ID:

dan_2220

 Coordinate:

scaffold_13150:3732-3882 -

 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 [dana_GLEANR_20368:9]; CDS [Dana\GF18978-cds]; intron [Dana\GF18978-in]

No Repeatable elements found

mature
  1. scaffold_2201:746-766 -
  2. scaffold_2466:712-732 -
  3. scaffold_2467:268-288 -
  4. scaffold_3295:715-735 -
  5. scaffold_5849:1118-1138 -
  6. scaffold_9170:2130-2150 -
  7. scaffold_9380:89-109 -
  8. scaffold_9380:2002-2022 -
  9. scaffold_9380:6553-6573 -
  10. scaffold_10119:1632-1652 -
  11. scaffold_12473:358-378 -
  12. scaffold_13026:1685-1705 -
  13. scaffold_13088:562997-563017 -
  14. scaffold_13088:566172-566192 -
  15. scaffold_13150:255-275 -
  16. dan_2220  scaffold_13150:3808-3828 -
  17. scaffold_13201:3463-3483 -
  18. scaffold_13201:3959-3979 -
  19. scaffold_13250:943-963 -
  20. scaffold_13250:5862-5882 -
  21. scaffold_1727:209-229 +
  22. scaffold_3648:280-300 +
  23. scaffold_4354:377-397 +
  24. scaffold_4644:701-721 +
  25. scaffold_4645:1307-1327 +
  26. scaffold_5058:1265-1285 +
  27. scaffold_5524:1846-1866 +
  28. scaffold_5989:724-744 +
  29. scaffold_6357:492-512 +
  30. scaffold_7316:266-286 +
  31. scaffold_7588:503-523 +
  32. scaffold_7737:62-82 +
  33. scaffold_8336:3920-3940 +
  34. scaffold_8751:2402-2422 +
  35. scaffold_8751:3888-3908 +
  36. scaffold_8751:4652-4672 +
  37. scaffold_9481:2096-2116 +
  38. scaffold_10377:2013-2033 +
  39. scaffold_11302:116-136 +
  40. scaffold_13674:893-913 +
  41. scaffold_1180:991-1011 -
  42. scaffold_2776:907-927 -
  43. scaffold_3084:88-108 -
  44. scaffold_4903:948-968 -
  45. scaffold_6550:127-147 -
  46. scaffold_12174:6973-6993 -
  47. scaffold_12260:230-250 -
star
  1. scaffold_2467:294-312 -
  2. scaffold_4355:924-942 +
  3. scaffold_5329:528-546 +
  4. scaffold_8795:2588-2606 -
  5. scaffold_9376:6381-6399 +
  6. scaffold_10046:5001-5019 +
  7. scaffold_10693:29-47 +
  8. scaffold_12139:1383-1401 +
  9. scaffold_12473:384-402 -
  10. scaffold_13150:281-299 -
  11. dan_2220  scaffold_13150:3834-3852 -

Sense Strand Reads

##################################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
CACCCAGGGAGGTCGCCTCCTCCAGCAGCCATCCAGGTCGCCTCCTCCAGGTTAGGGGCAGGGGCCAGCCAGGTCACATCCGCCAGCAGCCAGCCAGGTCGCCTCCTCCTGGTCAGGGGCGGGGGCGGGGAGTGCACCTCCTTCAGTCACCGGCTAGTCCGGCCGGTCTCCCCGTCAAGGGAAAGTGCCTGAGGGGTTATGAATTTCCCCTTTATATAGGCTTTGCCAGTACTAGAGGTGGGGAACTTGGT
********************************************************************************((((....(((((..(((......))).)))))....))))....****************************************************************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total V055
head
 M058
embryo
 V106
head
 V039
embryo
 M044
female body
...............................................................GCCAACCCGGTCAGATCCG......................................................................................................................................................................... 19 3 20 0.40 8 1 0 6 0 1
......................................................................AGGTCACATCCGACAGCAGCCACAC............................................................................................................................................................ 25 3 6 0.17 1 1 0 0 0 0
..........................................................................................................................GGGCGGGGAGTCTACCTC............................................................................................................... 18 2 9 0.11 1 1 0 0 0 0
....................................................................................................................................ACAACCTCCTTCAGTCACCG................................................................................................... 20 3 9 0.11 1 1 0 0 0 0
...................CTCCAGCAGCCATCCAGGTCG................................................................................................................................................................................................................... 21 0 20 0.10 2 0 0 0 2 0
........................................................................................................CCTCCTGGTCAGGGGCGGGGG.............................................................................................................................. 21 0 20 0.10 2 0 0 0 1 1
...............................................CAGGTTAGGGGCAGGGGCC......................................................................................................................................................................................... 19 0 20 0.10 2 0 0 2 0 0
................................................................................CGCCAGCAGCCAGCCAGGTCGCC.................................................................................................................................................... 23 0 11 0.09 1 0 1 0 0 0
................................................................................CGCCAGCAGCCAGCCAGGTCG...................................................................................................................................................... 21 0 11 0.09 1 0 0 0 1 0
................................................................................CGCCAGCAGCCAGCCAGGT........................................................................................................................................................ 19 0 11 0.09 1 0 1 0 0 0
................................................................................CGCCAGCAGCCAGCCAGGTC....................................................................................................................................................... 20 0 11 0.09 1 0 1 0 0 0
.........................................................................TCACATCCGCCAGGAGTGAGC............................................................................................................................................................. 21 3 11 0.09 1 1 0 0 0 0
.................................................................................GCCAGCAGCCAGCCAGGTCGCC.................................................................................................................................................... 22 0 15 0.07 1 0 1 0 0 0
.........................................................................................................CGCCTGGTCAGGGGCGGGGGC............................................................................................................................. 21 1 20 0.05 1 0 1 0 0 0
........................................................................................................CCTCCTGGTCAGGGGCGGGGGT............................................................................................................................. 22 1 20 0.05 1 0 0 0 1 0
.................................................................................GTCAGCAGCCAGCCAGGTCGCC.................................................................................................................................................... 22 1 20 0.05 1 0 1 0 0 0
................................................................................................................................................................................................................................GCCAGTACTAGAGGTGGGGAACTTGG. 26 0 20 0.05 1 0 0 0 0 1
.............CGCCTCCTCCAGCAGCCA............................................................................................................................................................................................................................ 18 0 20 0.05 1 0 0 0 1 0

Anti-sense strand reads

GTGGGTCCCTCCAGCGGAGGAGGTCGTCGGTAGGTCCAGCGGAGGAGGTCCAATCCCCGTCCCCGGTCGGTCCAGTGTAGGCGGTCGTCGGTCGGTCCAGCGGAGGAGGACCAGTCCCCGCCCCCGCCCCTCACGTGGAGGAAGTCAGTGGCCGATCAGGCCGGCCAGAGGGGCAGTTCCCTTTCACGGACTCCCCAATACTTAAAGGGGAAATATATCCGAAACGGTCATGATCTCCACCCCTTGAACCA
******************************************************************************************************************************((((....(((((..(((......))).)))))....))))....******************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 M044
female body
 V106
head
 V039
embryo
 V105
male body
.............................................................................TAGGCGGTCGTTGGTGGGTTC......................................................................................................................................................... 21 3 12 0.42 5 0 5 0 0 0
............................................................CCCCGGTCGGTCCAGTGTA............................................................................................................................................................................ 19 0 20 0.35 7 7 0 0 0 0
................................GGTCCAGCGGAGGAGGTCCAA...................................................................................................................................................................................................... 21 0 20 0.35 7 0 0 0 7 0
..................................................................................................................................................................................................................................GTCATGATCTCCACCCCTTGA.... 21 0 20 0.30 6 0 6 0 0 0
............................................................CCCCGGTCGGTCCAGTGTAG........................................................................................................................................................................... 20 0 20 0.30 6 6 0 0 0 0
.............................................................................TAGGCGGTCGTTCGTGGGTCC......................................................................................................................................................... 21 3 9 0.22 2 0 1 0 0 1
..............................................................CCGGTCGGTCCAGTGTAGGCGG....................................................................................................................................................................... 22 0 5 0.20 1 1 0 0 0 0
.......CCTCCAGCGGAGGAGGTCGTCG.............................................................................................................................................................................................................................. 22 0 5 0.20 1 0 0 1 0 0
........................................................CCGTCCCCGGTCGGTCCAGTGT............................................................................................................................................................................. 22 0 20 0.20 4 4 0 0 0 0
.......................................................................CCAGTGTAGGCGGTCGTCGGT............................................................................................................................................................... 21 0 6 0.17 1 1 0 0 0 0
.....................................................................GTCCAGTGTAGGCGGTCGTCGGTCG............................................................................................................................................................. 25 0 6 0.17 1 0 0 1 0 0
..............................................GGTCCAATCCCCGTCCCCGGTC....................................................................................................................................................................................... 22 0 20 0.15 3 3 0 0 0 0
...........................................................TCCCCGGTCGGTCCAGTGTAG........................................................................................................................................................................... 21 0 20 0.15 3 0 3 0 0 0
..........................................................GTCCCCGGTCGGTCCAGTGTA............................................................................................................................................................................ 21 0 20 0.15 3 0 3 0 0 0
.............................................................................TAGGCGGTCGTCCGTGGGTT.......................................................................................................................................................... 20 3 20 0.15 3 0 3 0 0 0
.........................................................CGTCCCCGGTCGGTCCAGTGT............................................................................................................................................................................. 21 0 20 0.15 3 0 3 0 0 0
.......................................................................................................................................................................................................ACTTAAAGGGGAAATAGATA................................ 20 2 7 0.14 1 0 1 0 0 0
.................................................................................CGGTCGTCGGTCGGTCCAGCGG.................................................................................................................................................... 22 0 15 0.13 2 2 0 0 0 0
................GAGGAGGTCGTCGGTAGGT........................................................................................................................................................................................................................ 19 0 20 0.10 2 0 0 2 0 0
........................................................................CAGTGTTCGCGGTCCTCGGTC.............................................................................................................................................................. 21 3 10 0.10 1 0 1 0 0 0
..............CGGAGGAGGTCGTCGGTAGG......................................................................................................................................................................................................................... 20 0 20 0.10 2 0 0 2 0 0
......................................................CCCCGTCCCCGGTCGGTCCAGTGTA............................................................................................................................................................................ 25 0 20 0.10 2 2 0 0 0 0
..............................................................CCGGTCGGTCCAGTGTAGG.......................................................................................................................................................................... 19 0 20 0.10 2 2 0 0 0 0
.............................................................CCCGGTCGGTCCAGTGTAGG.......................................................................................................................................................................... 20 0 20 0.10 2 0 2 0 0 0
................................................................................GCGGTCGTCGGTCGGTCCAGC...................................................................................................................................................... 21 0 11 0.09 1 0 0 0 1 0
.............................................................................TAGGCGGTCGTCCGTGGGTTC......................................................................................................................................................... 21 3 13 0.08 1 0 0 0 0 1
.................................................................................CGGTCGTCGGTCGGTCCAG....................................................................................................................................................... 19 0 16 0.06 1 0 0 1 0 0
..........................................................................................................................................AGGAAGTCACTGGCCAATA.............................................................................................. 19 3 18 0.06 1 0 1 0 0 0
...........................CGGTAGGTCCAGCGGAGGAGG........................................................................................................................................................................................................... 21 0 20 0.05 1 1 0 0 0 0
............................................................................GAAGGCGGTCGTCGGTCGGTC.......................................................................................................................................................... 21 1 20 0.05 1 0 0 0 1 0
..........................TCGGTAGGTCCAGCGGAGGAGGT.......................................................................................................................................................................................................... 23 0 20 0.05 1 1 0 0 0 0
..........CCAGCGGAGGAGGTCGTCGGTAG.......................................................................................................................................................................................................................... 23 0 20 0.05 1 0 0 1 0 0
.........................GTCGGTAGGTCCAGCGGA................................................................................................................................................................................................................ 18 0 20 0.05 1 0 0 1 0 0
...............................................................................GGCGTTCGTCGGTCGGTCC......................................................................................................................................................... 19 1 20 0.05 1 0 0 0 1 0
.........................................................CGTCCCCGGTCGGTCCAGTCT............................................................................................................................................................................. 21 1 20 0.05 1 1 0 0 0 0
.............GCGGAGGAGGTCGTCGGTAG.......................................................................................................................................................................................................................... 20 0 20 0.05 1 0 0 1 0 0
......................................................CCCCGTCCCCGGTCGGTCCAGTCTAG........................................................................................................................................................................... 26 1 20 0.05 1 1 0 0 0 0
...................GAGGTCGTCGGTAGGTCCAGC................................................................................................................................................................................................................... 21 0 20 0.05 1 0 1 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13150:3682-3932 - dan_2220 CACCCAGGGAGGTCGCCTCCTCCAGCAGCCATCCAGGTCGCCTCCTCCAGGTTAGGGGCAGGGGCCAGCCAGGTCACATCCGCCAGCAGCCAGCCAGGTCGCCTCCTCCTGGTCAGGGGCGGGGGCGGGGAGTGCACCTCCTTCAGTCACCGGCTAGTCCGGCCGGTCTCCCCGTCAAGGGAAAGTGCCTGAGGGGTTATGAATTTCCCCTTTATATAGGC---TTTGCCAGTACTAGAGGTGGGGAACTTGGT
droBip1 scf7180000395006:2025-2029 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droKik1 scf7180000301911:9327-9331 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droFic1 scf7180000451979:7114-7118 - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGAT
droEle1 scf7180000486991:11566-11570 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droBia1 scf7180000297283:23885-23889 - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droTak1 scf7180000414603:4485-4489 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droEug1 scf7180000409859:24886-24890 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
dp5 2:30224845-30224849 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT
droWil2 scf2_1100000004963:89124-89167 + ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTATGTAGGTCACTATCGAGGCACTATCGATGGCACTATCGAT

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
CACCCAGGGAGGTCGCCTCCTCCAGCAGCCATCCAGGTCGCCTCCTCCAGGTTAGGGGCAGGGGCCAGCCAGGTCACATCCGCCAGCAGCCAGCCAGGTCGCCTCCTCCTGGTCAGGGGCGGGGGCGGGGAGTGCACCTCCTTCAGTCACCGGCTAGTCCGGCCGGTCTCCCCGTCAAGGGAAAGTGCCTGAGGGGTTATGAATTTCCCCTTTATATAGGC---TTTGCCAGTACTAGAGGTGGGGAACTTGGTSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
...................CTCCAGCAGCCATCCAGGTCG......................................................................................................................................................................................................................21200.102002000
........................................................................................................CCTCCTGGTCAGGGGCGGGGG.................................................................................................................................21200.102101000
...............................................CAGGTTAGGGGCAGGGGCC............................................................................................................................................................................................19200.102000002
................................................................................CGCCAGCAGCCAGCCAGGTCGCC.......................................................................................................................................................23110.091010000
................................................................................CGCCAGCAGCCAGCCAGGTCG.........................................................................................................................................................21110.091001000
................................................................................CGCCAGCAGCCAGCCAGGT...........................................................................................................................................................19110.091010000
................................................................................CGCCAGCAGCCAGCCAGGTC..........................................................................................................................................................20110.091010000
.................................................................................GCCAGCAGCCAGCCAGGTCGCC.......................................................................................................................................................22150.071010000
........................................................................................................CCTCCTGGTCAGGGGCGGGGGT................................................................................................................................22200.051001000
...................................................................................................................................................................................................................................GCCAGTACTAGAGGTGGGGAACTTGG.26200.051100000
.............CGCCTCCTCCAGCAGCCA...............................................................................................................................................................................................................................18200.051001000
droBip1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
droKik1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
droFic1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGATSizeHit CountTotal NormTotal
No Reads
droEle1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
droBia1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
droTak1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
droEug1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit CountTotal NormTotal
No Reads
dp5
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGATSizeHit 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
droWil2
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTATGTAGGTCACTATCGAGGCACTATCGATGGCACTATCGATSizeHit CountTotal NormTotalM020
Head		M045
Female-body		V117
Male-body		V118
Embryo		V119
Head
No Reads

Generated: 05/18/2015 at 01:47 AM