FlyBase

General FlyBase FB2024_02 Statistics

Number of references in FlyBase

241488

Number of research papers

117266

Number of personal communications to FlyBase

7782

Number of fly stocks

167405

Number of fly images

1258

FlyBase changes in this release

Annotation Sources

Gene model annotations for D. melanogaster protein-coding and non-protein-coding genes are manually annotated by FlyBase (see FBrf0229216). The miRNA annotations are obtained from miRBase (see FBrf0220601).

FlyBase no longer reflects NCBI annotation or genome assembly updates for non-D. melanogaster fruit fly species. For the status of these gene model annotations, see the NCBI page Eukaryotic genomes annotated at NCBI. The FlyBase archived release FB2017_05 includes the last NCBI annotation update that was imported into FlyBase for these species.

Drosophila melanogaster (R6.57)

Statistics

Gene records

32151

Genes located to the genome

17873

Genes not located to the genome

14278

Alleles

221450

Alleles of located genes

212801

Alleles of unlocated genes

8649

Aberrations

21461

Deficiencies

8770

Deficiencies with mapped endpoints

2501

Transposable element insertions

218531

Insertions mapped to the sequence

72118

Annotation Release 6.57

Summary of changes from previous release

New Gene Models

Restored Gene Models

Deleted Gene Models

Merged Gene Models

Split Gene Models

Complex combinations

Annotated Gene Models

Count

Avg. size

Longest

Shortest

Change

Genes

17873

5753

1965857

Protein coding genes

13986

6956

1965857

162

Protein coding transcripts

30802

2889

71382

152

5' untranslated regions

28571

196

5416

3' untranslated regions

21861

504

18494

Exons (protein coding)

77850

539

28074

-1

Introns (protein coding)

58665

1711

268107

Unique polypeptides

22282

694

22949

rRNA genes

115

463

8118

rRNA

115

463

8118

tRNA genes

312

186

tRNA

312

snRNA genes

168

444

snRNA

168

444

snoRNA genes

269

119

316

snoRNA

270

119

316

miRNA genes

262

174

miRNA

485

Long non-coding RNA genes

2557

1978

239347

Long non-coding RNAs

3060

1093

21216

Long non-coding RNA exons

4450

697

21216

Long non-coding RNA introns

1590

2252

158159

Pseudogenes

339

973

13559

Transposable elements present in the sequenced strain

5896

1573

66001

Annotated repeat regions

9450

Other Annotated Gene Features

Mapped Nucleotide Changes

Annotated Gene Features

Count

Change

total mapped nucleotide changes

25531

226

aberration junction

9957

complex substitution

deletion

5538

insertion site

2745

103

point mutation

6843

sequence variant

TE target site duplication

uncharacterized change in nucleotide sequence

insertion

254

Mapped Regulatory Elements

Annotated Gene Features

Count

Change

total mapped regulatory elements

423708

19664

enhancer

poly A site

106698

protein binding site

1404

regulatory region

58283

19662

rescue fragment

877

origin of replication

8062

silencer

insulator

7684

transcription factor binding site

240700

Mapped Reagent Features

Annotated Gene Features

Count

Change

transposable element insertion site

72118

microarray amplicons

14095

BAC

50389

dsRNA amplicons (in vitro)

68437

dsRNA amplicons (in vivo)

48141

reporter constructs

48793

short guide RNA

16325

150

oligonucleotide

495232

Aligned Evidence Features

Nucleotide Alignments

Annotated Gene Features

Algorithm

Count

Change

D. melanogaster cDNA inserts

splign

22360

D. melanogaster EST

sim4,splign

671275

Other melanogaster DNA sequences

sim4tandem,splign

15768

Gene Predictions

Annotated Gene Features

Algorithm

Count

Change

BATZ Contrast

CONTRAST

14218

BATZ Contrast NA

CONTRAST

13585

CONGO exons

CONGO

40543

DGIL snap

SNAP

19630

DGIL snap homology

SNAP

22936

NCBI gnomon

GNOMON

19719

RGUI geneid

GENEID 1.2

12385

RGUI geneid u12

GENEID 1.2

12716

Proteins Aligned

Annotated Gene Features

Algorithm

Count

Change

D. melanogaster proteins

Prosplign

60247

Other proteins

Prosplign

6571523

96777

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

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	BDGP Collaborators: DHGP, BCM-HGSC, Celera Genomics
Sequenced Strain	iso-1 Flies available: 55 known mutations (see Table 5 below) Bloomington: 2057 DGRC-Kyoto: 106641 3 known duplications that may be polymorphic (see Table 6 below) 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
Additional information	BDGP readme file (in preparation).
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. 471,585 bp from sized gaps in major chromosome scaffolds. 18,800 bp from 188 unsized gaps in major chromosome scaffolds. 662,593 bp from sized and unsized gaps in minor scaffolds. 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 Length of Sized Gaps (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	6,000	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 Length of Sized Gaps (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 Length of Sized Gaps (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	Allele	Information About Mutation
α4GT2	FBgn0039378	CG5878	α4GT2¹	Mutation in sequenced strain: insertion of transposon.
AttC	FBgn0041579	CG4740	AttC^iso-1	Mutation in sequenced strain: deletion; 8bp deletion in first exon.
bw	FBgn0000241	CG17632	bw¹	Known mutation in sequenced strain: complex; multiple in-frame stops.
Cby	FBgn0067317	CG13415	Cby^iso-1	Mutation in sequenced strain: frameshift (-2).
CG2528	FBgn0032969	CG2528	CG2528^iso-1	Mutation in sequenced strain: insertion of transposon; transcription appears to terminate within the roo transposon or transcript is inappropriately spliced.
CG3894	FBgn0035059	CG3894	CG3894^iso-1	Mutation in sequenced strain: insertion of transposon; many ESTs correspond to an unspliced alternative transcript with readthrough into transposon sequences.
CG4892	FBgn0028884	CG4892	CG4892^iso-1	Mutation in sequenced strain: frameshift (-1).
CG7963	FBgn0037584	CG7963	CG7963^iso-1	Mutation in sequenced strain: complex; multiple indels.
CG8642	FBgn0033312	CG8642	CG8642^iso-1	Mutation in sequenced strain: frameshift; -2 frameshift at amino acid 78/79.
CG9812	FBgn0034860	CG9812	CG9812^iso-1	Mutation in strain: premature stop (nonsense mutation); mutation of cytosine residue to adenine at 2R:23,413,037.
CG9897	FBgn0034807	CG9897	CG9897^iso-1	Mutation in sequenced strain: frameshift (+1).
CG11891	FBgn0039309	CG11891	CG11891^iso-1	Mutation in sequenced strain: complex.
CG11951	FBgn0039656	CG11951	CG11951^iso-1	Mutation in sequenced strain: deletion; 251-bp deletion.
CG12224	FBgn0037974	CG12224	CG12224^iso-1	Mutation in sequenced strain: deletion; 7-bp deletion in first exon.
CG13749	FBgn0033353	CG13749	CG13749^iso-1	Mutation in sequenced strain: 10bp deletion in coding sequence.
CG14088	FBgn0036858	CG14088	CG14088^iso-1	Mutation in sequenced strain: frameshift.
CG14499	FBgn0034317	CG14499	CG14499^iso-1	Mutation in sequenced strain: deletion (-5).
CG14907	FBgn0038455	CG14907	CG14907^iso-1	Mutation in sequenced strain: frameshift (-1).
CG17267	FBgn0038821	CG17267	CG17267^iso-1	Mutation in sequenced strain: frameshift.
CG18787	FBgn0042125	CG18787	CG18787^iso-1	Mutation in strain: premature stop (nonsense mutation). Within a tandem duplication; copy of CG18789.
CG31013	FBgn0051013	CG31013	CG31013^iso-1	Mutation in strain: premature stop (nonsense mutation).
CG33267	FBgn0053267	CG33267	CG33267^iso-1	Mutation in sequenced strain: insertion of transposon.
CG33282	FBgn0053282	CG33282	CG33282^iso-1	Mutation in sequenced strain: premature stop in exon 3.
CG33301	FBgn0053301	CG33301	CG33301^iso-1	Mutation in strain: premature stop (nonsense mutation).
CG33346	FBgn0053346	CG33346	CG33346^iso-1	Mutation in strain: premature stop (nonsense mutation).
CG33511	FBgn0053511	CG33511	CG33511^iso-1	Mutation in sequenced strain: nonsense mutation at aa 362.
CG33632	FBgn0053632	CG33632	CG33632^iso-1	Mutation in strain: premature stop (nonsense mutation).
CG33964	FBgn0053964	CG33964	CG33964^iso-1	Mutation in sequenced strain: deletion; functional allele represented by GM20958.
CG34308	FBgn0085337	CG34308	CG34308^iso-1	Mutation in sequenced strain; frameshift (-1).
CG42335	FBgn0259237	CG42335	CG42335^iso-1	Mutation in sequenced strain: insertion of transposon; transcription appears to terminate within the mdg1 transposon.
CG42364	FBgn0259710	CG42364	CG42364^iso-1	Mutation in strain: single base change in start codon.
CG42395	FBgn0259741	CG42395	CG42395^iso-1	Mutation in sequenced strain: insertion of transposon.
CG42566	FBgn0260768	CG42566	CG42566^iso-1	Mutation in sequenced strain: frameshift; -2 frameshift at 2R:22,662,946.
CG43092	FBgn0262538	CG43092	CG43092^iso-1	Mutation in sequenced strain: 23-bp deletion.
CG46042	FBgn0267709	CG46042	CG46042^iso-1	Mutation in sequenced strain: deletion; 26-nt deletion.
CHKov1	FBgn0045761	CG10618	CHKov1^Doc1420	Mutation in sequenced strain: insertion of transposon; an insertion allele segregating in wild-type strains.
cn	FBgn0000337	CG1555	cn¹	Known mutation in sequenced strain: deletion of 3' end.
Cyp6a14	FBgn0033302	CG8687	Cyp6a14^iso-1	Mutation in sequenced strain: -2 frameshift at amino acid 74.
Cyp6a16	FBgn0031726	CG7249	Cyp6a16^iso-1	Mutation in sequenced strain: deletion; 11-bp deletion within coding region.
Cyp6a20	FBgn0033980	CG10245	Cyp6a20^iso-1	Mutation in sequenced strain: frameshift in exon 1.
Cyp6a9	FBgn0013771	CG10246	Cyp6a9^iso-1	Mutation in sequenced strain: single base change in start codon; G to A transition in start codon.
FucTC	FBgn0044872	CG40305	FucTC^iso-1	Mutation in sequenced strain: frameshift in exon 1.
Gr22b	FBgn0045500	CG31931	Gr22b^iso-1	Mutation in strain: premature stop (nonsense mutation).
Gr22d	FBgn0045498	CG31930	Gr22d^iso-1	Mutation in sequenced strain; frameshift mutation.
GstD5	FBgn0010041	CG12242	GstD5^iso-1	Mutation in strain: premature stop (nonsense mutation): full length CDS sequence can be obtained from FBrf0058802.
Ir10a	FBgn0083979	CG34143	Ir10a^iso-1	Mutation in sequenced strain: deletion; 31-bp deletion in exon 2.
Ir60e	FBgn0035019	CG13592	Ir60e^iso-1	Mutation in strain: premature stop (nonsense mutation).
Ir67a	FBgn0036010	CG12525	Ir67a^iso-1	Mutation in strain: premature stop (nonsense mutation).
Ir93a	FBgn0259215	CG42315	Ir93a^iso-1	Mutation in sequenced strain: insertion of transposon.
lectin-28C	FBgn0040099	CG7106	lectin-28C^iso-1	Mutation in sequenced strain: deletion; 28-bp deletion within coding region.
MstProx	FBgn0015770	CG1149	MstProx^iso-1	Mutation in strain: premature stop (nonsense mutation).
MtnD	FBgn0053192	CG33192	MtnD^OreR	Mutation in strain: premature stop (nonsense mutation).
nbs	FBgn0261530	CG6754	nbs^iso-1	Mutation in sequenced strain; G to A mutation in 2nd intron splice donor relative to other Drosophila species. Alternative downstream splice donor may be used.
Or85e	FBgn0026399	CG9700	Or85e^iso-1	Mutation in sequenced strain: deletion; truncated at 3' end.
Or98b	FBgn0039582	CG1867	Or98b^iso-1	Mutation in sequenced strain: frameshift (-1) in exon 2.
OSCP1	FBgn0033685	CG13178	OSCP1^iso-1	Mutation in sequenced strain: premature stop (nonsense mutation).
Rh6	FBgn0019940	CG5192	Rh6¹	Mutation in sequenced strain: deletion; 19-bp deletion spans first exon/intron boundary.
Rx	FBgn0020617	CG10052	Rx^iso-1	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.
Sirt6	FBgn0037802	CG6284	Sirt6^iso-1	Mutation in sequenced strain: insertion of transposon.
speck	FBgn0287831	CG3318	speck¹	Known mutation in sequenced strain: insertion of transposon.
teq	FBgn0023479	CG4821	teq^iso-1	Mutation in sequenced strain: insertion of transposon.
Ugt35C1	FBgn0040256	CG6633	Ugt35C1^iso-1	Mutation in sequenced strain: frameshift after amino acid residue 47 (exon 1).
y	FBgn0004034	CG3757	y¹	Known mutation in sequenced strain: single base change in start codon. 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 [-]	CG18477 (Repeat 1) and CG31780 (Repeat 2) are identical. CG18478 (Repeat 1) and CG31827 (Repeat 2) are identical. CG44141 (Repeat 1) and CG44140 (Repeat 2) are identical. CG43923 (Repeat 1) and CG43924 (Repeat 2) are identical.
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.

Ontology Versions

Ontology

version/date

ChEBI (chemical entities of biological interest)

2024-03-28

DO (human disease ontology)

2024-01-31

FBbi (image ontology)

2005-08-10

FBbt (fly_anatomy)

2024-02-22

FBdv (fly_development)

2019-10-21

FBcv (FlyBase controlled vocabulary)

2023-08-02

FBsv (stock ontology)

2022-09-26

GO (gene ontology)

2024-01-17

PSI-MI (molecular interactions)

2015-08-11

SO (sequence ontology)

2021-11-22