28. scaffold_12371:639-664 -
  29. scaffold_12944:180301-180326 -
  30. scaffold_13034:1002396-1002421 -
  31. scaffold_13099:931730-931755 -
  32. scaffold_13111:535262-535287 -
  33. scaffold_13258:1335494-1335519 -
  34. dan_2377  scaffold_13337:3166156-3166181 -
  35. scaffold_13339:2370885-2370910 -
  36. scaffold_13339:3006857-3006882 -
  37. scaffold_13339:3010445-3010470 -
  38. scaffold_13454:4363-4388 -
  39. scaffold_13499:257719-257744 -
  40. scaffold_13767:663649-663674 -

Sense Strand Reads

##################################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TGATCACAGCAAGCGTCTGGCCAACCCGAGCAGTCCCTTGCAGAATCCAGGTAAATTTAGTCAGGACTATTTACGGTTTTGACTACGACTCCGGGACCTACCGTTACTCCCGTGAGTTCAAGTTTGACGTAGTTGCCGCATAACGCTCTACGGACGAACAATGCCATTTGAAAATATTCTTGTTACCTTTAATATTAAGAAATAATAGTAAATAAAATAATAACTTAAAAATTTTTATGGACGTTTATATT
************************************************************************************************......((.................(((((.(((((..((........)).)))))..)))))...))*************************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total M044
female body
 M058
embryo
 V106
head
........................................................................................................................................CGCATAACGCTCTACGGACGAACAATGC....................................................................................... 28 0 5 0.20 1 1 0 0
.GATCACAGCAAGCGTCTGGCCAACCC................................................................................................................................................................................................................................ 26 0 20 0.10 2 2 0 0
...................................................................................................................................................CTACGTACCAAGAATGCCA..................................................................................... 19 3 18 0.06 1 1 0 0
.........CAAGCGTCTGGCCAACCCGAGCAGTCCC...................................................................................................................................................................................................................... 28 0 20 0.05 1 1 0 0
................................................................................................CCTACCGTTACTCCCGTGAGTTCAAG................................................................................................................................. 26 0 20 0.05 1 0 1 0
.........................................................................CGGTTTTGACTACGACTCCGGGACCTA....................................................................................................................................................... 27 0 20 0.05 1 1 0 0
.....................................................................TTTACGGTTTTGACTACGACTCCGGGA........................................................................................................................................................... 27 0 20 0.05 1 1 0 0
.....................................................................CGTACGGTTTAGACTACGA................................................................................................................................................................... 19 3 20 0.05 1 0 0 1
.....................CAACCCGAGCAGTCCCTTGCA................................................................................................................................................................................................................. 21 0 20 0.05 1 1 0 0
.......................................................................................ACTCCGGGACCTACCGTTACTCCCGT.......................................................................................................................................... 26 0 20 0.05 1 1 0 0

Anti-sense strand reads

ACTAGTGTCGTTCGCAGACCGGTTGGGCTCGTCAGGGAACGTCTTAGGTCCATTTAAATCAGTCCTGATAAATGCCAAAACTGATGCTGAGGCCCTGGATGGCAATGAGGGCACTCAAGTTCAAACTGCATCAACGGCGTATTGCGAGATGCCTGCTTGTTACGGTAAACTTTTATAAGAACAATGGAAATTATAATTCTTTATTATCATTTATTTTATTATTGAATTTTTAAAAATACCTGCAAATATAA
***************************************************************************************......((.................(((((.(((((..((........)).)))))..)))))...))************************************************************************************************ 		Read size # Mismatch Hit Count Total Norm Total M044
female body
 V039
embryo
 M058
embryo
 V105
male body		 V106
head
..................................................................................GATGCTGAGGCCCTGGATGGCAAT................................................................................................................................................. 24 0 20 3.40 68 68 0 0 0 0
..........................................................................................................................................................GCTTGTTAAGGTAGACTTT.............................................................................. 19 2 1 1.00 1 0 1 0 0 0
...................................................................................................................CAAGTTCAAACTGCATCAACGGCGT............................................................................................................... 25 0 20 0.50 10 9 0 1 0 0
........................................................................................................................TCAAACTGCATCAACGGCGTATTGCG......................................................................................................... 26 0 20 0.35 7 7 0 0 0 0
.............................................................................................................................CTGCATCAACGGCGTATTGCGAGAT..................................................................................................... 25 0 20 0.35 7 7 0 0 0 0
....................................................................................................GGCAATGAGGGCACTCAAGTTCAAACT............................................................................................................................ 27 0 20 0.35 7 7 0 0 0 0
..................................................................................................................TCAAGTTCAAACTGCATCAACGGCGT............................................................................................................... 26 0 20 0.35 7 7 0 0 0 0
................................................................................CTGATGCTGAGGCCCTGGATGGCAA.................................................................................................................................................. 25 0 20 0.30 6 6 0 0 0 0
.CTAGTGTCGTTCGCAGACCGGTT................................................................................................................................................................................................................................... 23 0 20 0.20 4 0 0 4 0 0
.........GTTCGCAGACCGGTTGGGCTCGTC.......................................................................................................................................................................................................................... 24 0 20 0.15 3 3 0 0 0 0
...............................................................................TCTGATGCTGAGGCCCTGGATGGCAAT................................................................................................................................................. 27 1 20 0.15 3 3 0 0 0 0
..........................................................................................................GAGGGCACTCAAGTTCAAACTGCATCA...................................................................................................................... 27 0 20 0.15 3 3 0 0 0 0
..........................................................................................................GAGGGCACTCAAGTTCAAACTGC.......................................................................................................................... 23 0 20 0.10 2 2 0 0 0 0
..........................GCTCGTCAGGGAACGTCTTAGGTCCA....................................................................................................................................................................................................... 26 0 20 0.10 2 2 0 0 0 0
.............................................................................................CCTGGATGGCAATGAGGGCACTC....................................................................................................................................... 23 0 20 0.10 2 2 0 0 0 0
..........................................................................................................GAGGGCACTCAAGTTCAAACTGCAT........................................................................................................................ 25 0 20 0.10 2 0 0 2 0 0
.............................................................................................................GGCACTCAAGTTCAAACTGCATCA...................................................................................................................... 24 0 20 0.10 2 2 0 0 0 0
...................................................................................ATGCTGAGGCCCTGGATGGCAATG................................................................................................................................................ 24 0 20 0.10 2 0 0 2 0 0
............................................................AGTCCTGATAAATGCCAAAAC.......................................................................................................................................................................... 21 0 20 0.05 1 0 0 1 0 0
.CTAGTGTCGTTCGCAGACCG...................................................................................................................................................................................................................................... 20 0 20 0.05 1 0 0 0 0 1
..............................................................TCCTGATAAATGCCAAAAC.......................................................................................................................................................................... 19 0 20 0.05 1 0 0 1 0 0
........CGGTCGCAGACCGGTTGGGCTCGTCA......................................................................................................................................................................................................................... 26 1 20 0.05 1 1 0 0 0 0
........................GGGCTCGTCAGGGAACGT................................................................................................................................................................................................................. 18 0 20 0.05 1 1 0 0 0 0
.............................................................................................................GGCACTCAAGTTCAAACTGCATCAACGG.................................................................................................................. 28 0 20 0.05 1 1 0 0 0 0
...TGTGTCGTTCGCAGACCGGTTGGGCT.............................................................................................................................................................................................................................. 26 1 20 0.05 1 0 0 1 0 0
.................................................CCATTTAAATCAGTCCTGATAAAT.................................................................................................................................................................................. 24 0 20 0.05 1 1 0 0 0 0
....................................................................................................................AAGTTCAAACTGCATCAACGGCGTAT............................................................................................................. 26 0 20 0.05 1 1 0 0 0 0
..............................GTCAGGGAACGTCTTAGGTCCA....................................................................................................................................................................................................... 22 0 20 0.05 1 1 0 0 0 0
...............................TCAGGGAACGTCTTAGGTCCATTTAAA................................................................................................................................................................................................. 27 0 20 0.05 1 0 0 1 0 0
..........................................................................CCAAAACTGATGCTGAGGCCCTGGAT....................................................................................................................................................... 26 0 20 0.05 1 0 0 1 0 0
.........GGTCGCAGACCGGTTGGGCTCGT........................................................................................................................................................................................................................... 23 1 20 0.05 1 1 0 0 0 0
.................................AGGGAACGTCTTAGGTCCATTTAAAT................................................................................................................................................................................................ 26 0 20 0.05 1 0 0 0 1 0
.......................................................................................TGAGGCCCTGGATGGCAATGAGTG............................................................................................................................................ 24 1 20 0.05 1 0 0 1 0 0
......................TTGGGCTCGTCAGGGAACGTCTT.............................................................................................................................................................................................................. 23 0 20 0.05 1 0 0 1 0 0
....................GGTTGGGCTCGTCAGGGAACGTCTTAG............................................................................................................................................................................................................ 27 0 20 0.05 1 1 0 0 0 0
........................................................................TGCCAAAACTGATGCTGAGGCCCT........................................................................................................................................................... 24 0 20 0.05 1 1 0 0 0 0
.............................................................................................................................CTGCATCAACGGCGTATTGCGAGATGC................................................................................................... 27 0 20 0.05 1 0 0 0 1 0
................................................................................................................................CATCAACGGCGTATTGCGAGATG.................................................................................................... 23 0 20 0.05 1 0 0 1 0 0
.......................................................................................................................................GGCGTATTGCGAGATGCCTGCTTGT........................................................................................... 25 0 20 0.05 1 0 1 0 0 0
.......................................................................................................................................GGCGTATTGCGAGATGCCTGCTTG............................................................................................ 24 0 20 0.05 1 1 0 0 0 0
ACTAGTGTCGTTCGCAGACCGGTTGGGC............................................................................................................................................................................................................................... 28 0 20 0.05 1 1 0 0 0 0
........CGTTCGCAGACCGGTTGGGC............................................................................................................................................................................................................................... 20 0 20 0.05 1 1 0 0 0 0
............................................................AGTCCTGATAAATGCCAAAACTGATGCT................................................................................................................................................................... 28 0 20 0.05 1 1 0 0 0 0
............................................................................................CCCTGGATGGCAATGAGGGCACTCAA..................................................................................................................................... 26 0 20 0.05 1 0 0 0 0 1
............................TCGTCAGGGAACGTCTTAGGTCCATT..................................................................................................................................................................................................... 26 0 20 0.05 1 0 0 1 0 0
.................ACCGGTTGGGCTCGTCAGGGAACGTCT............................................................................................................................................................................................................... 27 0 20 0.05 1 1 0 0 0 0
...................CGGTTGGGCTCGTCAGGGAACGT................................................................................................................................................................................................................. 23 0 20 0.05 1 0 1 0 0 0
..............................................................................................................GCACTCAAGTTCAAACTGCAT........................................................................................................................ 21 0 20 0.05 1 1 0 0 0 0
.........GTTCGCAGACCGGTTGGGCTCGTCAG........................................................................................................................................................................................................................ 26 0 20 0.05 1 1 0 0 0 0
....................................................................................TGCTGAGGCCCTGGATGGCAAT................................................................................................................................................. 22 0 20 0.05 1 0 0 0 1 0
...................................................................................................................CAAGTTCAAACTGCATCAACGGCG................................................................................................................ 24 0 20 0.05 1 1 0 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13337:3166027-3166277 - dan_2377 TGATCACAGCAAGCGTCTGGCCAACCCGAGCAGTCCCTTGCAGAATCCAGGTAAATTTAGTCAGGACTATTTACGGTTTTGACTACGACTCCGGGACCTACCGTTACTCCCGTGAGTTCAAGTTTGACGTAGTTGCCGCATAACGCTCTACGGACGAACAATGCCATTTGAAA----ATATTCTTGTTACCTTTAATATTAAGAAATAATAGTAAATAAAATAATAACTTAAAAAT------------------TTTTATGGACGTTTATATT
droBip1 scf7180000395962:7120-7232 - ----------------------------------------------------------------------------------------------------------------------------------------------------------------ATGCCATTTGAAAGTACATATTGTTGTTGCCTTTAAGATTATAAAATAATAGTAAATAAAGTTAAAAATAAAAGATATATACATAGAGCTTGGTTTATATGAGCGTTTGTATT

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TGATCACAGCAAGCGTCTGGCCAACCCGAGCAGTCCCTTGCAGAATCCAGGTAAATTTAGTCAGGACTATTTACGGTTTTGACTACGACTCCGGGACCTACCGTTACTCCCGTGAGTTCAAGTTTGACGTAGTTGCCGCATAACGCTCTACGGACGAACAATGCCATTTGAAA----ATATTCTTGTTACCTTTAATATTAAGAAATAATAGTAAATAAAATAATAACTTAAAAAT------------------TTTTATGGACGTTTATATTSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
........................................................................................................................................CGCATAACGCTCTACGGACGAACAATGC.............................................................................................................2850.201100000
.GATCACAGCAAGCGTCTGGCCAACCC......................................................................................................................................................................................................................................................26200.102200000
.........CAAGCGTCTGGCCAACCCGAGCAGTCCC............................................................................................................................................................................................................................................28200.051100000
................................................................................................CCTACCGTTACTCCCGTGAGTTCAAG.......................................................................................................................................................26200.051010000
.........................................................................CGGTTTTGACTACGACTCCGGGACCTA.............................................................................................................................................................................27200.051100000
.....................................................................TTTACGGTTTTGACTACGACTCCGGGA.................................................................................................................................................................................27200.051100000
.....................CAACCCGAGCAGTCCCTTGCA.......................................................................................................................................................................................................................................21200.051100000
.......................................................................................ACTCCGGGACCTACCGTTACTCCCGT................................................................................................................................................................26200.051100000
droBip1
----------------------------------------------------------------------------------------------------------------------------------------------------------------ATGCCATTTGAAAGTACATATTGTTGTTGCCTTTAAGATTATAAAATAATAGTAAATAAAGTTAAAAATAAAAGATATATACATAGAGCTTGGTTTATATGAGCGTTTGTATTSizeHit CountTotal NormTotal
No Reads

Generated: 05/18/2015 at 04:34 AM