ID:

dan_2874

 Coordinate:

scaffold_13340:3345702-3345852 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-13.6 -13.5 -13.3

Flybase annnotation

exon [dana_GLEANR_18553:5]; CDS [Dana\GF17286-cds]; intron [Dana\GF17286-in]

Repeatable elements

NameClassFamilyStrand
Hoana1DNAhAT-hobo-
mature
  1. scaffold_753:590-616 -
  2. scaffold_753:1150-1176 -
  3. scaffold_1799:273-299 -
  4. scaffold_13034:276172-276198 -
  5. scaffold_13089:243305-243331 -
  6. scaffold_13099:1596147-1596173 -
  7. scaffold_13111:411664-411690 -
  8. scaffold_13230:1397840-1397866 -
  9. scaffold_13230:1497068-1497094 -
  10. scaffold_13230:2285786-2285812 -
  11. scaffold_13239:512882-512908 -
  12. scaffold_13250:1311829-1311855 -
  13. scaffold_13258:1569006-1569032 -
  14. scaffold_13335:3134871-3134897 -
  15. scaffold_13339:1525181-1525207 -
  16. scaffold_13339:3002505-3002531 -
  17. dan_2874  scaffold_13340:3345755-3345781 -
  18. scaffold_13417:3192330-3192356 -
  19. scaffold_13417:3202138-3202164 -
  20. scaffold_13767:914190-914216 -
star
  1. scaffold_3910:1491-1519 -
  2. scaffold_5036:2363-2391 -
  3. scaffold_12600:980-1008 -
  4. scaffold_12943:958631-958659 -
  5. scaffold_13045:410956-410984 -
  6. scaffold_13089:325149-325177 -
  7. scaffold_13230:1869314-1869342 -
  8. scaffold_13230:2267563-2267591 -
  9. scaffold_13250:1311863-1311891 -
  10. scaffold_13280:1221796-1221824 -
  11. scaffold_13280:1223906-1223934 -
  12. scaffold_13337:13022253-13022281 -
  13. scaffold_13337:16911876-16911904 -
  14. scaffold_13339:4358025-4358053 -
  15. dan_2874  scaffold_13340:3345789-3345817 -
  16. scaffold_13417:5944006-5944034 -
  17. scaffold_13417:5960481-5960509 -
  18. scaffold_13767:613177-613205 -
  19. scaffold_13767:914224-914252 -
  20. scaffold_13767:1083464-1083492 -

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
AAAAATTAATGTAGAAAATCTGAGATTTCAACTTTGGATGAGTATTCCAAAGATATGGAAACTGCTAGCAACCATTTTTTAATTTTAGTTGGTACACATACATTTCAAAAATGATATGTACTAGAAACAATGATGGTCATCGCCATTACACGGCCTACATAATTCAATATATGGTAAAATTTGATCAATTTCTTTTCTTAGGTGTACCGCGGAAACTGTGGGTGATAGAACCTATGTTTGTTCTGAACTTT
*************************************************************************************...((((((((.((.(((((...))))))).))))))))......(((((((....)))))))******************************************************************************************************* 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 M044
female body
 V105
male body		 V039
embryo
.............................................TCCAAAGGTATGGAAACTGCTAGCAAC................................................................................................................................................................................... 27 1 1 1.00 1 1 0 0 0
.............................................TCCAAAGATATGGAAACTGCTAGC...................................................................................................................................................................................... 24 0 1 1.00 1 1 0 0 0
..............................................CCAAAGATATGGAAACTGCTAGCAAC................................................................................................................................................................................... 26 0 1 1.00 1 1 0 0 0
.........................................................................................................................TAGAAACAATGATGGTCATCGCCATTA....................................................................................................... 27 0 20 0.55 11 11 0 0 0
......................................................................................................................................................................................................TAGGTGTACCGCGGAAACTGT................................ 21 0 20 0.50 10 0 0 10 0
.............................AACTTTGGATGAGTATTCCA.......................................................................................................................................................................................................... 20 0 20 0.25 5 0 0 5 0
.....................................................................................TAGTTGGTACACATACATTTCAAAAATGA......................................................................................................................................... 29 0 20 0.20 4 4 0 0 0
......................................................................................................................TACTAGAAACAATGATGGTCATCGCC........................................................................................................... 26 0 20 0.20 4 0 4 0 0
......................................................................................................................................GGTCATCGCCATTACACGG.................................................................................................. 19 0 20 0.15 3 0 3 0 0
...................................................................................................................................................................................................TCTTAGGTGTACCGCGGAAACTGTG............................... 25 0 20 0.15 3 0 0 0 3
.............................................TCCAAAGATATGGAAACTGCT......................................................................................................................................................................................... 21 0 7 0.14 1 0 1 0 0
.....................................................................................................................................................................................................................AACTGTGGGTGATAGAACCTA................. 21 0 20 0.10 2 0 2 0 0
..........................................................................................................................................................................................................TGTACCGCGGAAACTGTGGGTGATA........................ 25 0 20 0.10 2 0 2 0 0
..................................................................................TTTTAGTTGGTACACATACATTTCAAA.............................................................................................................................................. 27 0 20 0.05 1 0 1 0 0
.............................................................................................................................AACAATGATGGTCATCGC............................................................................................................ 18 0 20 0.05 1 0 1 0 0
...................CTGAGATTTCAACTTTGGATGAG................................................................................................................................................................................................................. 23 0 20 0.05 1 0 0 1 0
.......................................................................................................................ACTAGAAACAATGATGGTCATCGCC........................................................................................................... 25 0 20 0.05 1 0 1 0 0
......TAATGTAGAAAATCTGAGATTTCAAC........................................................................................................................................................................................................................... 26 0 20 0.05 1 0 1 0 0
...................CTGAGATTTCAACTTTGGATGAGT................................................................................................................................................................................................................ 24 0 20 0.05 1 1 0 0 0

Anti-sense strand reads

TTTTTAATTACATCTTTTAGACTCTAAAGTTGAAACCTACTCATAAGGTTTCTATACCTTTGACGATCGTTGGTAAAAAATTAAAATCAACCATGTGTATGTAAAGTTTTTACTATACATGATCTTTGTTACTACCAGTAGCGGTAATGTGCCGGATGTATTAAGTTATATACCATTTTAAACTAGTTAAAGAAAAGAATCCACATGGCGCCTTTGACACCCACTATCTTGGATACAAACAAGACTTGAAA
*******************************************************************************************************...((((((((.((.(((((...))))))).))))))))......(((((((....)))))))************************************************************************************* 		Read size # Mismatch Hit Count Total Norm Total M044
female body
 M058
embryo
 V106
head
 V055
head
 V105
male body
..............................................................................................................................................GGTAATGTGCCGGATGTATTA........................................................................................ 21 0 20 0.75 15 14 0 0 1 0
....................................................................................................................................TACCAGTAGCGGTAATGTGCC.................................................................................................. 21 0 20 0.60 12 12 0 0 0 0
..............................................................................................................................................GGTAATGTGCCGGATGTAT.......................................................................................... 19 0 20 0.45 9 9 0 0 0 0
..................AGACTCTAAAGTTGAAACCTACTCAT............................................................................................................................................................................................................... 26 0 20 0.40 8 0 8 0 0 0
...............................................................................................................................................................................................................GCGCCTTTGACACCCACTATC....................... 21 0 20 0.25 5 5 0 0 0 0
.....................................................................................ATCAACCATGTGTATGTAAAG................................................................................................................................................. 21 0 20 0.15 3 0 0 3 0 0
................................................................................................................CTATACATGATCTTTGTTACT...................................................................................................................... 21 0 20 0.15 3 3 0 0 0 0
............................................................................................................................................................................................................................CCACTATCTTGGATACAAACAAGACTT.... 27 0 20 0.15 3 0 3 0 0 0
.....................................................................................................................................................................................................................TTGACACCCACTATCTTGGATACAAACAA......... 29 0 20 0.15 3 0 3 0 0 0
........................................................................................................................................................................................................CCACATGGCGCCTTTGACACCC............................. 22 0 20 0.15 3 0 3 0 0 0
......................................................................................................................................CCAGTAGCGGTAATGTGCC.................................................................................................. 19 0 20 0.10 2 2 0 0 0 0
..................................................................................................................................................................................................................CCTTTGACACCCACTATCTTGGAT................. 24 0 20 0.10 2 1 1 0 0 0
................TTAGACTCTAAAGTTGAAACCTACT.................................................................................................................................................................................................................. 25 0 20 0.10 2 0 2 0 0 0
.........................................................................................ACCATGTGTATGTAAAGTTTT............................................................................................................................................. 21 0 20 0.10 2 0 0 0 0 2
..................................................................................................................................................................................................AAGAATCCACATGGCGCCTTTGACAC............................... 26 0 20 0.10 2 0 2 0 0 0
..................................................................................................................................................................................TAAACTAGTTAAAGAAAAGAATCCAC............................................... 26 0 11 0.09 1 0 1 0 0 0
................................................................................................................................................................................TTTAAACTAGTTAAAGAAAAGAATCCAC............................................... 28 0 11 0.09 1 0 1 0 0 0
.................................................................................................................................................................................TTAAACTAGTTAAAGAAAAGAATCCACC.............................................. 28 1 13 0.08 1 0 1 0 0 0
...........................................................................................................................................AGCGGTAATGTGCCGGATGTATTAAG...................................................................................... 26 0 20 0.05 1 0 1 0 0 0
.......................................................................................................................................................................................................TCCACATGGCGCCTTTGACA................................ 20 0 20 0.05 1 0 0 1 0 0
...................................................................................................................................................................................................................................CTTGGATACAAACAAGACTTGAA. 23 0 20 0.05 1 0 1 0 0 0
...............................................................................................................................GTTACTACCAGTAGCGGTAA........................................................................................................ 20 0 20 0.05 1 1 0 0 0 0
....................................................................................................................................................................................................................TTTGACACCCACTATCTTGGATA................ 23 0 20 0.05 1 0 1 0 0 0
..............................................................................................................................................................................................................GGCGCCTTTGACACCCACTAT........................ 21 0 20 0.05 1 0 0 0 1 0
.....................................................................................................................................................................................................................TTGACACCCACTATCTTGGATACAAA............ 26 0 20 0.05 1 0 1 0 0 0
................................................................................................................................................................................................................CGCCTTTGACACCCACTATCTTGG................... 24 0 20 0.05 1 0 1 0 0 0
............................................................................................................................................................................................................ATGGCGCCTTTGACACCCACTATCTTG.................... 27 0 20 0.05 1 1 0 0 0 0
...........................................................................................CATGTGTATGTAAAGTTTTTA........................................................................................................................................... 21 0 20 0.05 1 0 0 1 0 0
.........................................................................................ACCATGTGTATGTAAAGTTTTTACT......................................................................................................................................... 25 0 20 0.05 1 0 1 0 0 0
..................................................................................................................................ACTACCAGTAGCGGTAATGTGCC.................................................................................................. 23 0 20 0.05 1 0 0 1 0 0
..........................................................................................................................................................................................................................ACCCACTATCTTGGATACAAACAAGACTT.... 29 0 20 0.05 1 0 1 0 0 0
.......................................................................................................................................CAGTAGCGGTAATGTGCCGGA............................................................................................... 21 0 20 0.05 1 1 0 0 0 0
.........................................................................................................................................GTAGCGGTAATGTGCCGGAT.............................................................................................. 20 0 20 0.05 1 1 0 0 0 0
.....................................................................................................................................ACCAGTAGCGGTAATGTGC................................................................................................... 19 0 20 0.05 1 1 0 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13340:3345652-3345902 - dan_2874 AAAAATTAATGTAGAAAAT--CTGAGATTTCAACTTTGGATGAGTATTCCAAAGATATGGAAACTGCTAGCAA-------CCATTTTTTA-ATTTTAGTTGGTACACATACATTTCAAAAATGATATGTACTAGAAACAATGATGGTCATCGCCATTACACGGCCTACATAATTCAATATATGGTAAAATTTGATCAATTTCTTTTCTTAGGTGTACCGCGGAAACTGTGGGTGATAGAACCTATGTTTGTTCT----GAACTTT
droBip1 scf7180000396730:444189-444434 + AAAAATAAATGTGTAAAAT---ACACATATAAACTTTGGATGAGTATTCCAAAGATGTGGTAACTGCTAGATA-------TCATTTTTTGCATTTGAGCTGGTATACATACATTTAAAAAATTATATGTACTAAAAACCATGATGGACAACGCAATTACGTGGCCTACATAAATCAATATATGGCAGAA---------TTTATTTTGTTAGGTGTACCGCGGAAACTGTGGGTGATAGAACCTATGTTTGTTTGCTCTCAACATT
droKik1 scf7180000302692:12459-12708 - ACAGA--AATGTTGAAAATTTTGGGAGTTTCAACTTTGGCGTCGAATTCCAAAGACATGGGCAATGGTCCACGATTGGGAC-------TA--TTTTTAGTAGTGCCCTGATGTATTGAGAGTAGGTCCTACCGAAAATAATAAAGGTAAGTCCAATTATATAGGCCACGTAATTCAAAATGTCGGCAAACATCGGTTTTTTGTATTCTTAGGTATACCGCGGAACCTGTAGGTGATGGAAAATAATTTTGTATG----GGACTTT
droEle1 scf7180000490527:7111-7298 - AAAAT----------------TAGAGATTTTTACTTTGACGTAATATTTAATATATATAGATAATGGTTAAAGCCGGTGAA------------TTTTAATAATGCGATGGTTTATTAAGAGTGTTTG-------------------TCA--------------GCAATACAAT----------GGT--AAATAGGATTTTCATATTCTTAGCTTTACTGCGGAACCCTTAGCTGGAGGAACATAAGTTTATATG----GAACTTT
droRho1 scf7180000777977:27422-27642 - GAACT--TGTGTAGAAA-------------------------TCAAAACCAAACAAATTATCAATGGTTGAAGTCAAGAAC-------G----TTTTTTTAACGTGGTGATGATTTGAAAGTGTTTA-ATCAGAAAACGAT-TTGGTCACTTCAATAATATAATCTACGTAATTTAAAATGTCTCCAAACTTAAAATTTTCTTATTCTAAACTATACTGCCGAACTTGTGGTTGATAAAACATAAGTTTGTATG----GGACTTT
droBia1 scf7180000302087:8787-8888 - A-------------------------------------------------------------------------------------------------------------------------------------------------------------CGTAGGCAACATAGTTCAATGTGTGAAAAAACATCG--TATTTGCATTCTCAGCTATACCGCGGAACCTGTAGGTGATTAAACACAAGTTTGTATA----AGACTTT
droTak1 scf7180000415242:413291-413539 + ACAAAT----TTTGAAAATTTTGGGAGTTTCAACTTTGGCGTCGAATTCCAAAGACATGGGCAATGCGTCACGATTGAGAC-------TA-ATTTTTAGTAGTGCCGTGATGTATTGAGAGTAGGTCCTACCGAAAATAATAAAGGTAAGTCCACTTATATTGGCCACGTAATTCAAAATGTCGGAAAACATCGGTTTTTTGTATTCTTAGGTATACCGCGGAACCTGTAGGTGATGGAAAATAATTTTGTATG----GGACTTT

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
AAAAATTAATGTAGAAAAT--CTGAGATTTCAACTTTGGATGAGTATTCCAAAGATATGGAAACTGCTAGCAA-------CCATTTTTTA-ATTTTAGTTGGTACACATACATTTCAAAAATGATATGTACTAGAAACAATGATGGTCATCGCCATTACACGGCCTACATAATTCAATATATGGTAAAATTTGATCAATTTCTTTTCTTAGGTGTACCGCGGAAACTGTGGGTGATAGAACCTATGTTTGTTCT----GAACTTTSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
...............................................TCCAAAGATATGGAAACTGCTAGC..................................................................................................................................................................................................2411.001010000
................................................CCAAAGATATGGAAACTGCTAGCAA-------C........................................................................................................................................................................................2611.001010000
...................................................................................................................................TAGAAACAATGATGGTCATCGCCATTA...........................................................................................................27200.55110110000
................................................................................................................................................................................................................TAGGTGTACCGCGGAAACTGT....................................21200.50100000100
...............................AACTTTGGATGAGTATTCCA......................................................................................................................................................................................................................20200.255000050
...............................................................................................TAGTTGGTACACATACATTTCAAAAATGA.............................................................................................................................................29200.204040000
................................................................................................................................TACTAGAAACAATGATGGTCATCGCC...............................................................................................................26200.204400000
................................................................................................................................................GGTCATCGCCATTACACGG......................................................................................................19200.153300000
.............................................................................................................................................................................................................TCTTAGGTGTACCGCGGAAACTGTG...................................25200.153003000
...............................................TCCAAAGATATGGAAACTGCT.....................................................................................................................................................................................................2170.141100000
...............................................................................................................................................................................................................................AACTGTGGGTGATAGAACCTA.....................21200.102200000
....................................................................................................................................................................................................................TGTACCGCGGAAACTGTGGGTGATA............................25200.102200000
............................................................................................TTTTAGTTGGTACACATACATTTCAAA..................................................................................................................................................27200.051100000
.......................................................................................................................................AACAATGATGGTCATCGC................................................................................................................18200.051100000
.....................CTGAGATTTCAACTTTGGATGAG.............................................................................................................................................................................................................................23200.051000010
.................................................................................................................................ACTAGAAACAATGATGGTCATCGCC...............................................................................................................25200.051100000
......TAATGTAGAAAAT--CTGAGATTTCAAC.......................................................................................................................................................................................................................................26200.051100000
.....................CTGAGATTTCAACTTTGGATGAGT............................................................................................................................................................................................................................24200.051010000
droBip1
AAAAATAAATGTGTAAAAT---ACACATATAAACTTTGGATGAGTATTCCAAAGATGTGGTAACTGCTAGATA-------TCATTTTTTGCATTTGAGCTGGTATACATACATTTAAAAAATTATATGTACTAAAAACCATGATGGACAACGCAATTACGTGGCCTACATAAATCAATATATGGCAGAA---------TTTATTTTGTTAGGTGTACCGCGGAAACTGTGGGTGATAGAACCTATGTTTGTTTGCTCTCAACATTSizeHit CountTotal NormTotal
No Reads
droKik1
ACAGA--AATGTTGAAAATTTTGGGAGTTTCAACTTTGGCGTCGAATTCCAAAGACATGGGCAATGGTCCACGATTGGGAC-------TA--TTTTTAGTAGTGCCCTGATGTATTGAGAGTAGGTCCTACCGAAAATAATAAAGGTAAGTCCAATTATATAGGCCACGTAATTCAAAATGTCGGCAAACATCGGTTTTTTGTATTCTTAGGTATACCGCGGAACCTGTAGGTGATGGAAAATAATTTTGTATG----GGACTTTSizeHit CountTotal NormTotal
No Reads
droEle1
AAAAT----------------TAGAGATTTTTACTTTGACGTAATATTTAATATATATAGATAATGGTTAAAGCCGGTGAA------------TTTTAATAATGCGATGGTTTATTAAGAGTGTTTG-------------------TCA--------------GCAATACAAT----------GGT--AAATAGGATTTTCATATTCTTAGCTTTACTGCGGAACCCTTAGCTGGAGGAACATAAGTTTATATG----GAACTTTSizeHit CountTotal NormTotal
No Reads
droRho1
GAACT--TGTGTAGAAA-------------------------TCAAAACCAAACAAATTATCAATGGTTGAAGTCAAGAAC-------G----TTTTTTTAACGTGGTGATGATTTGAAAGTGTTTA-ATCAGAAAACGAT-TTGGTCACTTCAATAATATAATCTACGTAATTTAAAATGTCTCCAAACTTAAAATTTTCTTATTCTAAACTATACTGCCGAACTTGTGGTTGATAAAACATAAGTTTGTATG----GGACTTTSizeHit CountTotal NormTotal
No Reads
droBia1
A-------------------------------------------------------------------------------------------------------------------------------------------------------------CGTAGGCAACATAGTTCAATGTGTGAAAAAACATCG--TATTTGCATTCTCAGCTATACCGCGGAACCTGTAGGTGATTAAACACAAGTTTGTATA----AGACTTTSizeHit CountTotal NormTotal
No Reads
droTak1
ACAAAT----TTTGAAAATTTTGGGAGTTTCAACTTTGGCGTCGAATTCCAAAGACATGGGCAATGCGTCACGATTGAGAC-------TA-ATTTTTAGTAGTGCCGTGATGTATTGAGAGTAGGTCCTACCGAAAATAATAAAGGTAAGTCCACTTATATTGGCCACGTAATTCAAAATGTCGGAAAACATCGGTTTTTTGTATTCTTAGGTATACCGCGGAACCTGTAGGTGATGGAAAATAATTTTGTATG----GGACTTTSizeHit CountTotal NormTotal
No Reads

Generated: 05/18/2015 at 05:49 AM