ID:

dan_1622

 Coordinate:

scaffold_13250:2802347-2802497 +

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-12.0 -11.3 -11.3 -11.1

Flybase annnotation

exon [dana_GLEANR_1274:2]; CDS [Dana\GF12722-cds]; intron [Dana\GF12722-in]

Repeatable elements

NameClassFamilyStrand
OSVALDO_I-intLTRGypsy+
mature
  1. scaffold_1164:1775-1798 +
  2. scaffold_3821:206-229 +
  3. scaffold_11535:1511-1534 +
  4. scaffold_12200:7802-7825 +
  5. scaffold_12911:1278807-1278830 +
  6. scaffold_12929:1482263-1482286 +
  7. scaffold_13043:212583-212606 +
  8. scaffold_13082:1095565-1095588 +
  9. scaffold_13099:408910-408933 +
  10. scaffold_13099:431712-431735 +
  11. scaffold_13099:3064731-3064754 +
  12. scaffold_13099:3083531-3083554 +
  13. scaffold_13177:33554-33577 +
  14. scaffold_13230:1392193-1392216 +
  15. scaffold_13250:1662177-1662200 +
  16. dan_1622  scaffold_13250:2802378-2802401 +
  17. scaffold_13339:1876034-1876057 +
  18. scaffold_13339:2921133-2921156 +
  19. scaffold_13417:1902771-1902794 +
  20. scaffold_13469:518075-518098 +
star
  1. scaffold_656:478-495 +
  2. scaffold_5292:12892-12909 +
  3. scaffold_10144:277-294 +
  4. scaffold_11535:1544-1561 +
  5. scaffold_12200:7835-7852 +
  6. scaffold_12929:1482296-1482313 +
  7. scaffold_12929:1489709-1489726 +
  8. scaffold_13045:492676-492693 +
  9. scaffold_13082:1095598-1095615 +
  10. scaffold_13082:1113040-1113057 +
  11. scaffold_13082:2449387-2449404 +
  12. scaffold_13099:408943-408960 +
  13. scaffold_13099:884921-884938 +
  14. scaffold_13177:33587-33604 +
  15. scaffold_13230:1392226-1392243 +
  16. dan_1622  scaffold_13250:2802411-2802428 +
  17. scaffold_13339:1869189-1869206 +
  18. scaffold_13339:1876067-1876084 +
  19. scaffold_13339:2921166-2921183 +
  20. scaffold_13469:518108-518125 +

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
TTAAATTTATTTTGATGATGTGTTATATGTATACATGAAAAGAACCACCCCCGTCCGCCCTTCACTCCCATCCTTACGTCCCCAAGGTATATCCTCTGGACCTTGCAGAAGATCTTGCAATTTGGTTCTGTTTTAACAACAGCTCGAACTACACACATTACAGTAGCATTACAGTATCAGTATAAAGTATCATCCATTCAGGGAAGAGCTGCTGTACTTGGGTCACCGAATAAAAAGCCAGGGAATCGGCA
*********************************************************************************..((............(((((((((((......))))))...)))))..))*********************************************************************************************************************** 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 V039
embryo
 M044
female body
..............................................................................................................................................................................................CATCTAATCAGGGAAGAGC.......................................... 19 2 1 1.00 1 0 1 0
..........................ATGTCTACATGAGAGGAACCAC........................................................................................................................................................................................................... 22 3 1 1.00 1 1 0 0
..........................ATGTCTACATGAACAGCACCA............................................................................................................................................................................................................ 21 3 3 0.33 1 0 1 0
........................................................................................................................................................................................................................................AAAATACAGGGAATCGGCA 19 2 5 0.20 1 0 0 1
.................................................................................CCAAGGTATATCCTCTGGACCTTG.................................................................................................................................................. 24 0 20 0.15 3 0 0 3
.................................................................................CCAAGGTATATCCTCTGGACCTT................................................................................................................................................... 23 0 20 0.10 2 0 0 2
..................................................................................CAAGGTATATCCTCTGGACCTTGC................................................................................................................................................. 24 0 20 0.10 2 0 0 2
...............................................................................................................................................................................................................GCGGCTGTACGTGGGGCACC........................ 20 3 16 0.06 1 1 0 0
......................................................................................GGATATCCTCTGGACCTTGC................................................................................................................................................. 20 1 20 0.05 1 1 0 0
.................................................................................CCAAGGTCTATCCTCTGGACCA.................................................................................................................................................... 22 2 20 0.05 1 1 0 0
...............................................................................CCCCATGGTATATCCTCTGGACCTT................................................................................................................................................... 25 1 20 0.05 1 0 0 1
..................................................................................CAAGGTATATCCTCTGGACCTTGCA................................................................................................................................................ 25 0 20 0.05 1 0 0 1
...................................................................................AAGGTATATCCTCTGGACCTTG.................................................................................................................................................. 22 0 20 0.05 1 0 0 1
...........................................................................ACGTCCCCAAGGTATATCCTC........................................................................................................................................................... 21 0 20 0.05 1 1 0 0
..................................................................................................................TTGCAATTTGGTTCTGTT....................................................................................................................... 18 0 20 0.05 1 1 0 0
...............................................................................CCCCAAGGTATATCCTCTGGACCTTGC................................................................................................................................................. 27 0 20 0.05 1 0 0 1
.........................................................................................TATCCTCTGGACCTTGAAA............................................................................................................................................... 19 2 20 0.05 1 1 0 0
...............................................................................CCCCAAGGTATATCCTCTGGAC...................................................................................................................................................... 22 0 20 0.05 1 0 0 1
..............................................................................TCCCCAAGCTATATCCTCTGGACCTTGC................................................................................................................................................. 28 1 20 0.05 1 0 0 1
..............................................................................TCCCCAAGGTATATCCTCTGGACCT.................................................................................................................................................... 25 0 20 0.05 1 1 0 0
...............................................................................CCCCAAGGTATATCCTCTGGACCT.................................................................................................................................................... 24 0 20 0.05 1 1 0 0

Anti-sense strand reads

AATTTAAATAAAACTACTACACAATATACATATGTACTTTTCTTGGTGGGGGCAGGCGGGAAGTGAGGGTAGGAATGCAGGGGTTCCATATAGGAGACCTGGAACGTCTTCTAGAACGTTAAACCAAGACAAAATTGTTGTCGAGCTTGATGTGTGTAATGTCATCGTAATGTCATAGTCATATTTCATAGTAGGTAAGTCCCTTCTCGACGACATGAACCCAGTGGCTTATTTTTCGGTCCCTTAGCCGT
***********************************************************************************************************************..((............(((((((((((......))))))...)))))..))********************************************************************************* 		Read size # Mismatch Hit Count Total Norm Total M044
female body
 V055
head
 M058
embryo
 V106
head
...................................CCTTTTCATCGTGGGGGCAGG................................................................................................................................................................................................... 21 3 1 1.00 1 0 1 0 0
................................................................GAGGGTAGGAATGCAGGGGTTCCAT.................................................................................................................................................................. 25 0 1 1.00 1 1 0 0 0
.........................................................................................ATAGGAGACCTGGAACGTCTTCTAGAAC...................................................................................................................................... 28 0 2 0.50 1 1 0 0 0
...........................................................................................AGGAGACCTGGAACGTCTTCTAGAAC...................................................................................................................................... 26 0 2 0.50 1 1 0 0 0
.......................................................................................................................................................................................ATTCATAGTAGGTGAGTCC................................................. 19 2 2 0.50 1 0 0 1 0
...........................................TGGTGGGGGCAGACGTGAGGTG.......................................................................................................................................................................................... 22 3 2 0.50 1 0 1 0 0
............................................................................................................................CAAGAAGAAATTGTTGTC............................................................................................................. 18 2 17 0.35 6 1 4 0 1
...........................................................................................AGGACACCTGGAACGTCTTCTAGAAC...................................................................................................................................... 26 1 3 0.33 1 1 0 0 0
.........................................CTTCGTGGGGGCAGGCGGC............................................................................................................................................................................................... 19 2 4 0.25 1 0 1 0 0
..........................................TTGGTGAGGGTAGGCAGGAAG............................................................................................................................................................................................ 21 3 5 0.20 1 0 1 0 0
.........................................................GGGAAGTGAGCGTAGCAA................................................................................................................................................................................ 18 2 6 0.17 1 0 0 0 1
.............................................GTGGGGGCAGGCGGGG.............................................................................................................................................................................................. 16 1 8 0.13 1 0 1 0 0
..............................................................GTGAGGGTAGTAATGGAG........................................................................................................................................................................... 18 2 12 0.08 1 1 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13250:2802297-2802547 + dan_1622 TTAAATTTATTTTGATGATGTGTTATATGTATACATGAA-AAGAACCACCCCCGTCC---------------------------------GCCCTTCACTCCCATCCTTACGTCCCCAAGGTATATCCTCTGGACCTTGCAGAAGATCTTGCAATTTGGTTCTGTTTTAACAACAGCTCGAACTACACACATTACAGTAGCATTACAGTAT-------CAGTATAAAGTATCATCCATTCAGGGAAGAGCTGCTGTACTTGGGTCACCGAATAAAAAGCCAGGGAATCGGCA
droBip1 scf7180000396583:97730-97956 - TTA-ATTTATTTTGATGATGTGTAGTATGGATACGTGAAAAAGAACCTCCCCCATCCGTCGAGCTAAGTCTAAGACCACAAGAAGTGCACGCCCTTCACTCCCATCCATACGTCCCTAAGGTATATCCTATGGACCTTGCAGAACACCTTGCATCTTGGTTCTGTTTTT----------GAACT---CACAGTACCCACACATTACAATATTTGGGCCCAATATGAAA-GTCAGCCAGTCAG--------------------------------------------------
droFic1 scf7180000454097:334-400 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGCCAGTTCTTCAGGCAAGAGTTGCTGTACCTAGGACACCGAGTAACAAGCCAAGGGATAGGGA
droEle1 scf7180000486270:8688-8755 + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGAGTCATTTCTTCAGAAGCGAGCTGCTTTACCTGGGGCACCGCGTTACAAATCAAGGAATCGGCT
droRho1 scf7180000774314:110-176 - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTCAGTTCTTCAAGCAGGAGCTGCTGTACCTGGGACATCGAGTAACAAGCCAAGGAATCGGTA
droBia1 scf7180000301342:42577-42644 + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATACCAGTTTTTCAAGAAGGAGCTGCTGTATTTGGGTCATAGAGTGACTAGCGACGGAATAGGCA
droTak1 scf7180000412828:9523-9589 - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTCAATTCTTCAAAAAGGAGCTGCTGTACCTGGGACATCGAGTAACAAGCCAAGGAATTGGCA
droYak3 v2_chr2L_random_011:34617-34684 + --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATGCCAGTTCTTCAAACAAGAACTTCTGTACCTAGGGCACCGTGTCACAAGCCAAGGAATAGGCA

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
TTAAATTTATTTTGATGATGTGTTATATGTATACATGAA-AAGAACCACCCCCGTCC---------------------------------GCCCTTCACTCCCATCCTTACGTCCCCAAGGTATATCCTCTGGACCTTGCAGAAGATCTTGCAATTTGGTTCTGTTTTAACAACAGCTCGAACTACACACATTACAGTAGCATTACAGTAT-------CAGTATAAAGTATCATCCATTCAGGGAAGAGCTGCTGTACTTGGGTCACCGAATAAAAAGCCAGGGAATCGGCASizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
...................................................................................................................CCAAGGTATATCCTCTGGACCTTG.........................................................................................................................................................24200.153300000
...................................................................................................................CCAAGGTATATCCTCTGGACCTT..........................................................................................................................................................23200.102200000
....................................................................................................................CAAGGTATATCCTCTGGACCTTGC........................................................................................................................................................24200.102200000
....................................................................................................................CAAGGTATATCCTCTGGACCTTGCA.......................................................................................................................................................25200.051100000
.....................................................................................................................AAGGTATATCCTCTGGACCTTG.........................................................................................................................................................22200.051100000
.............................................................................................................ACGTCCCCAAGGTATATCCTC..................................................................................................................................................................21200.051010000
....................................................................................................................................................TTGCAATTTGGTTCTGTT..............................................................................................................................18200.051010000
.................................................................................................................CCCCAAGGTATATCCTCTGGACCTTGC........................................................................................................................................................27200.051100000
.................................................................................................................CCCCAAGGTATATCCTCTGGAC.............................................................................................................................................................22200.051100000
................................................................................................................TCCCCAAGGTATATCCTCTGGACCT...........................................................................................................................................................25200.051010000
.................................................................................................................CCCCAAGGTATATCCTCTGGACCT...........................................................................................................................................................24200.051010000
droBip1
TTA-ATTTATTTTGATGATGTGTAGTATGGATACGTGAAAAAGAACCTCCCCCATCCGTCGAGCTAAGTCTAAGACCACAAGAAGTGCACGCCCTTCACTCCCATCCATACGTCCCTAAGGTATATCCTATGGACCTTGCAGAACACCTTGCATCTTGGTTCTGTTTTT----------GAACT---CACAGTACCCACACATTACAATATTTGGGCCCAATATGAAA-GTCAGCCAGTCAG--------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGCCAGTTCTTCAGGCAAGAGTTGCTGTACCTAGGACACCGAGTAACAAGCCAAGGGATAGGGASizeHit CountTotal NormTotal
No Reads
droEle1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGAGTCATTTCTTCAGAAGCGAGCTGCTTTACCTGGGGCACCGCGTTACAAATCAAGGAATCGGCTSizeHit CountTotal NormTotal
No Reads
droRho1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTCAGTTCTTCAAGCAGGAGCTGCTGTACCTGGGACATCGAGTAACAAGCCAAGGAATCGGTASizeHit CountTotal NormTotal
No Reads
droBia1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATACCAGTTTTTCAAGAAGGAGCTGCTGTATTTGGGTCATAGAGTGACTAGCGACGGAATAGGCASizeHit CountTotal NormTotal
No Reads
droTak1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGTGTCAATTCTTCAAAAAGGAGCTGCTGTACCTGGGACATCGAGTAACAAGCCAAGGAATTGGCASizeHit CountTotal NormTotal
No Reads
droYak3
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATGCCAGTTCTTCAAACAAGAACTTCTGTACCTAGGGCACCGTGTCACAAGCCAAGGAATAGGCASizeHit CountTotal NormTotalM026
Head		M043
Female-body		M056
Embryo		V046
Embryo		V052
Head		V058
Head		V120
Male-body		SRR1275488
Male larvae		SRR1275486
Male prepupae		SRR1275484
Male prepupae		GSM1528802
follicle cells
...................................................................................................................................................................................................................................................CAAGAACTTCTGTACCTAGGGCACC........................25200.20400400000000
..............................................................................................................................................................................................................................................TCAAACAAGAACTTCTGTACCTAGGGCAC.........................29200.10200200000000
...........................................................................................................................................................................................................................................TCTTCAAACAAGAACTTCTGTACC.................................24200.10200200000000
............................................................................................................................................................................................................................................CTTCAAACAAGAACTTCTGTACCT................................24200.05101000000000
............................................................................................................................................................................................................................................CTTCAAACAAGAACTTCTGTACCTAGGG............................28200.05101000000000
..............................................................................................................................................................................................................................................TCAAACAAGAACTTCTGTACCTAGGGC...........................27200.05100100000000
................................................................................................................................................................................................................................AAAATGCCAGTTCTTCAAACAAGAAC..........................................26200.05100100000000
..............................................................................................................................................................................................................................................TCAAACAAGAACTTCTGTACCTAGG.............................25200.05101000000000
...................................................................................................................................................................................................................................................CAAGAACTTCTGTACCTAGGGCAC.........................24200.05101000000000
...........................................................................................................................................................................................................................................TCTTCAAACAAGAACTTCTGTACCT................................25200.05100100000000

Generated: 05/18/2015 at 02:33 AM