ID:

dan_2200

 Coordinate:

scaffold_13335:494559-494709 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-39.8 -39.8

Flybase annnotation

CDS [Dana\GF19446-cds]; exon [dana_GLEANR_21487:1]; intron [Dana\GF19446-in]

No Repeatable elements found

mature
  1. scaffold_1736:188-208 +
  2. scaffold_1736:380-400 +
  3. scaffold_1736:764-784 +
  4. scaffold_1736:956-976 +
  5. scaffold_1736:1340-1360 +
  6. scaffold_1736:1724-1744 +
  7. scaffold_1736:1916-1936 +
  8. scaffold_3082:959-979 -
  9. scaffold_3355:931-951 -
  10. scaffold_11075:138-158 +
  11. scaffold_11075:329-349 +
  12. scaffold_11075:520-540 +
  13. scaffold_11075:711-731 +
  14. scaffold_13335:493991-494011 -
  15. dan_2200  scaffold_13335:494565-494585 -
  16. scaffold_13335:494758-494778 -
  17. scaffold_13335:2321622-2321642 -
  18. scaffold_13335:2326422-2326442 +
  19. scaffold_13335:2326613-2326633 +
  20. scaffold_13335:2326804-2326824 +
  21. scaffold_2790:1609-1629 -
  22. scaffold_2790:1993-2013 -
  23. scaffold_2790:2185-2205 -
  24. scaffold_3599:400-420 -
  25. scaffold_3599:592-612 -
  26. scaffold_3599:784-804 -
  27. scaffold_4762:295-315 -
  28. scaffold_4762:1833-1853 -
  29. scaffold_4762:3172-3192 -
  30. scaffold_4762:4690-4710 -
  31. scaffold_4762:5076-5096 -
  32. scaffold_4762:5649-5669 -
  33. scaffold_4763:326-346 -
  34. scaffold_4763:710-730 -
  35. scaffold_4763:1667-1687 -
  36. scaffold_4908:2193-2213 -
  37. scaffold_9045:72-92 -
  38. scaffold_9045:456-476 -
  39. scaffold_9045:1032-1052 -
  40. scaffold_11033:348-368 -
star

Sense Strand Reads

-----------------#################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
GTTCCCTGATTCGCAAAATGGTATCCCTTTTCCGGATCGGATTCGAAATGGTGGAGAATATTCACAAAAAAAGTGCCGGAAAAGCGTGGAGGGCACTTTTCCAGGGGTACACTCATGATTTTGAGCCAAAAATGAGGCCAAAATTTTATTTTGAGAATTTTAAGGATATTTTGATGCAGATCGACGGGGATTAGTTCCCTGATTCACAAATGGTATCCCTTTTCCGGATCGGATTCGAAATGGTTGAGATA
**************************************************(((((.....))))).......((((((((((((.((.....)).)))))))...))))).((((.(((((((.(((........))))))))))......))))...............(((((....)))))((((((.....))))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total V055
head
 M044
female body
 M058
embryo
.................................................................AAACAAATTGACGGAAAAGCGTG................................................................................................................................................................... 23 3 1 1.00 1 1 0 0
.............................................................................GGAAAAGCGTAGATGGTACT.......................................................................................................................................................... 20 3 6 0.17 1 1 0 0
.....................................................................................................................................................................ATATTTTGATGCAGATCGACGT................................................................ 22 1 20 0.05 1 0 1 0
.......................................................TAATATTCACAAAAAAAATCCC.............................................................................................................................................................................. 22 3 20 0.05 1 0 0 1
..............................................................................................................................................................................TGCAGATCGACGGGGATTAGT........................................................ 21 0 20 0.05 1 0 1 0

Anti-sense strand reads

CAAGGGACTAAGCGTTTTACCATAGGGAAAAGGCCTAGCCTAAGCTTTACCACCTCTTATAAGTGTTTTTTTCACGGCCTTTTCGCACCTCCCGTGAAAAGGTCCCCATGTGAGTACTAAAACTCGGTTTTTACTCCGGTTTTAAAATAAAACTCTTAAAATTCCTATAAAACTACGTCTAGCTGCCCCTAATCAAGGGACTAAGTGTTTACCATAGGGAAAAGGCCTAGCCTAAGCTTTACCAACTCTAT
**************************************************(((((.....))))).......((((((((((((.((.....)).)))))))...))))).((((.(((((((.(((........))))))))))......))))...............(((((....)))))((((((.....))))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total V039
embryo
 V105
male body		 M058
embryo
.....................................................................................CACCACCCGAGAAAACGTCCCC................................................................................................................................................ 22 3 2 0.50 1 1 0 0
..........................................................................................................CATGTGAGTTCCAAAATTCG............................................................................................................................. 20 3 7 0.14 1 0 1 0
................................................ACCACCTCTTATAAGACTTT....................................................................................................................................................................................... 20 2 7 0.14 1 0 0 1
..............................................................................................................................................................................ACGTCTAGCTGCCCCTAATCAAG...................................................... 23 0 20 0.05 1 0 1 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13335:494509-494759 - dan_2200 GTTCCCTGATTCGCAAAATGGTATCCCTTTTCCGGATCGGATTCG--------------------AAATGGTGGAGAA-TATTCACAAAAAAAGTGCCGGAAAAGCGTGGAGGGCACTTTTCCA-GGGGTACACTCATGAT-----------------------TTTGAGCCAAAAATGAGGCCAAAATTTTATTTTGAGAATTTTAAGGATATTTTGATGCAGATCGACGGGGATTAG-TTCCCTGATTCACAAATGGTATCCCTTTTCCGGATCGGATTCGAAATGGTTGAGATA
droBip1 scf7180000395498:256640-256886 + GATCCCCGATTCCC-AAATGGCATCCCTTTTCACGATCCGGTGCG--------------------AAATAGCCAAG-A-TATTCGCCA-AAAACTG-AGGAAAACCCGAATTCGCACTTTTCCAAGGGGTACCCCCAGGAT-----------------------TTTT-GCCAAAAATCGATCCAAAATTTTTTGTTGAGGATTTTAGGAATCCTTGGATGCAGATCGACGGTGAAAGG-ATCCCCGATTCCCAAATGGCATCCCTTTTCACGATCCGGTGCGAAATAGCCAAGATA
droBia1 scf7180000301345:79711-79958 - GTTTTACGATTCCA-AAGAGGTATGCCACTTTGGAATCTGATTTT--------------------AATTAGTGAAG-T-TAT-----------------------AGATGTTGGAACTCTCACT-GGGGTTACATTTTGACGAACTACCGAAAACTAGGAAATATGTGACATGAAAATGGGTCAAAAATTGAACATCAAAGAT-TTAAAAATGTTTTAATGCAGATTGTTTGGAATTTG-TTTTACGATTCCAAAGAGGTATGCCACTTTGGAATCGGACTCTTATTAGTGAACTTA
droEre2 scaffold_4644:1687180-1687432 - TATACCGAATTC-A-ACGAGGTATGACATTCCACAATCAGACCAATATTTTAGCTGCTGTGAACCAAAAACTGA-TAATTTTTAATCA-AAAAATC-AGGTTTAAAGAAAATCGCATTTTTGCAAGAGGTAACATCATAAT-----------------------TTTTTGCGAAAAATG--GCCAAAATTCAACATTTC----------AAACCTTGAATGCAATTCGATGGCAAATTTTATACCAAATTCA-GCGAGGTATGACATTCCCCAATCAGACC---AATATTTTAGCTA

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
GTTCCCTGATTCGCAAAATGGTATCCCTTTTCCGGATCGGATTCG--------------------AAATGGTGGAGAA-TATTCACAAAAAAAGTGCCGGAAAAGCGTGGAGGGCACTTTTCCA-GGGGTACACTCATGAT-----------------------TTTGAGCCAAAAATGAGGCCAAAATTTTATTTTGAGAATTTTAAGGATATTTTGATGCAGATCGACGGGGATTAG-TTCCCTGATTCACAAATGGTATCCCTTTTCCGGATCGGATTCGAAATGGTTGAGATASizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
..................................................................................................................................................................................................................ATATTTTGATGCAGATCGACGT.................................................................22200.051100000
...........................................................................................................................................................................................................................TGCAGATCGACGGGGATTAG-T........................................................21200.051100000
droBip1
GATCCCCGATTCCC-AAATGGCATCCCTTTTCACGATCCGGTGCG--------------------AAATAGCCAAG-A-TATTCGCCA-AAAACTG-AGGAAAACCCGAATTCGCACTTTTCCAAGGGGTACCCCCAGGAT-----------------------TTTT-GCCAAAAATCGATCCAAAATTTTTTGTTGAGGATTTTAGGAATCCTTGGATGCAGATCGACGGTGAAAGG-ATCCCCGATTCCCAAATGGCATCCCTTTTCACGATCCGGTGCGAAATAGCCAAGATASizeHit CountTotal NormTotal
No Reads
droBia1
GTTTTACGATTCCA-AAGAGGTATGCCACTTTGGAATCTGATTTT--------------------AATTAGTGAAG-T-TAT-----------------------AGATGTTGGAACTCTCACT-GGGGTTACATTTTGACGAACTACCGAAAACTAGGAAATATGTGACATGAAAATGGGTCAAAAATTGAACATCAAAGAT-TTAAAAATGTTTTAATGCAGATTGTTTGGAATTTG-TTTTACGATTCCAAAGAGGTATGCCACTTTGGAATCGGACTCTTATTAGTGAACTTASizeHit CountTotal NormTotal
No Reads
droEre2
TATACCGAATTC-A-ACGAGGTATGACATTCCACAATCAGACCAATATTTTAGCTGCTGTGAACCAAAAACTGA-TAATTTTTAATCA-AAAAATC-AGGTTTAAAGAAAATCGCATTTTTGCAAGAGGTAACATCATAAT-----------------------TTTTTGCGAAAAATG--GCCAAAATTCAACATTTC----------AAACCTTGAATGCAATTCGATGGCAAATTTTATACCAAATTCA-GCGAGGTATGACATTCCCCAATCAGACC---AATATTTTAGCTASizeHit CountTotal NormTotalM055
Female-body		M057
Embryo		V060
Head		V040
Embryo		V107
Male-body		V108
Head		GSM1528801
follicle cells
No Reads

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