FB2014_04, released July 21st, 2014
 
 

FB2014_04 Release Notes

show General FlyBase FB2014_04 Statistics
Number of references in FlyBase
208772
Number of research papers
91917
Number of personal communications to FlyBase
5763
Number of fly stocks
125541
Number of fly images
1258
Drosophila workers registered with FlyBase
2985
showDrosophila melanogaster (R6.01)
Statistics
Gene records
31701
Genes located to the genome
17262
Genes not located to the genome
14439
Alleles
167328
Alleles of located genes
148922
Alleles of unlocated genes
18406
Aberrations
20222
Deficiencies
8624
Deficiencies with mapped endpoints
2154
Transposable element insertions
149979
Insertions mapped to the sequence
65454
Annotation Release 6.01
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
31
Merged Gene Models
2 → 1
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17262
5685
396036
31
-32
Protein coding genes
13954
6722
396036
117
-1
Protein coding transcripts
30277
2868
71382
108
-29
5' untranslated regions
28354
195
3845
1
0
3' untranslated regions
21303
498
18494
1
-5
Exons (protein coding)
77571
537
28074
1
-5
Introns (protein coding)
58471
1656
189627
23
-2
Unique polypeptides
21955
690
22949
11
0
rRNA genes
142
414
6026
123
-19
rRNA
142
414
6026
123
-19
tRNA genes
314
75
186
61
0
tRNA
314
73
87
61
0
snRNA genes
31
164
444
71
0
snRNA
31
164
444
71
0
snoRNA genes
288
118
316
46
0
snoRNA
288
118
316
46
0
miRNA genes
238
94
215
54
0
miRNA
304
22
29
20
0
Long non-coding RNA genes
2085
1903
239347
31
-11
Long non-coding RNAs
2455
955
21216
31
-7
Long non-coding RNA exons
3634
607
21216
6
NA
Long non-coding RNA introns
1336
1979
110624
42
NA
Pseudogenes
209
1035
12415
53
-1
Transposable elements present in the sequenced strain
5579
1504
66001
6
-25
Annotated repeat regions
9450
Mapped Nucleotide Changes
Annotated Gene Features
Count
Change
total mapped nucleotide changes
12744
-5
aberration junction
6646
-3
complex substitution
80
1
deletion
819
1
insertion site
48
0
point mutation
4913
-4
sequence variant
216
0
TE target site duplication
0
0
uncharacterized change in nucleotide sequence
22
0
Mapped Regulatory Elements
Annotated Gene Features
Count
Change
total mapped regulatory elements
206464
-61
enhancer
103
0
poly A site
98
0
protein binding site
1404
0
regulatory region
2065
0
rescue fragment
688
0
origin of replication
8062
-7
silencer
537
0
insulator
7686
0
transcription factor binding site
185821
-54
Mapped Reagent Features
Annotated Gene Features
Count
Change
transposable element insertion site
65455
-1
microarray amplicons
14095
0
BAC
967
-6
dsRNA amplicons (in vitro)
68086
0
dsRNA amplicons (in vivo)
40960
0
reporter constructs
7176
1
oligonucleotide
668582
2
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster cDNA inserts
splign
22303
-1
D. melanogaster EST
sim4,splign
723462
-808
Other melanogaster DNA sequences
splign
5100
-8569
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast
CONTRAST
14218
-1
BATZ Contrast NA
CONTRAST
13585
-4
CONGO exons
CONGO
40543
-1
DGIL snap
SNAP
19630
-10
DGIL snap homology
SNAP
22936
-13
NCBI gnomon
GNOMON
19719
-10
RGUI geneid
GENEID 1.2
12385
-4
RGUI geneid u12
GENEID 1.2
12716
-1
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster proteins
Prosplign
52175
-24085
Other proteins
Prosplign
492304
-81
Translated Nucleotide Alignments
Annotated Gene Features
Algorithm
 
 
Insect ESTs
WU-tblastx 2.0
 
 
A. gambiae genomic
WU-tblastx 2.0
 
 
D. pseudoobscura genomic
WU-tblastx 2.0
 
 
hide Release 6 Sequence Assembly

Date updated: 11-SEP-2014

TABLE 1: Overview of the BDGP D. melanogaster Release 6 D. melanogaster Genome Assembly.

Current Release
Dmel_Release_6
Data Provider
Collaborators: DHGP, BCM-HGSC, Celera Genomics
Sequenced Strain
iso-1
52 known mutations (see Table 5 below)
3 known duplications that may be polymorphic (see Table 6 below)
Flies available:
Bloomington: 2057
DGRC-Kyoto: 106641
BAC clones available:
CHORI BPRC
Date Released
21-JUL-2014 (FlyBase, nuclear genome assembly)
25-JUL-2014 (GenBank, RefSeq)
NCBI Accessions
Release 6 plus MT
Assembly: GCA_000001215.3*
RefSeq: GCF_000001215.3*
BioProject: PRJNA13812
Assembly Statistics
  • Total sequence length = 143,726,002 bp.
  • Total gap length = 1,152,978 bp.
  • Total number of scaffolds = 1,870.
  • Seven chromosome arms (plus mitochondrial genome*): X, 2L, 2R, 3L, 3R, 4 and Y.
  • The vast majority of sequence, 137.6 Mbp, resides on the seven chromsome arms.
  • 1,862 “unlocalized” minor scaffolds are included, of which 884 have been mapped cytologically or genetically to a chromosome: X, 2CEN, 3CEN, Y, XY and rRNA.**
Major Changes Relative to Release 5
  • Release 6 is 4.2 Mbp (4,240,621 bp) larger.
  • Total gap length decreased by 1.5 Mbp.
  • The majority of new sequence (13.5 Mbp) has been added to the heterochromatic regions of the chromosome arm scaffolds, 10.0 Mbp of which derives from the BDGP Release 5 scaffolds XHet, 2LHet, 2RHet, 3LHet, 3RHet and U.
  • The chromosome Y scaffold is vastly improved and ten times larger at 3.1 Mbp.
  • Most gaps are in the heterochromatic regions of the assembly.
  • 1,862 minor scaffolds replace Release 5 concatenated pseudoscaffolds (e.g., U).
  • 48 minor scaffolds have been modified from Release 5; their names indicate their mapping (e.g. 2Cen_mapped_Scaffold_10_D1684). The remaining 1,814 “unmodified” minor scaffolds have numeric identifiers like 2110000...
  • All fragmented gene annotations from Release 5 have been resolved, largely as a result of improvements to the Y and 3R scaffolds.

* The assembly update in Dmel R6.01 (FB2014_04) is for the nuclear genome only and includes the old mitochondrial genome (GCA_000001215.3/GCF_000001215.3). The new iso-1 reference mitochondrial genome (GCA_000001215.4/GCF_000001215.4) will become the reference in the next FlyBase public update (FB2014_06).

** He et al., 2012.

TABLE 2: Detailed Information on the BDGP Release_6 Assembly

Chromosome Arm Scaffolds
Scaffold
Length (bp)
Sized
Gaps
Total Gap
Size (bp)
Unsized
Gaps
GenBank
Accession
Comparison to Release 5*
X
23,542,271
4
65,520
6
AE014298.5
  • Net gain of 0.9 Mb compared to r5 X plus XHet: most at scaffold's end.
  • Central 15.4 Mb of X sequence unchanged: r5:X:4,684,794..20,073,489 maps to r6:X:4,790,761..20,179,456.
  • About 103.6 kb of new sequence added at scaffold's start (14.1 kb from r5 scaffold U).
  • 1 Mb of new sequence added near scaffold end, including 208.9 kb and 204.1 kb from r5 scaffolds U and XHet, respectively.
2L
23,513,712
0
0
2
AE014134.6
  • Net gain of 133.3 kb compared to r5 2L plus 2LHet: all at scaffold's end.
  • Initial 21.5 Mb of 2L scaffold unchanged: r5:2L:1..21,485,538 maps to r6:2L:1..21,485,538.
  • New sequence at the end includes 293.3 kb and 40.2 kb from r5 scaffolds 2LHet and U, respectively.
2R
25,286,936
1
6,600
7
AE013599.5
  • Net gain of 0.9 Mb compared to r5 2R plus 2RHet: most at scaffold's start.
  • Central 16.7 Mb of 2R sequence unchanged: r5:2R:3,036..16,668,212 maps to r6:2R:4,115,531..20,780,707.
  • New sequence at the start includes 2.3 Mb and 987.3 kb from r5 scaffolds 2RHet and U, respectively.
3L
28,110,227
4
117,660
5
AE014296.5
  • Net gain of 1.0 Mb compared to r5 3L plus 3L Het: all at scaffold's end.
  • Initial 24.5 Mb of 3L sequence unchanged, except an unsized gap is now sized at 7kb: r5:3L:1..24,523,740 maps to r6:3L:1..24,530,640.
  • New sequence at the end includes 2.3 Mb, 328.2 kb and 150.2 kb from r5 scaffolds 3LHet, 2RHet and U, respectively.
3R
32,079,331
9
22,772
18
AE014297.3
  • Net gain of 1.7 Mb compared to r5 3R plus 3RHet: all at scaffold's start.
  • Last 27.9 Mb of 3R sequence unchanged: r5:3R:1..27,905,053 maps to r6:3R:4,174,278..32,079,331.
  • New sequence at the end includes 2.2 Mb and 1.0 Mb from r5 scaffolds 3RHet and U, respectively.
4
1,348,131
1
17,000
0
AE014135.4
  • Net loss of 3.7 kb compared to r5 scaffold 4.
  • Replacement of r5 scaffold start: 24.1 kb of sequence removed (some moved to r6 3R, X and Y) and replaced with 3.4 kb from the r5 scaffold U.
  • Change in start of r6 scaffold 4 completes the JYalpha gene annotation.
  • The remaining sequence is unchanged, but the unsized gap in r5 is now sized at 17kb.
Y Chromosome Scaffold
Scaffold
Length (bp)
Sized
Gaps
Total Gap
Size (bp)
Unsized
Gaps
GenBank
Accession
Comparison to Release 5*
Y
3,667,352
61
242,633
150
CP007106.1
  • Net gain of 3.3 Mb compared to r5 YHet: over a ten-fold increase.
  • 232.3 kb carried over from r5 scaffold YHet.
  • New sequence includes 702.5 kb and 84.2 kb from r5 scaffolds U and 3LHet, respectively.
Mitochondrial Scaffold
Scaffold
Length (bp)
Sized
Gaps
Total Gap
Size (bp)
Unsized
Gaps
GenBank
Accession
Comparison to Release 5*
M
19,517
0
0
0
U37541.1
  • Not changed this release (see footnotes in Table 1).
Minor Scaffold Groups (full list of individual minor scaffolds)**
Unordered
Scaffold Group
Number of
Scaffolds
Total Size
(bp)
Total Gap
Size (bp)
Unsized
Gaps
Comments*
X
446
1,005,345
72,915
0
2CEN
28
222,873
60,073
1
  • Chromosome 2 centromere.
3CEN
144
729,966
41,429
10
  • Chromosome 3 centromere.
Y
199
860,223
63,081
24
XY
66
209,541
806
1
rDNA
1
76,973
16,500
0
  • GenBank Accession CP007120.1.
unmapped
978
3,053,597
402,989
11
  • Net loss of 7.0 Mb, compared to r5 pseudoscaffold U, due to movement of sequences to chromosome arms or to mapped scaffold groups.
  • Now represented by separate scaffolds instead of a concatenated pseudoscaffold.

* The movement of sequence from Release 5 to Release 6 scaffolds was deduced from a review of the FlyBase r5-r6 liftover table, which was derived from NCBI mapping information.

** Scaffolds in the X, 2CEN, 3CEN, Y, XY and rDNA groups were mapped cytologically or genetically to a chromosome, as described in He et al., 2012.

TABLE 3: Known Gaps in the Chromosome Arm Scaffolds of the BDGP Release 6 Assembly*

  Scaffold GenBank
Accession
Gap Gap Type Comments
  X AE014298.5 X:21,907,216..21,907,315 unsized  
  X AE014298.5 X:22,260,555..22,260,654 unsized  
  X AE014298.5 X:22,281,173..22,281,192 sized  
  X AE014298.5 X:22,282,924..22,314,923 sized  
  X AE014298.5 X:22,317,805..22,349,804 sized  
  X AE014298.5 X:22,354,229..22,354,328 unsized  
  X AE014298.5 X:23,020,992..23,021,091 unsized  
  X AE014298.5 X:23,321,166..23,321,265 unsized  
  X AE014298.5 X:23,356,568..23,358,067 sized  
  X AE014298.5 X:23,473,919..23,474,018 unsized  
  2L AE014134.6 2L:21,485,539..21,485,638 unsized Histone gene cluster. **
  2L AE014134.6 2L:22,420,242..22,420,341 unsized  
  2R AE013599.5 2R:4,369..4,468 unsized  
  2R AE013599.5 2R:24,427..24,526 unsized  
  2R AE013599.5 2R:416,885..422,884 sized  
  2R AE013599.5 2R:748,932..749,031 unsized  
  2R AE013599.5 2R:1,472,351..1,472,450 unsized  
  2R AE013599.5 2R:1,826,184..1,826,283 unsized  
  2R AE013599.5 2R:3,759,568..3,759,667 unsized  
  2R AE013599.5 2R:20,780,708..20,780,807 unsized  
  3L AE014296.5 3L:5,107,767..5,114,766 sized Estimated to be 7 kb by optical mapping.
  3L AE014296.5 3L:24,592,985..24,593,084 unsized  
  3L AE014296.5 3L:24,637,106..24,637,205 unsized  
  3L AE014296.5 3L:26,400,915..26,401,014 unsized  
  3L AE014296.5 3L:26,404,000..26,406,999 sized  
  3L AE014296.5 3L:26,882,322..26,936,121 sized  
  3L AE014296.5 3L:26,952,526..27,006,385 sized  
  3L AE014296.5 3L:27,015,780..27,015,879 unsized  
  3L AE014296.5 3L:27,549,161..27,549,260 unsized  
  3R AE014297.3 3R:27,271..27,370 unsized  
  3R AE014297.3 3R:30,825..30,924 unsized  
  3R AE014297.3 3R:44,500..50,290 sized  
  3R AE014297.3 3R:52,605..52,704 unsized  
  3R AE014297.3 3R:122,626..122,725 unsized  
  3R AE014297.3 3R:168,640..168,739 unsized  
  3R AE014297.3 3R:169,034..172,514 sized  
  3R AE014297.3 3R:189,146..189,245 unsized  
  3R AE014297.3 3R:268,539..268,638 unsized  
  3R AE014297.3 3R:304,890..304,989 unsized  
  3R AE014297.3 3R:1,461,766..1,461,865 unsized  
  3R AE014297.3 3R:2,409,542..2,409,641 unsized  
  3R AE014297.3 3R:2,446,427..2,446,526 unsized  
  3R AE014297.3 3R:2,488,684..2,488,783 unsized  
  3R AE014297.3 3R:2,492,821..2,494,720 sized  
  3R AE014297.3 3R:2,498,073..2,499,972 sized  
  3R AE014297.3 3R:2,515,633..2,516,632 sized  
  3R AE014297.3 3R:2,519,339..2,520,338 sized  
  3R AE014297.3 3R:2,522,592..2,522,691 unsized  
  3R AE014297.3 3R:2,527,792..2,530,091 sized  
  3R AE014297.3 3R:2,536,032..2,539,431 sized  
  3R AE014297.3 3R:2,543,863..2,543,962 unsized  
  3R AE014297.3 3R:3,033,775..3,033,874 unsized  
  3R AE014297.3 3R:3,169,915..3,170,014 unsized  
  3R AE014297.3 3R:4,009,645..4,011,644 sized  
  3R AE014297.3 3R:4,012,025..4,012,124 unsized  
  3R AE014297.3 3R:4,174,179..4,174,278 unsized  
  4 AE014135.4 4:1,200,663..1,217,662 sized Estimated to be 17 kb by optical mapping.

* Unsized gaps are represented in the genome assembly sequence by a run of 100 Ns.

** About 20 copies of the approximately 100 copies of the 5 kb histone repeat unit are present in the release 6 AE014134.6 scaffold.

TABLE 4: Location of Heterochromatin in the Major Chromosome Arm Scaffolds of BDGP Release 6

  Scaffold GenBank
Accession
Boundary between Euchromatin and Heterochromatin* BACs
  X AE014298.5 22,628,490 BACR08A09
  2L AE014134.6 22,000,975 BACR10I13
  2R AE013599.5 5,398,184 BACR02D22
  3L AE014296.5 22,962,476 BACR17M18
  3R AE014297.3 4,552,934 BACR15E02

* The euchromatin-heterochromatin boundaries indicated were defined by FISH of mitotic chromosomes from third instar larval neuroblasts using BAC-derived probes, as compared to standard DNA banding patterns defined for mitotic chromosomes (bands h1-h61). Boundaries correspond to the distal end of the indicated BAC, and heterochromatin is provisionally defined as sequence that is proximal to these boundaries (i.e., closer to the centromere). Note that the transition from euchromatin to heterochromatin is gradual, and the resolution of this cytological mapping is about 100 kb. For more information, see Figure 8 and Table 1 of Hoskins et al., 2002.

TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence.*

  Gene Symbol Gene ID Annotation ID Information About Mutation
  alpha4GT2 FBgn0039378 CG5878 Mutation in sequenced strain: insertion of transposable element.
  attC FBgn0041579 CG4740 Mutation in sequenced strain; 8bp deletion in first exon.
  bw FBgn0000241 CG17632 Known mutation in sequenced strain: complex mutation pattern resulting in premature stop.
  Cby FBgn0067317 CG13415 Mutation in sequenced strain: small deletion, premature stop (FBrf0218054).
  CG11891 FBgn0039309 CG11891 Mutation in sequenced strain: complex.
  CG14088 FBgn0036858 CG14088 Mutation in sequenced strain: frameshift.
  CG14499 FBgn0034317 CG14499 Mutation in sequenced strain: frameshift.
  CG17267 FBgn0038821 CG17267 Mutation in sequenced strain: frameshift.
  CG18787 FBgn0042125 CG18787 Mutation in sequenced strain: premature stop. Within a tandem duplication; copy of CG18789.
  CG2528 FBgn0032969 CG2528 Mutation in sequenced strain: insertion of transposon.
  CG31013 FBgn0051013 CG31013 Mutation in sequenced strain: premature stop.
  CG33282 FBgn0053282 CG33282 Mutation in sequenced strain: premature stop in exon 3.
  CG33301 FBgn0053301 CG33301 Mutation in sequenced strain: premature stop.
  CG33346 FBgn0053346 CG33346 Mutation in sequenced strain: premature stop.
  CG33511 FBgn0053511 CG33511 Mutation in sequenced strain: nonsense mutation at aa 362.
  CG33632 FBgn0053632 CG33632 Mutation in sequenced strain: A-to-T mutation at 2R:12,522,216 results in premature stop codon.
  CG33964 FBgn0053964 CG33964 Mutation in sequenced strain: indel; functional allele represented by GM20958.
  CG3894 FBgn0035059 CG3894 Mutation in sequenced strain: insertion of transposon.
  CG42335 FBgn0259237 CG42335 Mutation in sequenced strain: insertion of transposon; frameshift.
  CG42364 FBgn0259710 CG42364 Mutation in sequenced strain: single nucleotide substitution destroys start codon.
  CG42566 FBgn0260768 CG42566 Mutation in sequenced strain: -2 frameshift at 2R:22,662,946.
  CG43092 FBgn0262538 CG43092 Mutation in sequenced strain: 23-bp indel that results in a frameshift and a premature stop.
  CG7448 FBgn0037143 CG7448 Mutation in sequenced strain: 22 bp deletion in exon 5 leading to a frameshift.
  CG7963 FBgn0037584 CG7963 Mutation in sequenced strain: deletion and downstream frameshift.
  CG8642 FBgn0033312 CG8642 Mutation in sequenced strain: -2 frameshift at amino acid 78/79.
  CG9812 FBgn0034860 CG9812 Mutation in sequenced strain: mutation of cytosine residue to adenine at 2R:23,413,037 resulting in premature stop.
  CHKov1 FBgn0045761 CG10618 Mutation in strain: the sequenced strain carries an insertion allele segregating in wild-type strains (insertion of Doc element, CHKov1Doc1420).
  cn FBgn0000337 CG1555 Known mutation in sequenced strain: deletion of 3' end.
  Cyp6a14 FBgn0033302 CG8687 Mutation in sequenced strain: -2 frameshift at amino acid 74.
  Cyp6a16 FBgn0031726 CG7249 Mutation in sequenced strain: indel resulting in frameshift.
  Cyp6a20 FBgn0033980 CG10245 Mutation in sequenced strain: frameshift in exon 1.
  Cyp6a9 FBgn0013771 CG10246 Mutation in sequenced strain: G to A transition in start codon.
  FucTC FBgn0044872 CG40305 Mutation in sequenced strain: frameshift in exon 1.
  Gr22b FBgn0045500 CG31931 Mutation in sequenced strain; premature stop.
  Gr22d FBgn0045498 CG31930 Mutation in sequenced strain; frameshift mutation.
  GstD5 FBgn0010041 CG12242 Mutation in sequenced strain: premature stop: full length CDS sequence can be obtained from FBrf0058802.
  Ir10a FBgn0083979 CG34143 Mutation in sequenced strain: 29-bp deletion in exon 2.
  Ir60e FBgn0035019 CG13592 Mutation in sequenced strain; premature stop.
  Ir67a FBgn0036010 CG12525 Mutation in sequenced strain; premature stop.
  lectin-28C FBgn0040099 CG7106 Mutation in sequenced strain: indel within coding region.
  LysC FBgn0004426 CG9111 Mutation in sequenced strain; premature stop.
  MstProx FBgn0015770 CG1149 Mutation in sequenced strain; premature stop.
  MtnD FBgn0053192 CG33192 Mutation in sequenced strain; premature stop.
  nbs FBgn0261530 CG6754 Mutation/variant in sequenced strain; G to A mutation in 2nd intron splice donor relative to other Dmel strains. Alternative downstream splice donor may be used.
  Or85e FBgn0026399 CG9700 Mutation in sequenced strain; truncated at 3' end (FBrf0168007).
  Or98b FBgn0039582 CG1867 Mutation in sequenced strain; frameshift mutation and premature stop.
  Rh6 FBgn0019940 CG5192 Mutation in sequenced strain, Rh61.
  Rx FBgn0020617 CG10052 Mutation in sequenced strain: single base deletion in first exon (2R:20,917,096) resulting in frameshift.
  sdk FBgn0021764 CG5227 Sequence error at position X:730,319 (inserted T) leads to premature translation stop in fifth exon. Will be corrected in future release.
  sp FBgn0003466 unidentified Known from strain genotype.
  Ugt86Dd FBgn0040256 CG6633 Mutation in sequenced strain: frameshift after amino acid residue 47 (exon 1).
  y FBgn0004034 CG3757 Known mutation in sequenced strain.

* The iso-1 reference strain was known to have the genotype y1; bw1, cn1, sp1. Additional disruptive mutations have been discovered during FlyBase gene model annotation.

TABLE 6: Known Large Tandem Duplications in the iso-1 Reference Sequence.*

Duplication Size
Affected Scaffold
Structure of Variation
Comments
32.4 kb
2L: AE014134.6
  • Repeat 1: 2L:15,654,568..15,686,758
  • Repeat 2: 2L:15,688,165..15,721,755
  • Repeat 1 is sequence identical to Repeat 2, except that 1,400 bp of Repeat 1 (2L:15,657,273..15,658,672) is tandemly duplicated in Repeat 2 (2L:15,690,870..15,692,269 and 2L:15,692,270..15,693,669).

  • Bracketed by sequence-identical Hobo elements:
    H{}377: 2L:15,653,162..15,654,567 [-]
    H{}380: 2L:15,686,759..15,688,164 [-]
    H{}382: 2L:15,721,756..15,723,161 [-]
26.7 kb
3L: AE014296.5
  • Repeat 1: 3L:19,713,242..19,739,963
  • Repeat 2: 3L:19,744,658..19,771,377
  • Repeat 1 and Repeat 2 are sequence identical at 26,720 of 26,722 bp.

  • Bracketed by Doc elements:
    Doc{}1052: 3L:19,708,521..19,713,241
    unannotated: 3L:19,739,964..19,744,657
    Doc{}1053: 3L:19,771,346..19,776,073
  • Trpml (Repeat 1) and
    CG42638 (Repeat 2) are identical.

  • CG42529 (Repeat 1) and
    ms(3)76Ca (Repeat 2) are identical.

  • CG42637 (Repeat 1) and
    Gyc76C (Repeat 2) are identical throughout the CDS, 3' UTR and portions of the 5' UTR..
994 bp
3L: AE014296.5
  • Repeat 1: 3L:1,245,256..1,246,249
  • Repeat 2: 3L:1,246,250..1,247,243
  • Repeat 1 and Repeat 2 are sequence identical.
  • Duplication of this region results in the chimeric annotation CG32318, which combines 3' Psf1 and 5' Klp61F sequences.

* These tandem duplications may be polymorphic in the iso-1 reference strain.

TABLE 7: Annotation Changes Directly Resulting from the Release 5 to Release 6 Migration.

  Name (R5.57) ID (R5.57) Annotation
(R5.57)
R5-to-R6
Scaffold Change
Comment
  CR41604 FBgn0085814 CR41604 Deleted in Dmel R6.01.
  CR41608 FBgn0085818 CR41608 Deleted in Dmel R6.01.
  CR40546 FBgn0085742 CR40546 Deleted in Dmel R6.01.
  CR40572 FBgn0085747 CR40572 Deleted in Dmel R6.01.
  CR40597 FBgn0085754 CR40597 Deleted in Dmel R6.01.
  CR40508 FBgn0085740 CR40508 Deleted in Dmel R6.01.
  CR40507 FBgn0085739 CR40507 Deleted in Dmel R6.01.
  CR41539 FBgn0085796 CR41539 Deleted in Dmel R6.01.
  CR41617 FBgn0085823 CR41617 Deleted in Dmel R6.01.
  CR40574 FBgn0085749 CR40574 Deleted in Dmel R6.01.
  CR40528 FBgn0085741 CR40528 Deleted in Dmel R6.01.
  CR41618 FBgn0085824 CR41618 Deleted in Dmel R6.01.
  CR40728 FBgn0085769 CR40728 Deleted in Dmel R6.01.
  CR40734 FBgn0085770 CR40734 Deleted in Dmel R6.01.
  CR40565 FBgn0085745 CR40565 Deleted in Dmel R6.01.
  CR40779 FBgn0085774 CR40779 Deleted in Dmel R6.01.
  CR40581 FBgn0085750 CR40581 Deleted in Dmel R6.01.
  CR41540 FBgn0085797 CR41540 Deleted in Dmel R6.01.
  CR40560 FBgn0085743 CR40560 Deleted in Dmel R6.01.
  CR41605 FBgn0085815 CR41605 Deleted in Dmel R6.01.
  Su(Ste):CR42405 FBgn0259836 CR42405 Deleted in Dmel R6.01.
  Su(Ste):CR42413 FBgn0259844 CR42413 Deleted in Dmel R6.01.
  Su(Ste):CR42423 FBgn0259854 CR42423 Deleted in Dmel R6.01.
  Su(Ste):CR42434 FBgn0259865 CR42434 Deleted in Dmel R6.01.
  Su(Ste):CR42435 FBgn0259866 CR42435 Deleted in Dmel R6.01.
  Su(Ste):CR42436 FBgn0259867 CR42436 Deleted in Dmel R6.01.
  Su(Ste):CR42437 FBgn0259868 CR42437 Deleted in Dmel R6.01.
  Su(Ste):CR42440 FBgn0259871 CR42440 Deleted in Dmel R6.01.
  Su(Ste):CR42441 FBgn0259872 CR42441 Deleted in Dmel R6.01.
  Su(Ste):CR42442 FBgn0259873 CR42442 Deleted in Dmel R6.01.
  Su(Ste):CR42443 FBgn0259874 CR42443 Deleted in Dmel R6.01.
  CG30271 FBgn0050271 CG30271 CDS changed in Dmel R6.01.
  CG40801 FBgn0085520 CG40801 U to Y CDS changed in Dmel R6.01.
  CG40813 FBgn0085521 CG40813 U to X CDS changed in Dmel R6.01.
  kl-2 FBgn0001313 CG17866 YHet to Y CDS changed in Dmel R6.01.
  Ory FBgn0046323 CG40446 YHet to Y CDS changed in Dmel R6.01.
  Parp FBgn0010247 CG40411 3RHet to 3R CDS changed in Dmel R6.01.
  Pp1-Y2 FBgn0046698 CG40448 YHet to Y CDS changed in Dmel R6.01.
  Sdic3 FBgn0052823 CG32823 CDS changed in Dmel R6.01.
  Sdic4 FBgn0053499 CG33499 CDS changed in Dmel R6.01.
  uex FBgn0262124 CG42595 2RHet to 2R CDS changed in Dmel R6.01.
  CG43176 FBgn0262795 CG43176 U to Y CDS changed in Dmel R6.01; converted to pseudogene CR43176 in Dmel R6.02.
  Pp1-Y1 FBgn0261399 CG41534 U to Y CDS changed in Dmel R6.01; no longer fragmented.
  JYalpha FBgn0040037 CG17923 U to Y CDS changed in Dmel R6.01; CG17923 merged with CG40625 into new annotation CG45760 (JYalpha) in Dmel R6.01.
  CG42644 FBgn0261404 CG42644 U to 2R CG42644 merged into new annotation CG45781 in Dmel R6.02; no longer fragmented.
  CG40378 FBgn0058378 CG40378 U to 2R CG40378 merged into new annotation CG45781 in Dmel R6.02; no longer fragmented.
  CG43676 FBgn0263759 CG43676 U to 2R CG43676 merged into new annotation CG45781 in Dmel R6.02; no longer fragmented.
  CG41343 FBgn0085625 CG41343 3LHet to 3L CG41343 merged into new annotation CG45782 in Dmel R6.02; no longer fragmented.
  CG41087 FBgn0069947 CG41087 U to 3L CG41087 merged into new annotation CG45782 in Dmel R6.02; no longer fragmented.
  CG40467 FBgn0069977 CG40467 3LHet to 3L CG40467 merged into new annotation CG45782 in Dmel R6.02; no longer fragmented.
  CG42617 FBgn0261280 CG42617 3RHet to 3R CG42617 merged into new annotation CG45783 in Dmel R6.02; no longer fragmented.
  CG40249 FBgn0058249 CG40249 U to 3R CG40249 merged into new annotation CG45783 in Dmel R6.02; no longer fragmented.
  CG40188 FBgn0058188 CG40188 U to 3R CG40188 merged into new annotation CG45783 in Dmel R6.02; no longer fragmented.
  CG42618 FBgn0261281 CG42618 3RHet to 3R CG42618 merged into new annotation CG45783 in Dmel R6.02; no longer fragmented.
  CG41056 FBgn0058232 CG41056 3RHet to 3R CG41056 merged into new annotation CG45783 in Dmel R6.02; no longer fragmented.
  CG15831 FBgn0040034 CG15831 3RHet to 3R CDS changed in Dmel R6.01; CG15831 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG40155 FBgn0058155 CG40155 3RHet to 3R CG40155 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG40204 FBgn0058204 CG40204 U to 3R CG40204 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG41281 FBgn0085597 CG41281 3RHet to 3R CG41281 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG41518 FBgn0085663 CG41518 U to 3R CG41518 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG41527 FBgn0085670 CG41527 U to 3R CG41527 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG42621 FBgn0261336 CG42621 3RHet to 3R CG42621 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG42622 FBgn0261337 CG42622 U to 3R CG42622 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG42623 FBgn0261338 CG42623 U to 3R CG42623 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG42624 FBgn0261339 CG42624 3RHet to 3R CG42624 merged into new annotation CG45784 in Dmel R6.02; no longer fragmented.
  CG40992 FBgn0085550 CG40992 U to Y CG40992 merged into new annotation CG45785 (kl-3) in Dmel R6.02; no longer fragmented.
  CG40936 FBgn0085539 CG40936 U to Y CG40936 merged into new annotation CG45785 (kl-3) in Dmel R6.02; no longer fragmented.
  kl-3 FBgn0001314 CG17629 YHet to Y CDS changed in Dmel R6.01; CG17629 merged into new annotation CG45785 (kl-3) in Dmel R6.02; no longer fragmented.
  kl-5 FBgn0001315 CG40444 YHet to Y CDS changed in Dmel R6.01; CG40444 merged into new annotation CG45786 (kl-5) in Dmel R6.02; no longer fragmented.
  CG41497 FBgn0085658 CG41497 U to Y CDS changed in Dmel R6.01; CG41497 merged into new annotation CG45786 (kl-5) in Dmel R6.02; no longer fragmented.
  CG41367 FBgn0085633 CG41367 U to Y CG41367 merged into new annotation CG45787 (PRY) in Dmel R6.02; no longer fragmented.
  CG42619 FBgn0261334 CG42619 U to Y CG42619 merged into new annotation CG45787 (PRY) in Dmel R6.02; no longer fragmented.
  CG40930 FBgn0085538 CG40930 U to Y CG40930 merged into new annotation CG45787 (PRY) in Dmel R6.02; no longer fragmented.
  CG40245 FBgn0058245 CG40245 U to Y CG40245 merged into new annotation CG45799 (WDY) in Dmel R6.02; no longer fragmented.
  CG40583 FBgn0085498 CG40583 U to Y CG40583 merged into new annotation CG45799 (WDY) in Dmel R6.02; no longer fragmented.
  CG40551 FBgn0085496 CG40551 U to Y CG40551 merged into new annotation CG45799 (WDY) in Dmel R6.02; no longer fragmented.
  CG41020 FBgn0085556 CG41020 U to Y CDS changed in Dmel R6.01; CG41020 merged into new annotation CG45799 (WDY) in Dmel R6.02; no longer fragmented.
  CG42620 FBgn0261335 CG42620 U to Y CG42620 merged into new annotation CG45930 (Ccy) in Dmel R6.02; no longer fragmented.
  CG40948 FBgn0085541 CG40948 U to Y CG40948 merged into new annotation CG45930 (Ccy) in Dmel R6.02; no longer fragmented.
  CG40968 FBgn0085546 CG40968 U to Y CG40968 merged into new annotation CG45930 (Ccy) in Dmel R6.02; no longer fragmented.
showDrosophila ananassae (R1.3)
Statistics
Gene records
16542
Genes located to the genome
15978
Genes not located to the genome
564
Alleles
599
Alleles of located genes
174
Alleles of unlocated genes
425
Aberrations
161
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
21
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15978
4029
1176744
49
0
Protein coding genes
15069
4266
1176744
102
0
Protein coding transcripts
15070
1471
26718
102
0
Exons
57154
389
13661
2
0
Introns
41345
1026
1034096
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14954
491
8905
33
0
rRNA genes
135
154
2010
76
0
rRNA
135
154
2010
76
0
tRNA genes
307
75
195
71
0
tRNA
307
74
94
71
0
snRNA genes
29
166
262
98
0
snRNA
29
166
262
98
0
snoRNA genes
194
112
219
49
0
snoRNA
194
112
219
49
0
miRNA genes
76
84
117
57
0
miRNA
82
22
35
19
0
Miscellaneous non-coding RNA genes
3
289
297
276
0
Miscellaneous non-coding RNA
3
289
297
276
0
Pseudogenes
165
72
75
67
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
18891
0
BREN N-Scan
N-Scan
20227
0
DGIL snap
SNAP
41918
0
DGIL snap homology
SNAP
41007
0
EISE exonerate
EXONERATE
33504
0
EISE genemapper
GENE MAPPER
32718
0
EISE genewise
Genewise
20081
0
GLEANR consensus
GLEANR
22551
0
NCBI gnomon
GNOMON
23784
0
OXFD exonerate
EXONERATE
12920
0
PACH genemapper
GENE MAPPER
17892
0
RGUI geneid
GENEID 1.2
30348
0
RGUI geneid u12
GENEID 1.2
30800
0
showDrosophila erecta (R1.3)
Statistics
Gene records
16214
Gene records
16213
Gene records
16214
Genes located to the genome
15810
Genes located to the genome
15810
Genes located to the genome
15810
Genes not located to the genome
404
Genes not located to the genome
403
Genes not located to the genome
404
Alleles
2
Alleles
2
Alleles
2
Alleles of located genes
0
Alleles of located genes
0
Alleles of located genes
0
Aberrations
0
Aberrations
0
Aberrations
0
Deficiencies
0
Deficiencies
0
Deficiencies
0
Deficiencies with mapped endpoints
0
Deficiencies with mapped endpoints
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Transposable element insertions
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
1
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15810
3553
1170937
30
-1
Protein coding genes
15044
3728
1170937
66
-1
Protein coding transcripts
15048
1455
26613
66
-1
Exons
56655
388
13790
1
-1
Introns
40986
835
1121756
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14868
488
8870
21
-1
rRNA genes
104
213
3518
30
0
rRNA
104
213
3518
30
0
tRNA genes
284
76
189
66
0
tRNA
284
74
86
70
0
snRNA genes
38
153
274
47
0
snRNA
38
153
274
47
0
snoRNA genes
252
111
316
45
0
snoRNA
252
111
316
45
0
miRNA genes
81
84
127
63
0
miRNA
88
22
29
20
0
Miscellaneous non-coding RNA genes
5
1178
3727
275
0
Miscellaneous non-coding RNA
5
1178
3727
275
0
Pseudogenes
2
72
73
72
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14863
0
BREN N-Scan
N-Scan
16723
0
DGIL snap
SNAP
25198
0
DGIL snap homology
SNAP
24654
0
EISE exonerate
EXONERATE
33587
0
EISE genemapper
GENE MAPPER
28987
0
EISE genewise
Genewise
43127
0
GLEANR consensus
GLEANR
16880
0
NCBI gnomon
GNOMON
18662
0
OXFD exonerate
EXONERATE
13568
0
PACH genemapper
GENE MAPPER
19020
0
RGUI geneid
GENEID 1.2
18654
0
RGUI geneid u12
GENEID 1.2
18866
0
showDrosophila grimshawi (R1.3)
Statistics
Gene records
15907
Genes located to the genome
15585
Genes not located to the genome
322
Alleles
6
Alleles of located genes
5
Alleles of unlocated genes
1
Aberrations
1
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15585
3993
238808
46
0
Protein coding genes
14982
4150
238808
117
0
Protein coding transcripts
14986
1488
26535
117
0
Exons
56795
393
13188
1
0
Introns
41370
965
216011
1
0
5' untranslated regions
1
2
2
2
1
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14741
500
8844
38
0
rRNA genes
70
132
180
97
0
rRNA
70
132
180
97
0
tRNA genes
260
76
191
71
0
tRNA
260
73
86
71
0
snRNA genes
32
155
266
98
0
snRNA
32
155
266
98
0
snoRNA genes
154
110
244
46
0
snoRNA
154
110
244
46
0
miRNA genes
82
83
126
63
0
miRNA
88
22
29
20
0
Miscellaneous non-coding RNA genes
4
308
348
293
0
Miscellaneous non-coding RNA
4
308
348
293
0
Pseudogenes
1
75
75
75
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14003
0
BREN N-Scan
N-Scan
17378
0
DGIL snap
SNAP
34975
0
DGIL snap homology
SNAP
34420
0
EISE exonerate
EXONERATE
34389
0
EISE genemapper
GENE MAPPER
32724
0
EISE genewise
Genewise
19258
0
GLEANR consensus
GLEANR
16901
0
NCBI gnomon
GNOMON
17922
0
OXFD exonerate
EXONERATE
11052
0
PACH genemapper
GENE MAPPER
16572
0
RGUI geneid
GENEID 1.2
29516
0
RGUI geneid u12
GENEID 1.2
30148
0
showDrosophila mojavensis (R1.3)
Statistics
Gene records
15570
Genes located to the genome
15179
Genes not located to the genome
391
Alleles
44
Alleles of located genes
36
Alleles of unlocated genes
8
Aberrations
10
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15179
4262
299059
60
0
Protein coding genes
14594
4429
299059
105
0
Protein coding transcripts
14595
1482
26781
105
0
Exons
55195
392
14595
2
0
Introns
40199
1075
245033
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14512
494
8926
34
0
rRNA genes
75
149
1990
103
0
rRNA
75
149
1990
103
0
tRNA genes
264
75
194
71
0
tRNA
264
73
86
71
0
snRNA genes
30
158
264
98
0
snRNA
30
158
264
98
0
snoRNA genes
139
116
273
60
0
snoRNA
139
116
273
60
0
miRNA genes
71
84
127
62
0
miRNA
78
22
29
20
0
Miscellaneous non-coding RNA genes
3
303
323
294
0
Miscellaneous non-coding RNA
3
303
323
294
0
Pseudogenes
3
78
91
72
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14779
0
BREN N-Scan
N-Scan
18863
0
DGIL snap
SNAP
34235
0
DGIL snap homology
SNAP
39387
0
EISE exonerate
EXONERATE
33573
0
EISE genemapper
GENE MAPPER
31926
0
EISE genewise
Genewise
41625
0
GLEANR consensus
GLEANR
17738
0
NCBI gnomon
GNOMON
17950
0
OXFD exonerate
EXONERATE
10902
0
PACH genemapper
GENE MAPPER
16684
0
RGUI geneid
GENEID 1.2
19994
0
RGUI geneid u12
GENEID 1.2
20482
0
showDrosophila persimilis (R1.3)
Statistics
Gene records
18137
Genes located to the genome
17573
Genes not located to the genome
564
Alleles
37
Alleles of located genes
8
Alleles of unlocated genes
29
Aberrations
32
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
1
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17573
3484
231798
45
-1
Protein coding genes
16874
3624
231798
72
-1
Protein coding transcripts
16878
1284
24363
72
-1
Exons
59145
367
9522
1
-1
Introns
41743
949
160788
1
0
5' untranslated regions
2
1
2
1
2
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
16741
429
8120
23
-1
rRNA genes
85
260
3969
103
0
rRNA
85
260
3969
103
0
tRNA genes
305
75
195
71
0
tRNA
305
74
93
71
0
snRNA genes
31
160
313
97
0
snRNA
31
160
313
97
0
snoRNA genes
199
110
277
45
0
snoRNA
199
110
277
45
0
miRNA genes
75
85
110
62
0
miRNA
81
22
29
20
0
Miscellaneous non-coding RNA genes
3
304
322
296
0
Miscellaneous non-coding RNA
3
304
322
296
0
Pseudogenes
1
75
75
75
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
18611
0
BREN N-Scan
N-Scan
19699
0
DGIL snap
SNAP
38209
0
DGIL snap homology
SNAP
36086
0
EISE exonerate
EXONERATE
35069
0
EISE genemapper
GENE MAPPER
32760
0
EISE genewise
Genewise
25594
0
GLEANR consensus
GLEANR
23029
0
NCBI gnomon
GNOMON
24696
0
OXFD exonerate
EXONERATE
11924
0
PACH genemapper
GENE MAPPER
17011
0
RGUI geneid
GENEID 1.2
28798
0
RGUI geneid u12
GENEID 1.2
28613
0
showDrosophila pseudoobscura pseudoobscura (R3.2)
Statistics
Gene records
19938
Genes located to the genome
16756
Genes not located to the genome
3182
Alleles
328
Alleles of located genes
70
Alleles of unlocated genes
258
Aberrations
61
Deficiencies
1
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 3.2
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
1
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16756
3467
204842
26
0
Protein coding genes
15864
3647
204842
36
0
Protein coding transcripts
16857
1532
55449
36
0
Exons
58514
408
16920
2
0
Introns
42391
873
167882
1
0
5' untranslated regions
1028
128
2871
1
0
3' untranslated regions
907
254
2005
1
0
Unique polypeptides
16740
502
18482
11
0
rRNA genes
56
151
1823
90
0
rRNA
56
151
1823
90
0
tRNA genes
294
75
195
71
0
tRNA
294
74
93
71
0
snRNA genes
31
159
311
85
0
snRNA
31
159
311
85
0
snoRNA genes
203
110
277
26
0
snoRNA
203
111
277
45
0
miRNA genes
232
98
120
62
0
miRNA
336
22
29
20
-1
Miscellaneous non-coding RNA genes
4
674
1905
174
0
Miscellaneous non-coding RNA
4
457
1038
174
0
Pseudogenes
72
2108
68089
75
0
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
D. pseudoobscura cDNA inserts
splign
11
0
D. pseudoobscura ESTs
splign
24851
0
Other insect cDNAs/mRNAs
splign
98521
191
Aligned Drosophila annotations
splign
274816
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
16158
0
BREN N-Scan
N-Scan
17088
0
DGIL snap
SNAP
23678
0
DGIL snap homology
SNAP
21676
0
EISE exonerate
EXONERATE
34828
0
EISE genemapper
GENE MAPPER
32857
0
EISE genewise
Genewise
42938
0
GLEANR consensus
GLEANR
17328
0
Genewise
Genewise
17878
-4
Genscan
Genscan 1.0
16822
-7
NCBI gnomon
GNOMON
19259
0
OXFD exonerate
EXONERATE
11690
0
PACH genemapper
GENE MAPPER
17265
0
RGUI geneid
GENEID 1.2
19060
0
RGUI geneid u12
GENEID 1.2
18970
0
Twinscan
Twinscan
18078
-4
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
Other proteins
Prosplign
587617
49997
D. pseudoobscura proteins
Prosplign
15745
830
showDrosophila sechellia (R1.3)
Statistics
Gene records
17943
Genes located to the genome
17273
Genes not located to the genome
670
Alleles
13
Alleles of located genes
4
Alleles of unlocated genes
9
Aberrations
1
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17273
3172
215256
27
0
Protein coding genes
16467
3321
215256
27
0
Protein coding transcripts
16471
1305
43656
27
0
Exons
58765
367
11004
1
0
Introns
41665
799
173070
1
0
5' untranslated regions
2
1
1
1
2
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
16125
440
14551
8
0
rRNA genes
139
235
1997
30
0
rRNA
139
235
1997
30
0
tRNA genes
299
75
189
70
-9
tRNA
299
74
86
70
-9
snRNA genes
30
156
273
98
0
snRNA
30
156
273
98
0
snoRNA genes
242
112
315
46
0
snoRNA
242
112
315
46
0
miRNA genes
78
84
127
63
0
miRNA
85
22
29
20
0
Miscellaneous non-coding RNA genes
5
1178
3707
277
0
Miscellaneous non-coding RNA
5
1178
3707
277
0
Pseudogenes
13
74
75
71
9
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
15887
0
BREN N-Scan
N-Scan
18367
0
DGIL snap
SNAP
36782
0
DGIL snap homology
SNAP
31358
0
EISE exonerate
EXONERATE
34854
0
EISE genemapper
GENE MAPPER
28216
0
EISE genewise
Genewise
25095
0
GLEANR consensus
GLEANR
21332
0
NCBI gnomon
GNOMON
25689
0
OXFD exonerate
EXONERATE
14423
0
PACH genemapper
GENE MAPPER
18928
0
RGUI geneid
GENEID 1.2
29159
0
RGUI geneid u12
GENEID 1.2
29186
0
showDrosophila simulans (R1.4)
Statistics
Gene records
17627
Genes located to the genome
16169
Genes not located to the genome
1458
Alleles
428
Alleles of located genes
201
Alleles of unlocated genes
227
Aberrations
33
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
7
Annotation Release 1.4
Summary of changes from previous release
New Gene Models
65
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16169
3221
179058
30
65
Protein coding genes
15413
3373
179058
54
0
Protein coding transcripts
15415
1234
25239
54
0
Exons
53314
356
7825
1
-636
Introns
37899
869
168520
1
-72
5' untranslated regions
4
1
2
1
1
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15346
411
8412
17
0
rRNA genes
72
158
180
30
0
rRNA
72
158
180
30
0
tRNA genes
266
75
189
58
0
tRNA
266
73
86
59
0
snRNA genes
32
156
273
97
0
snRNA
32
156
273
97
0
snoRNA genes
246
111
315
46
0
snoRNA
246
111
315
46
0
miRNA genes
135
93
127
63
65
miRNA
185
22
29
20
110
Miscellaneous non-coding RNA genes
3
1426
3706
277
0
Miscellaneous non-coding RNA
3
1426
3706
277
0
Pseudogenes
2
73
74
73
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
15530
0
BREN N-Scan
N-Scan
18989
0
DGIL snap
SNAP
28265
0
DGIL snap homology
SNAP
24623
0
EISE exonerate
EXONERATE
35213
0
EISE genemapper
GENE MAPPER
27790
0
EISE genewise
Genewise
27426
0
GLEANR consensus
GLEANR
17049
0
NCBI gnomon
GNOMON
19856
0
OXFD exonerate
EXONERATE
12420
0
PACH genemapper
GENE MAPPER
18260
0
RGUI geneid
GENEID 1.2
13797
0
RGUI geneid u12
GENEID 1.2
14128
0
showDrosophila virilis (R1.2)
Statistics
Gene records
16041
Genes located to the genome
15343
Genes not located to the genome
698
Alleles
572
Alleles of located genes
112
Alleles of unlocated genes
460
Aberrations
83
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
5
Annotation Release 1.2
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15343
4220
565985
49
0
Protein coding genes
14491
4461
565985
93
0
Protein coding transcripts
14491
1500
40500
93
0
Exons
55557
393
23577
1
0
Introns
40386
1071
535952
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14382
501
13499
30
0
rRNA genes
299
189
1995
49
0
rRNA
299
189
1995
49
0
tRNA genes
277
76
191
71
0
tRNA
277
73
86
71
0
snRNA genes
31
158
261
98
0
snRNA
31
158
261
98
0
snoRNA genes
165
113
282
57
0
snoRNA
165
113
282
57
0
miRNA genes
74
84
126
58
0
miRNA
81
22
29
20
0
Miscellaneous non-coding RNA genes
4
303
330
294
0
Miscellaneous non-coding RNA
4
303
330
294
0
Pseudogenes
2
87
89
85
0
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
Other insect cDNAs/mRNAs
splign
29348
171
Aligned Drosophila annotations
splign
318968
0
D. virilis ESTs
splign
21383
0
D. virilis cDNA inserts
splign
0
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14476
0
BREN N-Scan
N-Scan
18350
0
DGIL snap
SNAP
35378
0
DGIL snap homology
SNAP
35285
0
EISE exonerate
EXONERATE
33940
0
EISE genemapper
GENE MAPPER
32430
0
EISE genewise
Genewise
19550
0
GLEANR consensus
GLEANR
17679
0
NCBI gnomon
GNOMON
18636
0
OXFD exonerate
EXONERATE
11117
0
PACH genemapper
GENE MAPPER
16744
0
RGUI geneid
GENEID 1.2
26095
0
RGUI geneid u12
GENEID 1.2
27145
0
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
Other proteins
Prosplign
464023
51657
D. virilis proteins
Prosplign
14697
0
showDrosophila willistoni (R1.3)
Statistics
Gene records
16938
Genes located to the genome
16385
Genes not located to the genome
553
Alleles
203
Alleles of located genes
6
Alleles of unlocated genes
197
Aberrations
57
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16385
4318
683577
30
0
Protein coding genes
15512
4555
683577
90
0
Protein coding transcripts
15513
1462
27624
90
0
Exons
57093
399
21318
2
0
Introns
40896
1203
682464
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15434
488
9207
29
0
rRNA genes
80
308
1987
30
0
rRNA
80
308
1987
30
0
tRNA genes
296
76
191
62
0
tRNA
296
73
84
62
0
snRNA genes
37
160
363
97
0
snRNA
37
160
363
97
0
snoRNA genes
216
119
209
57
0
snoRNA
216
119
209
57
0
miRNA genes
77
85
138
63
0
miRNA
83
22
29
20
0
Miscellaneous non-coding RNA genes
3
314
346
298
0
Miscellaneous non-coding RNA
3
314
346
298
0
Pseudogenes
164
72
79
65
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
12928
0
BREN N-Scan
N-Scan
16784
0
DGIL snap
SNAP
53474
0
DGIL snap homology
SNAP
50296
0
EISE exonerate
EXONERATE
34660
0
EISE genemapper
GENE MAPPER
32996
0
EISE genewise
Genewise
19279
0
GLEANR consensus
GLEANR
20211
0
NCBI gnomon
GNOMON
24902
0
OXFD exonerate
EXONERATE
10778
0
PACH genemapper
GENE MAPPER
16855
0
RGUI geneid
GENEID 1.2
25184
0
RGUI geneid u12
GENEID 1.2
27260
0
showDrosophila yakuba (R1.3)
Statistics
Gene records
17524
Genes located to the genome
16891
Genes not located to the genome
633
Alleles
7
Alleles of located genes
4
Alleles of unlocated genes
3
Aberrations
0
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16891
3422
252576
39
0
Protein coding genes
16077
3590
252576
39
0
Protein coding transcripts
16082
1408
26793
39
0
Exons
59388
382
13188
2
0
Introns
42642
824
161037
1
0
5' untranslated regions
1
1
1
1
1
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15940
471
8930
12
0
rRNA genes
57
242
3981
91
0
rRNA
57
242
3981
91
0
tRNA genes
328
75
191
71
-46
tRNA
328
74
86
71
-46
snRNA genes
37
158
276
98
0
snRNA
37
158
276
98
0
snoRNA genes
255
110
316
45
0
snoRNA
255
110
316
45
0
miRNA genes
80
85
127
63
0
miRNA
87
22
29
20
0
Miscellaneous non-coding RNA genes
5
1169
3705
275
0
Miscellaneous non-coding RNA
5
1169
3705
275
0
Pseudogenes
52
72
76
62
46
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
16923
0
BREN N-Scan
N-Scan
19482
0
DGIL snap
SNAP
32761
0
DGIL snap homology
SNAP
32029
0
EISE exonerate
EXONERATE
34716
0
EISE genemapper
GENE MAPPER
29982
0
EISE genewise
Genewise
20916
0
GLEANR consensus
GLEANR
18816
0
NCBI gnomon
GNOMON
20302
0
OXFD exonerate
EXONERATE
14290
0
PACH genemapper
GENE MAPPER
18907
0
RGUI geneid
GENEID 1.2
15647
0
RGUI geneid u12
GENEID 1.2
16037
0