ID:

dan_2230

 Coordinate:

scaffold_13150:40547-40697 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-29.9 -29.8 -29.8

Flybase annnotation

CDS [Dana\GF18978-cds]; exon [dana_GLEANR_20368:4]; intron [Dana\GF18978-in]

Repeatable elements

NameClassFamilyStrand
Hoana2DNAhAT-Ac-
mature
  1. scaffold_5382:599-620 -
  2. scaffold_7652:895-916 +
  3. scaffold_13150:31252-31273 -
  4. scaffold_13150:33593-33614 -
  5. scaffold_13150:36612-36633 -
  6. scaffold_13150:38675-38696 -
  7. dan_2230  scaffold_13150:40604-40625 -
  8. dan_1441  scaffold_13150:41359-41380 -
  9. scaffold_13150:41958-41979 -
  10. scaffold_13150:43930-43951 -
  11. scaffold_13150:45766-45787 -
  12. scaffold_13150:49912-49933 -
  13. scaffold_13150:51973-51994 -
  14. scaffold_13150:53823-53844 -
  15. scaffold_13150:54519-54540 -
  16. scaffold_13150:60666-60687 -
  17. scaffold_13150:61120-61141 -
  18. scaffold_13150:62210-62231 -
star

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
TGTGAATTTCCGCCTTATATAGGCTTAGCCAGTACTAGAGGTGGGGAACTTGGTAGTTTGAGAAAAACTATCGCTCGCTACCGATGGTGCCGATATCGATAGTTCCCCACCTCTAGTCAGAACAGGTGGCGAATAATTGACCGATCTGAAATAAAAACAAACTATTAAATACAAAAAATTTAACCGCTTTACCTCCTGCAGGGTCAGGGCAAAATGGGTGCGCCTCCTCCAGCAGTGTCAGGTGGGGTCGC
**************************************************((((((((((......(((((((.(((.((((...)))).)))...)))))))((.((((((...........)))))).)).........................))))))))))..................((..........))..************************************************** 		Read size # Mismatch Hit Count Total Norm Total V039
embryo
 M058
embryo
 M044
female body
.........................................................................................................................................................................................GCTTTACCTCCTGCAGGGTC.............................................. 20 0 6 0.17 1 1 0 0
..........................................................................................................................CAGGTGGCGAATAATTGACCGA........................................................................................................... 22 0 18 0.06 1 0 1 0
..................................................................................................................................................................................................................ATCATGGGTGCGCCACCTCC..................... 20 3 20 0.05 1 0 1 0
.......................CTTAGCCAGTACTAGAGGTGGG.............................................................................................................................................................................................................. 22 0 20 0.05 1 0 1 0
..................................................................................................................................................................................................................................CTCCAGCAGTGTCAGGTGGGG.... 21 0 20 0.05 1 0 0 1
.........................TAGCCAGTACTAGAGGTGGGG............................................................................................................................................................................................................. 21 0 20 0.05 1 0 0 1
..........................AGCCAGTACTAGAGGTGGGG............................................................................................................................................................................................................. 20 0 20 0.05 1 0 1 0
.........................TAGCCAGTACTAGAGGTTGGG............................................................................................................................................................................................................. 21 1 20 0.05 1 1 0 0
....................................AGAGGTGGGGAACTTGGTAGT.................................................................................................................................................................................................. 21 0 20 0.05 1 0 1 0
..................ATAGGCTTAGCCAGTACTAGA.................................................................................................................................................................................................................... 21 0 20 0.05 1 1 0 0
...........................................................................................................................AGGTGGCGAATAATTGCGA............................................................................................................. 19 3 20 0.05 1 1 0 0
..............................................................................................ATCGATAGTTCCCCACCTCTAGTCAGAAC................................................................................................................................ 29 0 20 0.05 1 0 0 1

Anti-sense strand reads

ACACTTAAAGGCGGAATATATCCGAATCGGTCATGATCTCCACCCCTTGAACCATCAAACTCTTTTTGATAGCGAGCGATGGCTACCACGGCTATAGCTATCAAGGGGTGGAGATCAGTCTTGTCCACCGCTTATTAACTGGCTAGACTTTATTTTTGTTTGATAATTTATGTTTTTTAAATTGGCGAAATGGAGGACGTCCCAGTCCCGTTTTACCCACGCGGAGGAGGTCGTCACAGTCCACCCCAGCG
**************************************************((((((((((......(((((((.(((.((((...)))).)))...)))))))((.((((((...........)))))).)).........................))))))))))..................((..........))..************************************************** 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 M044
female body
 V055
head
 V039
embryo
.......................................................................................................................................................................................................................CCCACGCGGAGGAGGTCGTCA............... 21 0 20 1.20 24 23 1 0 0
......................................................................................................................................................................................................................ACCCACGCGGAGGAGGTCGTC................ 21 0 20 0.55 11 11 0 0 0
...............................................................................................................................................................................................................................GAGGAGGTCGTCACAGTCCAC....... 21 0 20 0.40 8 6 2 0 0
..........................................................................................................GGTGGAGATCAGTCTTGTCCA............................................................................................................................ 21 0 20 0.35 7 0 7 0 0
........................................................................CGAGCGATGGCTACCACGGCT.............................................................................................................................................................. 21 0 20 0.35 7 7 0 0 0
..........................................CCCCTTGAACCATCAAACTCT............................................................................................................................................................................................ 21 0 20 0.30 6 5 1 0 0
....................TCCGAATCGGTCATGATCTCC.................................................................................................................................................................................................................. 21 0 20 0.25 5 5 0 0 0
.....................CCGAATCGGTCATGATCTCC.................................................................................................................................................................................................................. 20 0 20 0.20 4 4 0 0 0
...........CGGAATATATCCGAATCGGGC........................................................................................................................................................................................................................... 21 1 20 0.20 4 4 0 0 0
.......................................................................................................AGGGGTGGAGATCAGTCTTGT............................................................................................................................... 21 0 20 0.15 3 3 0 0 0
...................................................................................................ATCAAGGGGTGGAGATCAGTC................................................................................................................................... 21 0 20 0.15 3 3 0 0 0
..................................................................................................................................................................................................GGACGACACAGTCCCGTTATA.................................... 21 3 7 0.14 1 0 0 1 0
.............................GTCATGATCTCCGCCCCTTGA......................................................................................................................................................................................................... 21 1 20 0.10 2 0 2 0 0
..............................................................................................................................................................................................................................GGAGGAGGTCGTCACAGTCC......... 20 0 20 0.10 2 0 2 0 0
............................................................................................................TGGAGATCAGTCTTGTCCACC.......................................................................................................................... 21 0 20 0.10 2 2 0 0 0
......................................................................................................AAGGGGTGGAGATCAGTCTTG................................................................................................................................ 21 0 20 0.10 2 2 0 0 0
...........................CGGTCATGATCTCCACCCCTT........................................................................................................................................................................................................... 21 0 20 0.10 2 2 0 0 0
.........................................................................................................................................................................................................CCAGTCCCGTTTTACCCACGC............................. 21 0 10 0.10 1 0 1 0 0
..........................................................................AGCGATGGCTACCACGGCTA............................................................................................................................................................. 20 0 15 0.07 1 1 0 0 0
...................................................................................................................................................................................AATTGGCGAGACGGAGGA...................................................... 18 2 16 0.06 1 0 0 1 0
....................................................................................................................................................................................................................TTCCCCACGCGGAGGAGGTCGT................. 22 1 16 0.06 1 0 1 0 0
.....................................................................................................................................................................................................CGTCGCAGTCCCGTTATA.................................... 18 2 18 0.06 1 0 0 1 0
.....................................................................................................................................................................................................................................GTCGTCACAGTCCACCCCAGC. 21 0 20 0.05 1 0 1 0 0
......................CGAATCGGTCATGATCTCCAC................................................................................................................................................................................................................ 21 0 20 0.05 1 1 0 0 0
............................................................................................................................................................................TTTTTTAAATTGGCGAGA............................................................. 18 1 20 0.05 1 1 0 0 0
..................................................................TGATAGCGAGCGATGGCTACCACG................................................................................................................................................................. 24 0 20 0.05 1 1 0 0 0
...................................................................................................................................................................................................................TTTCCCCACGCGGAGGAGGCC................... 21 2 20 0.05 1 0 0 1 0
....................TCCGAATCGGTCATGGTCTCC.................................................................................................................................................................................................................. 21 1 20 0.05 1 1 0 0 0
...........................................................................................................................................................................................................................CGCGGAGGAGGTCGTCACTG............ 20 1 20 0.05 1 1 0 0 0
................................................................................................................................CGATCATTAACTGGCTAGA........................................................................................................ 19 2 20 0.05 1 0 0 1 0
......................................................................................................................................................................................................................ACCCACGCGGAGGAGGTCCTC................ 21 1 20 0.05 1 1 0 0 0
...........................................................CTCTTTTTGATAGCGAGCGATGGC........................................................................................................................................................................ 24 0 20 0.05 1 1 0 0 0
................................................................TTTGATAGCGAGCGATGGCTA...................................................................................................................................................................... 21 0 20 0.05 1 1 0 0 0
..............................................................................................................................................................................................................................GGAGGAGGTCGTCACAGTCCA........ 21 0 20 0.05 1 1 0 0 0
........................................................................................................TGGGTGGAGATCAGTCTTGT............................................................................................................................... 20 1 20 0.05 1 1 0 0 0
.........................................................................................................GGGTGGAGATCAGTCTTGTCC............................................................................................................................. 21 0 20 0.05 1 0 1 0 0
........................................................................................................................................................................................................................CCACGCGGAGGAGGTCGTCACA............. 22 0 20 0.05 1 0 1 0 0
............................................................................................................................................................................................................................GCGGAGGAGGTCGTCACA............. 18 0 20 0.05 1 0 1 0 0
............................GGTCATGATCTCCACCCCTTGAACCAT.................................................................................................................................................................................................... 27 0 20 0.05 1 0 1 0 0
..............................................................................................................................................................................................................................GGAGGAGGTCGTCACTGTC.......... 19 1 20 0.05 1 1 0 0 0
.............................................................................................................................................................................................................................CGGAGGAGGTCGTCACAGTCC......... 21 0 20 0.05 1 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13150:40497-40747 - dan_2230 TGTGAATTTCCGCCTTATATAGGCTTAGCCAGTACTAGAGGTGGGGAACTTGGTAGTTTGAGAAAAACTATCGCTCGCTACCGATGGTGCCGA-TATCGATAGTTCCCCACCTCTAG----TCAGAACAGGTG----------------GCGAATAATTGACCGATCTGAAATAAAAACAAACTATT----AAATACAAAAAATTTAACCGCTTTACCTCCTGCAGGGTCAGGGCAAAATGGGTGCGCCTCCTCCAGCAGTGTCAGGTGGGGTCGC
droBip1 scf7180000395149:21977-22132 - T-------------------------------------------------CGATGGTTTGAAAAAAATAATCGCTCGCTATCGATGGCGCCT-CTATTGATAGTTTTCTACCTCTAG----TCAGAGTA------CTAGACTTAACTAAGCGAATAAAAGACCGAGTCCAATACTAAATAAATCCGAGCAAAAAAAAAATCCTTCTACTATATACA------------------------------------------------------------
droKik1 scf7180000301911:9327-9402 + T-------------------------------------------------CGATGGTTTGAGAAAAATAATCGCTCGCTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTAA----TAAGCACA---------------------------------------------------------------------------------------------------------------------------------------------------
droFic1 scf7180000454043:391680-391816 - -------------------------------------------------------GTTCGAGAAAAACAATCGTCGGCTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTATGTCATCAG------AGCTTTACAGTAA-------AAATAATCGATAATTTTAATATAATAATA-----------ATATACAATGCATCTAATCAATATA------------------------------------------------------------
droEle1 scf7180000486991:11566-11640 + T-------------------------------------------------CGATGGTTTGA-AAAAACAATCGCTCACTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTAT----TAACAACA---------------------------------------------------------------------------------------------------------------------------------------------------
droTak1 scf7180000414518:5755-5855 - T-------------------------------------------------CGATAGTTTAAAATAAACTATCGTATACTATCGATGGCGCCCACTATCGATAGTTCTCCACCTCTAG----TTGGAAA--------------------------TGATTGTCGGATGTACCGCGAAAGCA------------------------------------------------------------------------------------------------
droEug1 scf7180000409695:25226-25300 - T-------------------------------------------------CGATGGTTTGAGAATAATAATCGCTAGCTATCGATGGCGCCGACTATCGATATTTCTCCACCTCTAA----TCAAGAC----------------------------------------------------------------------------------------------------------------------------------------------------
dp5 2:30224845-30224924 + T-------------------------------------------------CGATGGTTTTGAAAATACTATCGTCCACTAACGATGGAGCCTACTATCGATAGTTCTCCACCTCTAG----TTGGGACCAGTG-----------------------------------------------------------------------------------------------------------------------------------------------
droPer2 scaffold_6:5614172-5614251 + T-------------------------------------------------CGATGGTTTTGAAAATACTATCGTCCACTAACGATGGAGCCTACTATCGATAGTTCTCCACCTCTAG----TTGGGACCAGTG-----------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TGTGAATTTCCGCCTTATATAGGCTTAGCCAGTACTAGAGGTGGGGAACTTGGTAGTTTGAGAAAAACTATCGCTCGCTACCGATGGTGCCGA-TATCGATAGTTCCCCACCTCTAG----TCAGAACAGGTG----------------GCGAATAATTGACCGATCTGAAATAAAAACAAACTATT----AAATACAAAAAATTTAACCGCTTTACCTCCTGCAGGGTCAGGGCAAAATGGGTGCGCCTCCTCCAGCAGTGTCAGGTGGGGTCGCSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
..................................................................................................................................................................................................................GCTTTACCTCCTGCAGGGTC..............................................2060.171001000
...............................................................................................................................CAGGTG----------------GCGAATAATTGACCGA...............................................................................................................22180.061010000
.......................CTTAGCCAGTACTAGAGGTGGG.......................................................................................................................................................................................................................................22200.051010000
...........................................................................................................................................................................................................................................................CTCCAGCAGTGTCAGGTGGGG....21200.051100000
.........................TAGCCAGTACTAGAGGTGGGG......................................................................................................................................................................................................................................21200.051100000
..........................AGCCAGTACTAGAGGTGGGG......................................................................................................................................................................................................................................20200.051010000
....................................AGAGGTGGGGAACTTGGTAGT...........................................................................................................................................................................................................................21200.051010000
..................ATAGGCTTAGCCAGTACTAGA.............................................................................................................................................................................................................................................21200.051001000
................................................................................................................................AGGTG----------------GCGAATAATTGCGA.................................................................................................................19200.051001000
...............................................................................................ATCGATAGTTCCCCACCTCTAG----TCAGAAC....................................................................................................................................................29200.051100000
droBip1
T-------------------------------------------------CGATGGTTTGAAAAAAATAATCGCTCGCTATCGATGGCGCCT-CTATTGATAGTTTTCTACCTCTAG----TCAGAGTA------CTAGACTTAACTAAGCGAATAAAAGACCGAGTCCAATACTAAATAAATCCGAGCAAAAAAAAAATCCTTCTACTATATACA------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droKik1
T-------------------------------------------------CGATGGTTTGAGAAAAATAATCGCTCGCTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTAA----TAAGCACA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
-------------------------------------------------------GTTCGAGAAAAACAATCGTCGGCTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTATGTCATCAG------AGCTTTACAGTAA-------AAATAATCGATAATTTTAATATAATAATA-----------ATATACAATGCATCTAATCAATATA------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
T-------------------------------------------------CGATGGTTTGA-AAAAACAATCGCTCACTATCGATGGCGCCGACTATCGATAGTTCTCCACCTCTAT----TAACAACA---------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droTak1
T-------------------------------------------------CGATAGTTTAAAATAAACTATCGTATACTATCGATGGCGCCCACTATCGATAGTTCTCCACCTCTAG----TTGGAAA--------------------------TGATTGTCGGATGTACCGCGAAAGCA------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEug1
T-------------------------------------------------CGATGGTTTGAGAATAATAATCGCTAGCTATCGATGGCGCCGACTATCGATATTTCTCCACCTCTAA----TCAAGAC----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
dp5
T-------------------------------------------------CGATGGTTTTGAAAATACTATCGTCCACTAACGATGGAGCCTACTATCGATAGTTCTCCACCTCTAG----TTGGGACCAGTG-----------------------------------------------------------------------------------------------------------------------------------------------SizeHit 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
.................................................................................................CGATAGTTCTCCACCTCTAG----T..........................................................................................................................................................21100.1010100000000
droPer2
T-------------------------------------------------CGATGGTTTTGAAAATACTATCGTCCACTAACGATGGAGCCTACTATCGATAGTTCTCCACCTCTAG----TTGGGACCAGTG-----------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM021
Embryo		M042
Female-body		V042
Embryo		V050
Head		V057
Head		V111
Male-body
...............................................................................................ATCGATAGTTCTCCACCT...................................................................................................................................................................18200.051100000

Generated: 05/18/2015 at 01:48 AM