FB2016_04, released July 28, 2016
 
 

A Database of Drosophila Genes & Genomes

FB2016_04 Release Notes

hide General FlyBase FB2016_04 Statistics
Number of references in FlyBase
215813
Number of research papers
97371
Number of personal communications to FlyBase
6228
Number of fly stocks
142428
Number of fly images
1258
Drosophila workers registered with FlyBase
3213

hideDrosophila melanogaster (R6.12)
Statistics
Gene records
32076
Genes located to the genome
17728
Genes not located to the genome
14348
Alleles
179515
Alleles of located genes
161547
Alleles of unlocated genes
17968
Aberrations
20665
Deficiencies
8762
Deficiencies with mapped endpoints
2400
Transposable element insertions
170592
Insertions mapped to the sequence
69039
Annotation Release 6.12
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
hide Annotated Gene Models
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17728
5747
1965857
30
0
Protein coding genes
13907
6951
1965857
162
0
Protein coding transcripts
30443
2880
71382
152
3
5' untranslated regions
28444
196
5416
1
2
3' untranslated regions
21440
503
18494
1
0
Exons (protein coding)
77675
539
28074
1
2
Introns (protein coding)
58529
1704
268107
23
0
Unique polypeptides
21955
693
22949
11
2
rRNA genes
147
529
8118
30
0
rRNA
147
547
8118
30
0
tRNA genes
313
75
186
61
0
tRNA
313
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
289
118
316
46
0
miRNA genes
256
92
215
50
0
miRNA
340
22
27
20
0
Long non-coding RNA genes
2470
1911
239347
31
0
Long non-coding RNAs
2914
994
21216
31
0
Long non-coding RNA exons
4228
639
21216
6
0
Long non-coding RNA introns
1499
2142
158159
42
0
Pseudogenes
315
1022
13559
30
0
Transposable elements present in the sequenced strain
5578
1504
66001
6
0
Annotated repeat regions
9450
hide Other Annotated Gene Features
Mapped Nucleotide Changes
Annotated Gene Features
Count
Change
total mapped nucleotide changes
15048
652
aberration junction
7746
568
complex substitution
107
0
deletion
1300
45
insertion site
48
0
point mutation
5609
39
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
261459
-5
enhancer
103
0
poly A site
86
-12
protein binding site
1404
0
regulatory region
2067
0
rescue fragment
757
7
origin of replication
8062
0
silencer
537
0
insulator
7687
0
transcription factor binding site
240756
0
Mapped Reagent Features
Annotated Gene Features
Count
Change
transposable element insertion site
69040
42
microarray amplicons
14095
0
BAC
50389
0
dsRNA amplicons (in vitro)
68437
0
dsRNA amplicons (in vivo)
44364
0
reporter constructs
50578
0
oligonucleotide
686920
0
hide Aligned Evidence Features
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster cDNA inserts
splign
22357
0
D. melanogaster EST
sim4,splign
671275
0
Other melanogaster DNA sequences
sim4tandem,splign
13847
5
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast
CONTRAST
14218
0
BATZ Contrast NA
CONTRAST
13585
0
CONGO exons
CONGO
40543
0
DGIL snap
SNAP
19630
0
DGIL snap homology
SNAP
22936
0
NCBI gnomon
GNOMON
19719
0
RGUI geneid
GENEID 1.2
12385
0
RGUI geneid u12
GENEID 1.2
12716
0
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster proteins
Prosplign
58272
-1
Other proteins
Prosplign
1324294
1293
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
55 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)
Publications
Release 6 reference genome assembly, Hoskins et al., 2015
Migration of FlyBase features to Release 6, dos Santos et al., 2015
NCBI Accessions
Release 6 plus MT
Assembly: GCA_000001215.4*
RefSeq: GCF_000001215.4*
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) was for the nuclear genome only and included the old mitochondrial genome. In update FB2015_01 (Dmel R6.04), the old mitochondrial reference genome assembly was replaced with one from the iso-1 sequenced strain.

** 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
Accessions (GenBank, RefSeq)
Comparison to Release 5*
X
23,542,271
4
65,520
6
AE014298.5, NC_004354.4
  • 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, NT_033779.5
  • 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, NT_033778.4
  • 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, NT_037436.4
  • 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, NT_033777.3
  • 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, NC_004353.4
  • 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
Accessions (GenBank, RefSeq)
Comparison to Release 5*
Y
3,667,352
61
242,633
150
CP007106.1, NC_024512.1
  • 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
Accessions (GenBank, RefSeq)
Comparison to Release 5*
M
19,524
0
0
0
KJ947872.2, NC_024511.2
  • Derived from the iso-1 sequenced strain.
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 Epigenomic border* Cytogenomic border** BAC**
          X 21,368,973 to 22,958,164 22,628,490 BACR08A09
          2L 21,090,000 to 22,170,000 22,000,975 BACR10I13
          2R 5,692,495 to 6,612,495 5,398,184 BACR02D22
          3L 22,256,900 to 23,026,900 22,962,476 BACR17M18
          3R not defined 4,552,934 BACR15E02

        * The locations of sharp transitions in the level of H3K9me2 histone modification were identified in cell lines, embryos, larvae and adult heads by ChIP-chip. The range of transition locations in different samples is shown. In some cases, an H3K9me2-based boundary was not observed. See Table 1 and Figure 3 of Riddle et al., 2011.

        ** 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 transposon; see alpha4GT2[1].
          attC FBgn0041579 CG4740 Mutation in sequenced strain: deletion; 8bp deletion in first exon.
          bw FBgn0000241 CG17632 Known mutation in sequenced strain: complex; multiple in-frame stops.
          Cby FBgn0067317 CG13415 Mutation in sequenced strain: frameshift (-2) (FBrf0218054).
          CG11891 FBgn0039309 CG11891 Mutation in sequenced strain: complex.
          CG14088 FBgn0036858 CG14088 Mutation in sequenced strain: frameshift.
          CG14499 FBgn0034317 CG14499 Mutation in sequenced strain: deletion (-5).
          CG17267 FBgn0038821 CG17267 Mutation in sequenced strain: frameshift.
          CG18787 FBgn0042125 CG18787 Mutation in strain: premature stop (nonsense mutation). Within a tandem duplication; copy of CG18789.
          CG2528 FBgn0032969 CG2528 Mutation in sequenced strain: insertion of transposon; transcription appears to terminate within the roo transposon or transcript is inappropriately spliced.
          CG31013 FBgn0051013 CG31013 Mutation in strain: premature stop (nonsense mutation).
        CG33267 FBgn0053267 CG33267 Mutation in sequenced strain: insertion of transposon.
          CG33282 FBgn0053282 CG33282 Mutation in sequenced strain: premature stop in exon 3.
          CG33301 FBgn0053301 CG33301 Mutation in strain: premature stop (nonsense mutation); see CG33301[R4.3].
          CG33346 FBgn0053346 CG33346 Mutation in strain: premature stop (nonsense mutation).
          CG33511 FBgn0053511 CG33511 Mutation in sequenced strain: nonsense mutation at aa 362.
          CG33632 FBgn0053632 CG33632 Mutation in strain: premature stop (nonsense mutation); see CG33632[R4.2].
          CG33964 FBgn0053964 CG33964 Mutation in sequenced strain: deletion; see CG33964[R4.2]; functional allele represented by GM20958.
          CG3894 FBgn0035059 CG3894 Mutation in sequenced strain: insertion of transposon; many ESTs correspond to an unspliced alternative transcript with readthrough into transposon sequences.
          CG42335 FBgn0259237 CG42335 Mutation in sequenced strain: insertion of transposon; transcription appears to terminate within the mdg1 transposon.
          CG42364 FBgn0259710 CG42364 Mutation in strain: single base change in start codon.
          CG42395 FBgn0259741 CG42395 Mutation in sequenced strain: insertion of transposon.
          CG42566 FBgn0260768 CG42566 Mutation in sequenced strain: frameshift; -2 frameshift at 2R:22,662,946.
          CG43092 FBgn0262538 CG43092 Mutation in sequenced strain: 23-bp deletion.
          CG7963 FBgn0037584 CG7963 Mutation in sequenced strain: complex; multiple indels.
          CG8642 FBgn0033312 CG8642 Mutation in sequenced strain: frameshift; -2 frameshift at amino acid 78/79.
          CG9812 FBgn0034860 CG9812 Mutation in strain: premature stop (nonsense mutation); mutation of cytosine residue to adenine at 2R:23,413,037.
          CHKov1 FBgn0045761 CG10618 Mutation in sequenced strain: insertion of transposon; an insertion allele segregating in wild-type strains; see HKov1[Doc1420].
          cn FBgn0000337 CG1555 Known mutation in sequenced strain: deletion of 3' end; see cn[1].
          Cyp6a14 FBgn0033302 CG8687 Mutation in sequenced strain: -2 frameshift at amino acid 74.
          Cyp6a16 FBgn0031726 CG7249 Mutation in sequenced strain: deletion; 11-bp deletion within coding region.
          Cyp6a20 FBgn0033980 CG10245 Mutation in sequenced strain: frameshift in exon 1.
          Cyp6a9 FBgn0013771 CG10246 Mutation in sequenced strain: single base change in start codon; G to A transition in start codon.
          FucTC FBgn0044872 CG40305 Mutation in sequenced strain: frameshift in exon 1; see FucTC[R4.3].
          Gr22b FBgn0045500 CG31931 Mutation in strain: premature stop (nonsense mutation); see Gr22b[1].
          Gr22d FBgn0045498 CG31930 Mutation in sequenced strain; frameshift mutation; see Gr22d[1].
          GstD5 FBgn0010041 CG12242 Mutation in strain: premature stop (nonsense mutation): full length CDS sequence can be obtained from FBrf0058802; see GstD5[1].
          Ir10a FBgn0083979 CG34143 Mutation in sequenced strain: deletion; 31-bp deletion in exon 2.
          Ir60e FBgn0035019 CG13592 Mutation in strain: premature stop (nonsense mutation).
          Ir67a FBgn0036010 CG12525 Mutation in strain: premature stop (nonsense mutation).
        Ir93a FBgn0259215 CG42315 Mutation in sequenced strain: insertion of transposon.
          lectin-28C FBgn0040099 CG7106 Mutation in sequenced strain: deletion; 28-bp deletion within coding region.
          MstProx FBgn0015770 CG1149 Mutation in strain: premature stop (nonsense mutation); see MstProx[1].
          MtnD FBgn0053192 CG33192 Mutation in strain: premature stop (nonsense mutation); see MtnD[OreR].
          nbs FBgn0261530 CG6754 Mutation in sequenced strain; G to A mutation in 2nd intron splice donor relative to other Dmel species. Alternative downstream splice donor may be used.
          Or85e FBgn0026399 CG9700 Mutation in sequenced strain: deletion; truncated at 3' end (FBrf0168007).
          Or98b FBgn0039582 CG1867 Mutation in sequenced strain: frameshift (-1) in exon 2.
          Rh6 FBgn0019940 CG5192 Mutation in sequenced strain: deletion; see Rh6[1]; 19-bp deletion spans first exon/intron boundary.
          Rx FBgn0020617 CG10052 Mutation in sequenced strain: frameshift; single base deletion in first exon (2R:20,917,096).
          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.
          Sirt6 FBgn0037802 CG6284 Mutation in sequenced strain: insertion of transposon.
          sp FBgn0003466 unidentified Known from strain genotype.
          Tequila FBgn0023479 CG4821 Mutation in sequenced strain: insertion of transposon.
          Ugt86Dd FBgn0040256 CG6633 Mutation in sequenced strain: frameshift after amino acid residue 47 (exon 1).
          y FBgn0004034 CG3757 Known mutation in sequenced strain: single base change in start codon; see y[1]. Compare with GB:X04427.

        * 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 CDS changed in Dmel R6.01; CG17923 merged with CG40625 into new annotation CG45760 (JYalpha) in Dmel R6.01.
          CG40625 FBgn0085503 CG40625 U to 4 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.
        hideDrosophila ananassae (R1.05)
        Statistics
        Gene records
        18520
        Genes located to the genome
        15807
        Genes not located to the genome
        2713
        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 1.05
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        13
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        15807
        6112
        1010801
        49
        -13
        Protein coding genes
        14365
        6511
        1010801
        108
        0
        Protein coding transcripts
        21191
        2529
        58287
        66
        0
        5' untranslated regions
        20482
        158
        4721
        1
        0
        3' untranslated regions
        14382
        252
        5229
        1
        0
        Exons (protein coding)
        68108
        456
        13661
        1
        0
        Introns (protein coding)
        52203
        1608
        170805
        30
        0
        Unique polypeptides
        19344
        671
        18780
        21
        0
        rRNA genes
        122
        160
        2010
        111
        -13
        rRNA
        122
        160
        2010
        111
        -13
        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
        29
        19
        0
        Long non-coding RNA genes
        660
        8394
        371486
        187
        0
        Long non-coding RNA exons
        3294
        306
        10345
        2
        0
        Long non-coding RNA introns
        2514
        1733
        95797
        36
        0
        Pseudogenes
        274
        5213
        73103
        178
        0
        Long non-coding RNA
        988
        1413
        28029
        65
        0
        hide Aligned Evidence Features
        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
        hideDrosophila erecta (R1.05)
        Statistics
        Gene records
        17374
        Genes located to the genome
        14758
        Genes not located to the genome
        2616
        Alleles
        2
        Alleles of located genes
        0
        Aberrations
        0
        Deficiencies
        0
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        0
        Annotation Release 1.05
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        2
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        14758
        5409
        326098
        45
        -2
        Protein coding genes
        13605
        5672
        326098
        111
        0
        Protein coding transcripts
        19592
        2433
        57919
        90
        0
        5' untranslated regions
        18193
        149
        2846
        1
        0
        3' untranslated regions
        12843
        226
        5809
        1
        0
        Exons (protein coding)
        64567
        447
        13188
        1
        0
        Introns (protein coding)
        49322
        1317
        188202
        30
        0
        Unique polypeptides
        18256
        667
        18493
        11
        0
        rRNA genes
        102
        216
        3518
        110
        -2
        rRNA
        102
        216
        3518
        110
        -2
        tRNA genes
        284
        76
        189
        66
        0
        tRNA
        284
        74
        86
        66
        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
        Long non-coding RNA genes
        299
        10760
        121709
        143
        0
        Long non-coding RNA exons
        1393
        246
        7478
        1
        0
        Long non-coding RNA introns
        1073
        2585
        77133
        30
        0
        Pseudogenes
        200
        4446
        61482
        147
        0
        Long non-coding RNA
        383
        1164
        16924
        33
        0
        hide Aligned Evidence Features
        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
        hideDrosophila 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
        hide Annotated Gene Models
        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
        hide Aligned Evidence Features
        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
        hideDrosophila mojavensis (R1.04)
        Statistics
        Gene records
        17197
        Genes located to the genome
        14680
        Genes not located to the genome
        2517
        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 1.04
        Summary of changes from previous release
        New Gene Models
        1626
        Restored Gene Models
        0
        Deleted Gene Models
        2125
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        14680
        6743
        326744
        60
        -499
        Protein coding genes
        13425
        7070
        326744
        69
        -1169
        Protein coding transcripts
        20110
        2387
        49912
        69
        5515
        5' untranslated regions
        19859
        164
        4436
        1
        19859
        3' untranslated regions
        14046
        223
        2907
        1
        14046
        Exons (protein coding)
        67288
        439
        14742
        1
        67288
        Introns (protein coding)
        51781
        1679
        195040
        30
        51781
        Unique polypeptides
        18142
        644
        15766
        23
        3630
        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
        Long non-coding RNA genes
        679
        7520
        195947
        246
        679
        Long non-coding RNAs
        983
        1012
        8904
        99
        983
        Long non-coding RNA exons
        3056
        255
        4366
        3
        3056
        Long non-coding RNA introns
        2240
        2050
        126396
        35
        2240
        Pseudogenes
        165
        8417
        149632
        214
        162
        hide Aligned Evidence Features
        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
        hideDrosophila 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
        hide Annotated Gene Models
        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
        hide Aligned Evidence Features
        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
        hideDrosophila pseudoobscura pseudoobscura (R3.04)
        Statistics
        Gene records
        22458
        Genes located to the genome
        16959
        Genes not located to the genome
        5499
        Alleles
        329
        Alleles of located genes
        71
        Alleles of unlocated genes
        258
        Aberrations
        61
        Deficiencies
        1
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        0
        Annotation Release 3.04
        Summary of changes from previous release
        New Gene Models
        2
        Restored Gene Models
        0
        Deleted Gene Models
        0
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        16959
        5692
        347323
        26
        2
        Protein coding genes
        14574
        6085
        347323
        108
        0
        Protein coding transcripts
        23456
        2619
        59456
        66
        0
        5' untranslated regions
        23435
        196
        4824
        1
        0
        3' untranslated regions
        16119
        295
        6655
        1
        0
        Exons (protein coding)
        71399
        480
        16920
        1
        0
        Introns (protein coding)
        54406
        1437
        174425
        30
        0
        Unique polypeptides
        21107
        660
        18779
        21
        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
        233
        98
        120
        62
        1
        miRNA
        337
        22
        29
        20
        1
        Long non-coding RNA genes
        1660
        7102
        336175
        170
        0
        Long non-coding RNA exons
        7854
        351
        5855
        1
        0
        Long non-coding RNA introns
        5565
        1830
        104169
        30
        0
        Pseudogenes
        273
        7820
        129883
        208
        0
        Long non-coding RNA
        3005
        1311
        11179
        76
        0
        hide Aligned Evidence Features
        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
        98972
        54
        Aligned Drosophila annotations
        splign
        445970
        158669
        Gene Predictions
        Annotated Gene Features
        Algorithm
        Count
        Change
        BATZ Contrast NA
        CONTRAST
        16148
        -10
        BREN N-Scan
        N-Scan
        17081
        -7
        DGIL snap
        SNAP
        23677
        -1
        DGIL snap homology
        SNAP
        21674
        -2
        EISE exonerate
        EXONERATE
        34778
        -50
        EISE genemapper
        GENE MAPPER
        32850
        -7
        EISE genewise
        Genewise
        42899
        -39
        GLEANR consensus
        GLEANR
        17321
        -7
        Genewise
        Genewise
        17878
        0
        Genscan
        Genscan 1.0
        16822
        0
        NCBI gnomon
        GNOMON
        19242
        -17
        OXFD exonerate
        EXONERATE
        11686
        -4
        PACH genemapper
        GENE MAPPER
        17264
        -1
        RGUI geneid
        GENEID 1.2
        18948
        -112
        RGUI geneid u12
        GENEID 1.2
        18860
        -110
        Twinscan
        Twinscan
        18078
        0
        Proteins Aligned
        Annotated Gene Features
        Algorithm
        Count
        Change
        Other proteins
        Prosplign
        1254777
        58223
        D. pseudoobscura proteins
        Prosplign
        23570
        7808
        hideDrosophila 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
        hide Annotated Gene Models
        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
        hide Aligned Evidence Features
        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
        hideDrosophila simulans (R2.02)
        Statistics
        Gene records
        20485
        Genes located to the genome
        16000
        Genes not located to the genome
        4485
        Alleles
        429
        Alleles of located genes
        192
        Alleles of unlocated genes
        237
        Aberrations
        33
        Deficiencies
        0
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        10
        Annotation Release 2.02
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        16
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        16000
        5641
        395700
        30
        -16
        Protein coding genes
        14179
        5974
        395700
        70
        0
        Protein coding transcripts
        24119
        2827
        58688
        70
        0
        5' untranslated regions
        25081
        240
        12550
        1
        0
        3' untranslated regions
        16231
        346
        10146
        1
        0
        Exons (protein coding)
        72161
        496
        18352
        1
        0
        Introns (protein coding)
        55058
        1366
        172145
        30
        0
        Unique polypeptides
        20922
        678
        18668
        11
        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
        245
        111
        315
        46
        0
        snoRNA
        245
        111
        315
        46
        0
        miRNA genes
        119
        92
        127
        63
        -16
        miRNA
        161
        22
        29
        20
        -24
        Long non-coding RNA genes
        1185
        7264
        263401
        157
        0
        Long non-coding RNA exons
        4867
        567
        14055
        1
        0
        Long non-coding RNA introns
        3439
        1825
        115321
        38
        0
        Pseudogenes
        187
        7508
        155275
        114
        0
        Long non-coding RNA
        1675
        2083
        27217
        95
        0
        hide Aligned Evidence Features
        Gene Predictions
        Annotated Gene Features
        Algorithm
        Count
        Change
        BATZ Contrast NA
        CONTRAST
        0
        -15530
        BREN N-Scan
        N-Scan
        0
        -18989
        DGIL snap
        SNAP
        0
        -28265
        DGIL snap homology
        SNAP
        0
        -24623
        EISE exonerate
        EXONERATE
        0
        -35213
        EISE genemapper
        GENE MAPPER
        0
        -27790
        EISE genewise
        Genewise
        0
        -27426
        GLEANR consensus
        GLEANR
        0
        -17049
        NCBI gnomon
        GNOMON
        0
        -19856
        OXFD exonerate
        EXONERATE
        0
        -12420
        PACH genemapper
        GENE MAPPER
        0
        -18260
        RGUI geneid
        GENEID 1.2
        0
        -13797
        RGUI geneid u12
        GENEID 1.2
        0
        -14128
        hideDrosophila virilis (R1.06)
        Statistics
        Gene records
        17674
        Genes located to the genome
        15078
        Genes not located to the genome
        2596
        Alleles
        574
        Alleles of located genes
        107
        Alleles of unlocated genes
        467
        Aberrations
        83
        Deficiencies
        0
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        6
        Annotation Release 1.06
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        7
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        15078
        7048
        410143
        57
        60
        Protein coding genes
        13620
        7536
        410143
        118
        0
        Protein coding transcripts
        20548
        2406
        54868
        54
        0
        5' untranslated regions
        20700
        166
        2671
        1
        0
        3' untranslated regions
        14143
        235
        4090
        1
        0
        Exons (protein coding)
        68491
        445
        15873
        1
        0
        Introns (protein coding)
        52868
        1795
        180607
        30
        0
        Unique polypeptides
        18239
        637
        17765
        17
        0
        rRNA genes
        288
        193
        1995
        110
        0
        rRNA
        288
        193
        1995
        110
        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
        116
        660
        57
        0
        snoRNA
        165
        113
        282
        57
        0
        miRNA genes
        134
        96
        187
        58
        60
        miRNA
        185
        22
        29
        18
        104
        Long non-coding RNA genes
        565
        11025
        308185
        273
        0
        Long non-coding RNAs
        846
        1373
        9108
        125
        0
        Long non-coding RNA exons
        2811
        285
        4133
        1
        0
        Long non-coding RNA introns
        2139
        2575
        188685
        48
        0
        Pseudogenes
        199
        6687
        143960
        188
        0
        hide Aligned Evidence Features
        Nucleotide Alignments
        Annotated Gene Features
        Algorithm
        Count
        Change
        Other insect cDNAs/mRNAs
        splign
        29810
        72
        D. virilis ESTs
        splign
        21383
        0
        D. virilis cDNA inserts
        splign
        0
        0
        Aligned Drosophila annotations
        splign
        445531
        107830
        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
        1080781
        306
        D. virilis proteins
        Prosplign
        13919
        -792
        hideDrosophila willistoni (R1.05)
        Statistics
        Gene records
        18541
        Genes located to the genome
        14857
        Genes not located to the genome
        3684
        Alleles
        207
        Alleles of located genes
        9
        Alleles of unlocated genes
        198
        Aberrations
        57
        Deficiencies
        0
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        0
        Annotation Release 1.05
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        5
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        14857
        4953
        540477
        57
        -5
        Protein coding genes
        13783
        5205
        540477
        88
        0
        Protein coding transcripts
        15182
        1763
        62819
        78
        0
        5' untranslated regions
        9225
        70
        1158
        1
        0
        3' untranslated regions
        7625
        104
        1357
        1
        0
        Exons (protein coding)
        57880
        404
        22491
        2
        0
        Introns (protein coding)
        44152
        1200
        169666
        30
        0
        Unique polypeptides
        14961
        552
        20907
        23
        0
        rRNA genes
        75
        323
        1987
        119
        -5
        rRNA
        75
        323
        1987
        119
        -5
        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
        Long non-coding RNA genes
        107
        5730
        90430
        244
        0
        Long non-coding RNAs
        120
        353
        3098
        47
        0
        Long non-coding RNA exons
        351
        107
        1354
        4
        0
        Long non-coding RNA introns
        240
        2441
        81159
        51
        0
        Pseudogenes
        277
        4679
        132507
        217
        0
        hide Aligned Evidence Features
        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
        hideDrosophila yakuba (R1.05)
        Statistics
        Gene records
        19504
        Genes located to the genome
        16262
        Genes not located to the genome
        3242
        Alleles
        7
        Alleles of located genes
        3
        Alleles of unlocated genes
        4
        Aberrations
        0
        Deficiencies
        0
        Deficiencies with mapped endpoints
        0
        Transposable element insertions
        0
        Annotation Release 1.05
        Summary of changes from previous release
        New Gene Models
        0
        Restored Gene Models
        0
        Deleted Gene Models
        3
        Merged Gene Models
        0
        Split Gene Models
        0
        Complex combinations
        0
        hide Annotated Gene Models
        Annotated Gene Models
        Count
        Avg. size
        Longest
        Shortest
        Change
        Genes
        16262
        5648
        535474
        45
        -3
        Protein coding genes
        14824
        6002
        535474
        89
        0
        Protein coding transcripts
        23304
        2681
        52458
        84
        0
        5' untranslated regions
        23460
        184
        13701
        1
        0
        3' untranslated regions
        16037
        310
        8874
        1
        0
        Exons (protein coding)
        71824
        474
        13753
        1
        0
        Introns (protein coding)
        54540
        1442
        186244
        30
        0
        Unique polypeptides
        20701
        675
        17154
        11
        0
        rRNA genes
        54
        249
        3981
        113
        -3
        rRNA
        54
        249
        3981
        113
        -3
        tRNA genes
        328
        75
        191
        71
        0
        tRNA
        328
        74
        86
        71
        0
        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
        Long non-coding RNA genes
        590
        9396
        282527
        172
        0
        Long non-coding RNA exons
        3016
        340
        13188
        1
        0
        Long non-coding RNA introns
        2356
        1920
        83974
        39
        0
        Pseudogenes
        338
        4041
        99128
        61
        0
        Long non-coding RNA
        820
        1637
        45736
        63
        0
        hide Aligned Evidence Features
        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