ID:

dan_3362

 Coordinate:

scaffold_13499:218058-218208 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-25.7 -25.6 -25.3 -25.0

Flybase annnotation

CDS [Dana\GF23829-cds]; exon [dana_GLEANR_86:2]; intron [Dana\GF23829-in]

Repeatable elements

NameClassFamilyStrand
Hoana8DNAhAT-hobo+
mature
  1. scaffold_12911:189862-189883 -
  2. scaffold_12928:277622-277643 -
  3. scaffold_13082:1880872-1880893 -
  4. scaffold_13099:1170651-1170672 -
  5. scaffold_13099:1562210-1562231 -
  6. scaffold_13099:3059832-3059853 -
  7. scaffold_13186:1599-1620 -
  8. scaffold_13248:4017868-4017889 -
  9. scaffold_13250:1141634-1141655 -
  10. scaffold_13250:1191845-1191866 -
  11. scaffold_13260:177610-177631 -
  12. scaffold_13260:1016251-1016272 -
  13. scaffold_13260:1024268-1024289 -
  14. scaffold_13280:997377-997398 -
  15. scaffold_13333:156699-156720 -
  16. scaffold_13335:3147524-3147545 -
  17. scaffold_13339:1797155-1797176 -
  18. scaffold_13417:3824158-3824179 -
  19. scaffold_13499:214415-214436 -
  20. dan_3362  scaffold_13499:218127-218148 -
star

Sense Strand Reads

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------##################################################
ACATAGCCCGCAATCATGAATTAAGTGATATTTTTGACCATAATGATTATTTGGGACTTTTATTTTTTCGCTCAGATAATAATAATGATTATTTCGGACCGAAGTGTATATACCCTTGCAGTTAGGTAGCAGCTTATAATTTTATATATATATCGGATCGTATATAGCTGACCGATCCTTATGAGAATTTCATCATCACAGGTGCCGGTCATCGCACAGGTTTTTATGCACGAAACTTCGCAGTTCGCGAC
**************************************************(((.((.((((((....(((.((((...................(((.((((.(((((((((..........(((((....)))))......))))))))).)))).))).......)))).))).....)))))).........)).)))************************************************** 		Read size # Mismatch Hit Count Total Norm Total M044
female body
 V055
head
 M058
embryo
 V105
male body		 V106
head
......................................CGTAATGATTATTAGGGAC.................................................................................................................................................................................................. 19 2 2 0.50 1 1 0 0 0 0
......................................CGTAATGATTAATTGGGAC.................................................................................................................................................................................................. 19 2 3 0.33 1 1 0 0 0 0
.....................................CCGTAATGATTAATAGGGAC.................................................................................................................................................................................................. 20 3 8 0.13 1 0 1 0 0 0
..............................................................................................................................................................................................................................TTTATGGTCGAAACTTCG........... 18 2 8 0.13 1 0 1 0 0 0
...............ATGAATTAAGTGTTGTTCTTG....................................................................................................................................................................................................................... 21 3 16 0.06 1 1 0 0 0 0
....................................ATCGTAATGATTATTAGGGAC.................................................................................................................................................................................................. 21 3 17 0.06 1 0 0 0 1 0
..............................................................................................................TAACCTTGCAGTTAGGTAGCAGCTTA................................................................................................................... 26 1 20 0.05 1 0 0 1 0 0
...........................................TGATTATGTGGGACGTGTAT............................................................................................................................................................................................ 20 3 20 0.05 1 0 1 0 0 0
..............................................................................................................TACCCTTGCAGTTAGGTAGCAG....................................................................................................................... 22 0 20 0.05 1 0 0 1 0 0
...................................................................................................................................................................................................TCTCCGGTGCCGATCATCG..................................... 19 3 20 0.05 1 0 0 0 0 1
.......................................GTAATGATTATTAGGGAC.................................................................................................................................................................................................. 18 2 20 0.05 1 1 0 0 0 0

Anti-sense strand reads

TGTATCGGGCGTTAGTACTTAATTCACTATAAAAACTGGTATTACTAATAAACCCTGAAAATAAAAAAGCGAGTCTATTATTATTACTAATAAAGCCTGGCTTCACATATATGGGAACGTCAATCCATCGTCGAATATTAAAATATATATATAGCCTAGCATATATCGACTGGCTAGGAATACTCTTAAAGTAGTAGTGTCCACGGCCAGTAGCGTGTCCAAAAATACGTGCTTTGAAGCGTCAAGCGCTG
**************************************************(((.((.((((((....(((.((((...................(((.((((.(((((((((..........(((((....)))))......))))))))).)))).))).......)))).))).....)))))).........)).)))************************************************** 		Read size # Mismatch Hit Count Total Norm Total M058
embryo
 V105
male body		 M044
female body
 V039
embryo
......................................................................................................................................................................................................GTCCACGGCCAGTAGCGTGTCCAAA............................ 25 0 2 0.50 1 1 0 0 0
........................................................GAGAAAAAACAAGCGAGTCTA.............................................................................................................................................................................. 21 3 6 0.17 1 0 1 0 0
.................................................................................................................GGAACGTCAATCCATCGTCGAATAT................................................................................................................. 25 0 20 0.15 3 3 0 0 0
TGTATCGGCCGTTAGAAC......................................................................................................................................................................................................................................... 18 2 16 0.13 2 2 0 0 0
TGTATCGGCCGTTAGAACA........................................................................................................................................................................................................................................ 19 3 20 0.10 2 1 0 1 0
..............................................................................................................................................................GCATATATCGACTGGCTAGGAA....................................................................... 22 0 10 0.10 1 0 0 0 1
............................................................................................................ATATGGGAACGTCAATCCATCGTCGA..................................................................................................................... 26 0 20 0.05 1 1 0 0 0
..........................................................................................................................................................................................................ACCGTCAGTAGCGTGTCCC.............................. 19 3 20 0.05 1 0 0 1 0
.............................................................................................................TATGGGAACGTCAATCCATCGTCGAAT................................................................................................................... 27 0 20 0.05 1 0 0 1 0
.....................................................................................................................CGTCAATCCATCGTCGAATA.................................................................................................................. 20 0 20 0.05 1 1 0 0 0
....................................................................................................................................................................................TACTCTTGGAGTAGTAGT..................................................... 18 2 20 0.05 1 1 0 0 0
................................................................................................................GGGAACGTCAATCCATCGTCGAAT................................................................................................................... 24 0 20 0.05 1 1 0 0 0
.....................................................................................................................................................CATAGCCTAGCATATATCGAC................................................................................. 21 1 20 0.05 1 1 0 0 0
...............................................................................................................TGGGAACGTCAATCCATCGTCGAACAT................................................................................................................. 27 1 20 0.05 1 1 0 0 0
..............................................................................................................ATGGGAACGTCAATCCATCGTCGAATAT................................................................................................................. 28 0 20 0.05 1 1 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droAna3 scaffold_13499:218008-218258 - dan_3362 ACATAGCCCGCAATCATGAATTAAGTGATATTTTTGACCATAATGATTATTTGGGACTTTTATTTTTTCGCTCAGATAATAATAAT-GA------------------TTATTTCGG-----ACCGAAGTGTATATACCCTTGCAGTTAGGTAGCAGCTTATAATTTTATATATATATCGG--ATCGTATATAGCTGACCGATCCTTATGAGAATTTCATCATCACAGGTGCCGGTCATCGCACAGGTTTTTATGCACGAAACTTCGCAGTTCGCGAC
droBip1 scf7180000395478:41240-41416 + CCATAGCGCGAAATCATGAATTGAGTGATATTTTTGAGCAAAA--------------------------------ATAATAAAAAT-CAAAAACAAGAAAGGAAAGCTAACTTCGGGCGGAGCCGAAGTTGATATACCCTTGCAGTTA------------AAACCGGATATATATCACAAATATCGGATATAGTTGGCCGATCCTTATAAGAATATGATAAT-------------------------------------------------------
droFic1 scf7180000454069:158277-158359 + GGTTATCTAAAAA--------------------------------------------CTTTATTTTAACT----GATA--------------ACAAGAAAGGA-AGCCAGCTTCGGCA--AGCCGAAGCTTATATACCCTTGCAGTCA---------------------------------------------------------------------------------------------------------------------------------
droEle1 scf7180000489338:948-1043 + AAATAAATCGAAAAAATAAATAAAA--AAAATTATAACTTTGCTGTTTATTAATTTTTTTTAGTTCTTCGA-CATATAGTAATGGTTAA------------------ATATTTCAG-----A-----------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1 scf7180000778355:6019-6105 + CCT------GCAATC--GACTTTAGTGAGTTTTTTGA-------------------------GTTTTTCCC-T------------------------CCAGGA-AGCAAACTTCGGCC--AGCTGAAGTTTATATACCCTTGCAGTTA---------------------------------------------------------------------------------------------------------------------------------
droBia1 scf7180000301495:203527-203563 + ACT-------------------------------------------------------------------------------------------------------------TCGGCA--AGCCGAAGTTTGTATACCCTTGCAGTTA---------------------------------------------------------------------------------------------------------------------------------
droSec2 scaffold_87:94286-94311 + GA-----------------------------------------------------------------------------------------------------------------------ACCGAAGTTTATATACCCTTGCAG------------------------------------------------------------------------------------------------------------------------------------
dp5 Unknown_singleton_3462:99-125 - GGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCTTCGCACAGGTTTTTAT------------------------
droPer2 scaffold_121:43703-43733 - GGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCATCGCACAGGGTTTTG-GCACG-------------------
droMoj3 scaffold_1874:5671-5673 + GAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droAna3
ACATAGCCCGCAATCATGAATTAAGTGATATTTTTGACCATAATGATTATTTGGGACTTTTATTTTTTCGCTCAGATAATAATAAT-GA------------------TTATTTCGG-----ACCGAAGTGTATATACCCTTGCAGTTAGGTAGCAGCTTATAATTTTATATATATATCGG--ATCGTATATAGCTGACCGATCCTTATGAGAATTTCATCATCACAGGTGCCGGTCATCGCACAGGTTTTTATGCACGAAACTTCGCAGTTCGCGACSizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
......................................................................................................................................TACCCTTGCAGTTAGGTAGCAG.........................................................................................................................22200.051010000
droBip1
CCATAGCGCGAAATCATGAATTGAGTGATATTTTTGAGCAAAA--------------------------------ATAATAAAAAT-CAAAAACAAGAAAGGAAAGCTAACTTCGGGCGGAGCCGAAGTTGATATACCCTTGCAGTTA------------AAACCGGATATATATCACAAATATCGGATATAGTTGGCCGATCCTTATAAGAATATGATAAT-------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droFic1
GGTTATCTAAAAA--------------------------------------------CTTTATTTTAACT----GATA--------------ACAAGAAAGGA-AGCCAGCTTCGGCA--AGCCGAAGCTTATATACCCTTGCAGTCA---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droEle1
AAATAAATCGAAAAAATAAATAAAA--AAAATTATAACTTTGCTGTTTATTAATTTTTTTTAGTTCTTCGA-CATATAGTAATGGTTAA------------------ATATTTCAG-----A-----------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droRho1
CCT------GCAATC--GACTTTAGTGAGTTTTTTGA-------------------------GTTTTTCCC-T------------------------CCAGGA-AGCAAACTTCGGCC--AGCTGAAGTTTATATACCCTTGCAGTTA---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droBia1
ACT-------------------------------------------------------------------------------------------------------------TCGGCA--AGCCGAAGTTTGTATACCCTTGCAGTTA---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
droSec2
GA-----------------------------------------------------------------------------------------------------------------------ACCGAAGTTTATATACCCTTGCAG------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054
Female-body		V113
Male-body		V114
Embryo		V115
Head
No Reads
dp5
GGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCTTCGCACAGGTTTTTAT------------------------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
..T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCTTCGCACAGGTTTTTA.........................2450.6030000000030
......................................................................................................................................................................................................................................CTGGTCTTCGCACAGGTTTTT..........................2170.2920200000000
..T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCTTCGCACAGGTTTTT..........................2360.1710100000000
..T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCTTCGCACAGGTTT............................21130.0810100000000
droPer2
GGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGGTCATCGCACAGGGTTTTG-GCACG-------------------SizeHit CountTotal NormTotalM021
Embryo		M042
Female-body		V042
Embryo		V050
Head		V057
Head		V111
Male-body
No Reads
droMoj3
GAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
No Reads

Generated: 05/18/2015 at 07:14 AM