ID:

dmo_539

 Coordinate:

scaffold_6359:417694-417844 -

 Confidence:

Candidate

 Type:

Unknown

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

Predicted structure

-39.4 -39.2 -39.1

Flybase annnotation

CDS [Dmoj\GI21621-cds]; exon [dmoj_GLEANR_6617:1]; intron [Dmoj\GI21621-in]

No Repeatable elements found

mature
  1. dmo_539  scaffold_6359:417747-417767 -
  2. scaffold_6680:19620207-19620227 -
  3. scaffold_6680:19637788-19637808 +
star

Sense Strand Reads

##################################################---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
AAAGCGGCGCAAGATCAAGAGCAATTGCCGGAGTCAGCTTTACGGTTCCTGTTTGTGTTGTTGCTGCTGTTGTTGAGCTCAACGCCGCATTTAATACGCCAACTCGTTGCACTTCATTCATTATTAACAGCAACAGCAACAGCTGCAACTGCGCTGCCAGCGTCAATGCGAAATATTGACATATTGACGGATATTTAAGCGAATGACTGAATGTGTGAGGCGAACTTAGATTGGCGGAGATATTTTATAGA
**************************************************..((((((((((((((.(((((((((...(((((..((.........)).....)))))..............))))))))).)))))))))).))))...((((.....(((((((((((....)))...))))))))........))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total M046
female body
 V110
male body
....................................................................................................................................................................................................................................GATTGGTGGATCTATTTTAT... 20 3 11 0.55 6 6 0
...............................................................................................................................CAGCAACAGCAACAGCTGCAA....................................................................................................... 21 0 3 0.33 1 0 1

Anti-sense strand reads

TTTCGCCGCGTTCTAGTTCTCGTTAACGGCCTCAGTCGAAATGCCAAGGACAAACACAACAACGACGACAACAACTCGAGTTGCGGCGTAAATTATGCGGTTGAGCAACGTGAAGTAAGTAATAATTGTCGTTGTCGTTGTCGACGTTGACGCGACGGTCGCAGTTACGCTTTATAACTGTATAACTGCCTATAAATTCGCTTACTGACTTACACACTCCGCTTGAATCTAACCGCCTCTATAAAATATCT
**************************************************..((((((((((((((.(((((((((...(((((..((.........)).....)))))..............))))))))).)))))))))).))))...((((.....(((((((((((....)))...))))))))........))))************************************************** 		Read size # Mismatch Hit Count Total Norm Total M060
embryo
 V110
male body		 M046
female body
..............................................................................................................................................................................................CACAAATTCGCTTACTGTCTT........................................ 21 3 9 0.11 1 1 0 0
............................................................................CTAGTAGCGGGGTAAATTA............................................................................................................................................................ 19 3 17 0.06 1 0 1 0
..............................................AGGAGAAACTCAACAACG........................................................................................................................................................................................... 18 2 20 0.05 1 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droMoj3 scaffold_6359:417644-417894 - dmo_539 AAAGCGGC-------GCAAGATCAAGAGCAATTGCCGGAGTCA-GCTTTACGGTTCCTGTTTGTGTTG---TTGCTGCTGTTGTTGAG-CT--CAACGCCGCATTTAATACGCCAACTCGTTGCACTTCATTCATTATTAACAGCAACAGCAACAGCTGCAACT----------------------------GCGCTGCCAGCGTCAATGCGAAATATTGACATATTGACGGATATTTAAGCGAATGACTGAATGTGTGAGGCGAACTTAGATTGGCGGAGATATTTTATAGA
droVir3 scaffold_12928:3845256-3845461 + AAACGGGC-------GCAGGATCAGCAGCAATTGCCGATGCCA-GCTTTGCTGT------TG-----TCCATTGTTGTTGTTGTTGAG-GT--CAGCGCCGCATTTAATACGCCAACTCGTTGCAGTT-GTTCATTATTAACAGCGACAGC------TGCAACT----------------TCGATGCCGACGTCGACGCCGGCGCCGACGCCAAATGTCGCCATATTGACAGTCATTAAAGCGAATAAATG------------------------------------------
droGri2 scaffold_15081:3901507-3901742 - AGATCAGCAGCAGCAGCAGCAGCAGCAGCAATTGACATTGCCAGGCTTTACTTT------TA-----T---TTGCTGTTGTTGTTGAG-GT--CAGCTTCGCATTTAATACGCCAACTCGTTGCAGCTCATTCATTATTAACAGGCACAGC------TGCAGC-AGTTGCAATGTTGACGTCGACCCCGACCCCGACACCGACACCGACGCCCAACGTTGCCATATTGACAGTTATTAAAGCGATTGAATGAATGAATGA---------------------------------
droWil2 scf2_1100000004513:2022029-2022117 - GTTACT----------------------------------------------G------TTGCTGTTG---TTGCTGTTGTTGTCGCT-CT--------TGTG-TTGTTGCTGCTGCTTATTACACATTGCCCACCATTGGTAGTGGCAGC------GGC-------------------------------------------------------------------------------------------------------------------------------------
dp5 4_group3:5318454-5318496 - AACAGC----------------------------------------------A------ACAGCAACA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAACAGCAGCAACAACG-----------------------------------------------------------------------------------
droPer2 scaffold_2:487472-487531 + CGCACC-----------------------------------CA-GCTTTTAATTTTGCGTCTGTTTCG---CTGCCGTCGTCGTCGCT-CT---------------------------------------------------------------------------------------------------------------CACCGCCGC----------------------------------------------------------------------------------
droKik1 scf7180000302592:198990-199102 - ACG-------------------------------------------------GTTCCGGTAACTGTTG---TTGTTGTTGTTGTTGCCGCTTCAGCTGCCAGATGCCATGGCCCAAAGTGTCGCATT---------ACTGAAAGT----------GCGAC-------------------------------------------------------------------------AGTCACAGCGAATGCAAG---------------------------GG-----CACT----
droBia1 scf7180000301754:4770757-4770830 - GATACA-----------------------------------TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATACATAGATACATAGATACACAGATACATAGATACATAGA---TACATAGATGCATAGA-----TACATAGA
droSec2 scaffold_15:1293691-1293726 - TGCT------------------------------------------------GCTGCTGTTTTTGCTG---CTGCTGTTGTTGTTGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droMoj3
AAAGCGGC-------GCAAGATCAAGAGCAATTGCCGGAGTCA-GCTTTACGGTTCCTGTTTGTGTTG---TTGCTGCTGTTGTTGAG-CT--CAACGCCGCATTTAATACGCCAACTCGTTGCACTTCATTCATTATTAACAGCAACAGCAACAGCTGCAACT----------------------------GCGCTGCCAGCGTCAATGCGAAATATTGACATATTGACGGATATTTAAGCGAATGACTGAATGTGTGAGGCGAACTTAGATTGGCGGAGATATTTTATAGASizeHit CountTotal NormTotalM046
Female-body		V041
Embryo		V049
Head		V056
Head		M060
Embryo		V110
Male-body
.............................................................................................................................................CAGCAACAGCAACAGCTGCAA...................................................................................................................................2130.331000001
droVir3
AAACGGGC-------GCAGGATCAGCAGCAATTGCCGATGCCA-GCTTTGCTGT------TG-----TCCATTGTTGTTGTTGTTGAG-GT--CAGCGCCGCATTTAATACGCCAACTCGTTGCAGTT-GTTCATTATTAACAGCGACAGC------TGCAACT----------------TCGATGCCGACGTCGACGCCGGCGCCGACGCCAAATGTCGCCATATTGACAGTCATTAAAGCGAATAAATG------------------------------------------SizeHit CountTotal NormTotalM027
Male-body		M028
Head		M047
Female-body		M061
Embryo		SRR060654
Ovary		SRR060655
Testis		SRR060656
Ovary		SRR060657
Testis		SRR060658
Ovary		SRR060659
Testis		SRR060660
Ovary		SRR060661
Embryo		SRR060662
Embryo		SRR060663
Embryo		SRR060664
Male-body		SRR060665
Female-body		SRR060666
Male-body		SRR060667
Female-body		SRR060668
Male-body		SRR060669
Female-body		SRR060670
Testis		SRR060671
Male-body		SRR060672
Female-body		SRR060673
Ovary		SRR060674
Ovary		SRR060675
Ovary		SRR060676
Ovary		SRR060677
Ovary		SRR060678
Testis		SRR060679
Testis		SRR060680
Testis		SRR060681
Testis		SRR060682
Embryo		SRR060683
Testis		SRR060684
Embryo		SRR060685
Embryo		SRR060686
Embryo		SRR060687
Embryo		SRR060688
Ovary		SRR060689
Testis		SRR1106712
embryo_0-2h		SRR1106713
embryo_0-2h		SRR1106714
embryo_2-4h		SRR1106715
embryo_4-6h		SRR1106716
embryo_4-6h		SRR1106717
embryo_6-8h		SRR1106718
embryo_6-8h		SRR1106719
embryo_8-10h		SRR1106720
embryo_8-10h		SRR1106721
embryo_10-12h		SRR1106722
embryo_10-12h		SRR1106723
embryo_12-14h		SRR1106724
embryo_12-14h		SRR1106725
embryo_14-16h		SRR1106726
embryo_14-16h		SRR1106727
larvae		SRR1106728
larvae		SRR1106729
mixed whole adult body		SRR1106730
embryo_16-30h		V047
Embryo		V053
Head		V116
Male-body		GSM1528803
follicle cells
No Reads
droGri2
AGATCAGCAGCAGCAGCAGCAGCAGCAGCAATTGACATTGCCAGGCTTTACTTT------TA-----T---TTGCTGTTGTTGTTGAG-GT--CAGCTTCGCATTTAATACGCCAACTCGTTGCAGCTCATTCATTATTAACAGGCACAGC------TGCAGC-AGTTGCAATGTTGACGTCGACCCCGACCCCGACACCGACACCGACGCCCAACGTTGCCATATTGACAGTTATTAAAGCGATTGAATGAATGAATGA---------------------------------SizeHit CountTotal NormTotalM041
Female-body		V109
Male-body
...........AGCAGCAGCAGCAGCAGCAA......................................................................................................................................................................................................................................................................20200.05110
droWil2
GTTACT----------------------------------------------G------TTGCTGTTG---TTGCTGTTGTTGTCGCT-CT--------TGTG-TTGTTGCTGCTGCTTATTACACATTGCCCACCATTGGTAGTGGCAGC------GGC-------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM020
Head		M045
Female-body		V117
Male-body		V118
Embryo		V119
Head
No Reads
dp5
AACAGC----------------------------------------------A------ACAGCAACA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAACAGCAGCAACAACG-----------------------------------------------------------------------------------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
..................................................................CA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAACAGCAGCAACAAC....................................................................................28110.0910100000000
................................................................................................................................................................AGCA----------------------------ACAACAGCAGCAACAAC....................................................................................21200.0510100000000
.............................................................AGCAACA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAAC................................................................................................21200.0510100000000
...............................................................CAACA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAACAGCA............................................................................................23200.0510100000000
...........................................................................................................................................................ACAGCAGCA----------------------------ACAACAGCAGCAAC.......................................................................................23200.0510001000000
.................................................................ACA---------------------------------------------------------------------------------------ACAGCAGCA----------------------------ACAACAGC.............................................................................................20200.0510100000000
droPer2
CGCACC-----------------------------------CA-GCTTTTAATTTTGCGTCTGTTTCG---CTGCCGTCGTCGTCGCT-CT---------------------------------------------------------------------------------------------------------------CACCGCCGC----------------------------------------------------------------------------------SizeHit CountTotal NormTotalM021
Embryo		M042
Female-body		V042
Embryo		V050
Head		V057
Head		V111
Male-body
No Reads
droKik1
ACG-------------------------------------------------GTTCCGGTAACTGTTG---TTGTTGTTGTTGTTGCCGCTTCAGCTGCCAGATGCCATGGCCCAAAGTGTCGCATT---------ACTGAAAGT----------GCGAC-------------------------------------------------------------------------AGTCACAGCGAATGCAAG---------------------------GG-----CACT----SizeHit CountTotal NormTotal
No Reads
droBia1
GATACA-----------------------------------TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATACATAGATACATAGATACACAGATACATAGATACATAGA---TACATAGATGCATAGA-----TACATAGASizeHit CountTotal NormTotal
No Reads
droSec2
TGCT------------------------------------------------GCTGCTGTTTTTGCTG---CTGCTGTTGTTGTTGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalM054
Female-body		V113
Male-body		V114
Embryo		V115
Head
No Reads

Generated: 05/17/2015 at 10:33 PM