FB2012_01 Release Notes

FB2012_01, released January 20th, 2012
 
show General FlyBase FB2012_01 Statistics
Number of references in FlyBase
200539
Number of research papers
85880
Number of abstracts
37610
Number of personal communications to FlyBase
5269
Number of fly stocks
114779
Number of fly images
981
Drosophila workers registered with FlyBase
5634
showDrosophila melanogaster (R5.43)
Statistics
Gene records
30465
Genes located to the genome
15494
Genes not located to the genome
14971
Alleles
142352
Alleles of located genes
123834
Alleles of unlocated genes
18518
Aberrations
19826
Deficiencies
8344
Deficiencies with mapped endpoints
2099
Transposable element insertions
134709
Insertions mapped to the sequence
60765
Annotation Release 5.43
Summary of changes from previous release
New Gene Models
39
Restored Gene Models
0
Deleted Gene Models
3
Merged Gene Models
16 → 8
Split Gene Models
6 → 14
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15494
5751
395988
31
36
Protein coding genes
13920
6321
395988
117
7
Protein coding transcripts
24500
2674
69439
105
202
Exons
71231
499
27708
1
282
Introns
54584
1868
17650844
23
193
5' untranslated regions
24335
185
3845
1
206
3' untranslated regions
17011
2481
17651548
1
188
Unique polypeptides
19773
647
22971
11
99
rRNA genes
160
500
6026
123
0
rRNA
160
500
6026
123
0
tRNA genes
314
75
186
61
0
tRNA
314
73
87
61
0
snRNA genes
46
113
275
36
0
snRNA
46
115
275
36
0
snoRNA genes
287
118
316
46
0
snoRNA
287
118
316
46
0
miRNA genes
238
95
215
54
0
miRNA
304
22
29
20
0
Miscellaneous non-coding RNA genes
356
2118
92118
31
20
Miscellaneous non-coding RNA
475
1192
15466
31
21
Pseudogenes
172
1112
12115
53
9
Transposable elements present in the sequenced strain
5600
1515
66001
6
0
Annotated repeat regions
10159
Mapped Nucleotide Changes
Annotated Gene Features
Count
Change
total mapped nucleotide changes
10163
120
aberration junction
6386
6
complex substitution
57
2
deletion
320
32
insertion site
48
0
point mutation
3126
80
sequence variant
204
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
204582
6
enhancer
103
0
poly A site
98
0
protein binding site
1397
1
regulatory region
235
0
rescue fragment
582
4
origin of replication
8069
0
silencer
537
0
insulator
7686
1
transcription factor binding site
185875
0
Mapped Reagent Features
Annotated Gene Features
Count
Change
transposable element insertion site
60765
338
microarray amplicons
14095
0
BAC
973
0
dsRNA amplicons (in vitro)
67448
-3482
dsRNA amplicons (in vivo)
30273
0
reporter constructs
7150
0
oligonucleotide
654156
-6964
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster cDNA inserts
sim4tandem,splign
21089
106
D. melanogaster EST
sim4,splign
724270
0
Other melanogaster DNA sequences
sim4tandem,splign
13429
2
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
Augustus prediction
Augustus 1.0
12292
0
BATZ Contrast
CONTRAST
14219
0
BATZ Contrast NA
CONTRAST
13589
0
CONGO exons
CONGO
40544
0
DGIL snap
SNAP
19640
0
DGIL snap homology
SNAP
22949
0
Genie prediction
Genie v2.2/flyGenie
11248
0
Genscan prediction
Genscan 1.0
18909
0
NCBI gnomon
GNOMON
19729
0
RGUI geneid
GENEID 1.2
12389
0
RGUI geneid u12
GENEID 1.2
12717
0
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
D. melanogaster proteins
WU-blastx 2.0, Prosplign
65647
120
Other insect proteins
WU-blastx 2.0
7076
0
Nematode proteins
WU-blastx 2.0
6361
0
Yeast proteins
WU-blastx 2.0
2170
0
Plant proteins
WU-blastx 2.0
8396
0
Rodent proteins
WU-blastx 2.0
14824
0
Primate proteins
WU-blastx 2.0
13691
0
Other invertebrate proteins
WU-blastx 2.0
13070
0
Other vertebrate proteins
WU-blastx 2.0
10443
0
Other proteins
Prosplign
373969
5309
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
 
 

Date updated: 20-FEB-2009

TABLE 1: Overview of the Release_5 Assembly (from BDGP)

Current Release
Release 5
 
Sequencing Center
Primary Center: BDGP
Collaborating Centers: DHGP, BCM-HGSC, Celera
Sequenced Strain
y1; cn1 bw1 sp1
Flies available:
Bloomington: 2057
DGRC-Kyoto: 106641
Tucson: 14021-0231.36
BAC clones available:
CHORI BPRC
Date Released:
Finished Arms
See Table 2 for arm accessions
18-APR-2006
WGS Heterochromatin
AABU01000000
20-NOV-2007

TABLE 2: Detailed Information on the Release_5 Assembly

Scaffold
Length (bp)
Internal Gaps
(see Table 3)
GenBank
Accession
Major Difference Compared to Release 4 (Arm Scaffolds Only)
ArmX
22,422,827
3
AE014298
8kb added to the distal end.
Gaps filled in regions 1-11.
Arm2L
23,011,544
2
AE014134
591kb added to the proximal end of the arm.
Arm2R
21,146,708
1
AE013599
380kb added to the proximal end.
Arm3L
24,543,557
1
AE014296
16kb added on distal end.
718kb added to proximal end.
Other gaps filled
Arm3R
27,905,053
0
AE014297
None.
Arm4
1,351,857
1
AE014135
70kbp added to the distal end.
XHet
204,112
0
CM000460
WGS
YHet
347,038
Draft
CM000461
WGS - Unordered
2LHet
368,872
2
CM000456
WGS
2RHet
3,288,761
Draft
CM000457
WGS - Unordered
3LHet
2,555,491
Draft
CM000458
WGS - Unordered
3RHet
2,517,507
Draft
CM000459
WGS - Unordered
ArmUn
10,049,037
Draft
FA000001
WGS - Unordered

Please note that the terminal portions of the chromosome arms are not complete. The centromeric regions contain many partial and nested repeats and a high percentage of low complexity sequence; this makes assembly of the sequence extremely difficult. The telomeric regions are slightly less difficult, since they are primarily composed of members of several telomere-specific transposon families. The telomeres of XL and 4R are the closest to being completely represented.

TABLE 3: Known Gaps in the Release 5 Major Arms Assembly

Scaffold
GenBank
Accession
Gaps
Notes
Gene Association
ArmX
AE014298
111523..129522
sized
 
ArmX
AE014298
21684450..21684549
unsized
 
ArmX
AE014298
21687344..21759343
sized
 
Arm2L
AE014134
21485539..21485638
unsized
Histone Gene Cluster *
Arm2L
AE014134
22420242..22420341
unsized
 
Arm2R
AE013599
16668213..16668312
unsized
 
Arm3L
AE014296
5107767..5107866
unsized
 
Arm3R
AE014297
None
--
 
Arm4
AE014135
1221289..1221388
unsized
 
* 20 copies of the ca. 100 copies of the 5kb histone repeat unit are present in the Release 5 AE014134 scaffold.

TABLE 4: Distribution of Centric Heterochromatin in Release 5 Scaffolds

Locations of the euchromatin/heterochromatin boundaries on the five major chromosome arm scaffolds has been determined by the DHGP.

Chr. Arm
Major Arm Scaffold GenBank Accessions & Seq. Coordinates
Associated
Heterochromatin Scaffold
Heterochromatin Scaffold GenBank Accessions &
Seq. Coordinates
X
AE014298 : 22030326..22422827
XHet
CM000460 : 1..204112
2L
AE014134 : 22000975..23011544
2LHet
CM000456 : 1..368872
2R
AE013599 : 1..1285689
2RHet
CM000457 : 1..3288761
3L
AE014296 : 22955576..24543557
3LHet
CM000458 : 1..2555491
3R
AE014297 : 1..378656
3RHet
CM000459 : 1..2517507
4
AE014135 : undefined
-
none
Y
none
Y
CM000461 : 1..347038
U*
none
U*
FA000001 : 1..10049037
* Unmapped Scaffolds

The sequenced strain, usually described as the y1; cn1 bw1 sp1 strain, was known to carry mutations in those four genes. During annotation, mutations in other genes have been discovered (Table 5). To allow compilation of a comprehensive proteome, wild-type protein sequences for these genes have been included in sequence entries in FlyBase and GenBank.

TABLE 5: Genes with Known Mutations in the Release 5 Sequence

Gene_Symbol
Gene_ID
Annotation_ID
Information about Mutation
bw
Known from strain genotype
CG9812
Discovered during genome annotation
CG31013
Discovered during genome annotation
CG33282
Discovered during genome annotation
CG33301
Discovered during genome annotation
CG33632
Discovered during genome annotation
CG33964
Discovered during genome annotation
CG34143
Discovered during genome annotation
cn
Known from strain genotype
FucTC
Discovered during genome annotation
LysC
Discovered during genome annotation
MstProx
Discovered during genome annotation
Rh6
Discovered during genome annotation
sdk
Sequencing error in Release 5: Incorrect insertion of a T at position X:587140.
sp
unidentified
Known from strain genotype
Ugt86Dd
Discovered during genome annotation
y
Known from strain genotype

TABLE 6: Known Polymorphisms in the Sequenced Strain

Type of
Polymorphism
Affected Scaffold
Structure of Variation
Comments
35KB Tandem Duplication
2L: AE014134
Repeat 1: 15654568..15686758
Repeat 2: 15688165..15721755
(Repeat 1 and Repeat 2 are sequence Identical)

Bracketed by Sequence-Identical Hobo Elements:
H{}377 = 15653162..15654567 [-]
H{}380 = 15686759..15688164 [-]
H{}382 = 15721756..15723161 [-]
Polymorphic with single copy of this 35KB sequence.

Reference sequence includes tandem duplication.

CG18477 (in Repeat 1) and CG31780 (in Repeat 2) are sequence-identical.

CG18478 (in Repeat 1) and CG31827 (in Repeat 2) are sequence-identical.
31.4KB Tandem Duplication
3L: AE014296
Repeat 1: 19706342..19733063
Repeat 2: 19737758.19764477
(26,720bp identical of 26,722bp)
The Doc elements are omitted.

The tandem duplication occurs between Doc{}1052 (3L:19701621..19706341) and an unannotated Doc element at 3L:19733064..19737758 and is bounded by a third Doc element, Doc{}1053.
Reference sequence includes tandem duplication.

CG42529 and CG14101 are sequence-identical.

trpml is also duplicated, but the second copy is not annotated.

Gyc76C 3' exons duplicated, but deliberately omitted from the annotation.
994bp Tandem Duplication
3L: AE014296
Repeat 1: 1246250..1247243
Repeat 2: 1245256..1246249
(Repeat 1 and Repeat 2 are sequence Identical)
Reference sequence includes tandem duplication.

Duplication upstream of Klf61F, creating chimeric annotation CG32318.
Abbreviations Used:
  • BAC: Bacterial Articifical Chromosome
  • BCM-HGSC: Baylor College of Medicine - Human Genome Sequencing Center
  • BDGP: Berkeley Drosophila Genome Project
  • CHORI BPRC: Childrens Hospital of Oakland Research Institute, BAC PAC Resource Center
  • DGRC-Kyoto: Drosophila Genetic Resource Center (Kyoto, Japan)
  • DHGP: Drosophila Heterochromatin Genome Project
  • WGS: Whole Genome Shotgun sequencing and assembly
showDrosophila ananassae (R1.3)
Statistics
Gene records
16622
Genes located to the genome
15978
Genes not located to the genome
644
Alleles
598
Alleles of located genes
173
Alleles of unlocated genes
425
Aberrations
161
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
21
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15978
4029
1176744
49
0
Protein coding genes
15069
4266
1176744
102
0
Protein coding transcripts
15070
1471
26718
102
0
Exons
57154
389
13661
2
0
Introns
41345
1026
1034096
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14954
491
8905
33
0
rRNA genes
135
154
2010
76
0
rRNA
135
154
2010
76
0
tRNA genes
307
75
195
71
0
tRNA
307
74
94
71
0
snRNA genes
29
166
262
98
0
snRNA
29
166
262
98
0
snoRNA genes
194
112
219
49
0
snoRNA
194
112
219
49
0
miRNA genes
76
84
117
57
0
miRNA
82
22
35
19
0
Miscellaneous non-coding RNA genes
3
289
297
276
0
Miscellaneous non-coding RNA
3
289
297
276
0
Pseudogenes
165
72
75
67
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
18891
0
BREN N-Scan
N-Scan
20227
0
DGIL snap
SNAP
41918
0
DGIL snap homology
SNAP
41007
0
EISE exonerate
EXONERATE
33504
0
EISE genemapper
GENE MAPPER
32718
0
EISE genewise
Genewise
20081
0
GLEANR consensus
GLEANR
22551
0
NCBI gnomon
GNOMON
23784
0
OXFD exonerate
EXONERATE
12920
0
PACH genemapper
GENE MAPPER
17892
0
RGUI geneid
GENEID 1.2
30348
0
RGUI geneid u12
GENEID 1.2
30800
0
showDrosophila erecta (R1.3)
Statistics
Gene records
16214
Genes located to the genome
15810
Genes not located to the genome
404
Alleles
2
Alleles of located genes
0
Aberrations
0
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
1
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15810
3553
1170937
30
-1
Protein coding genes
15044
3728
1170937
66
-1
Protein coding transcripts
15048
1455
26613
66
-1
Exons
56655
388
13790
1
-1
Introns
40986
835
1121756
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14868
488
8870
21
-1
rRNA genes
104
213
3518
30
0
rRNA
104
213
3518
30
0
tRNA genes
284
76
189
66
0
tRNA
284
74
86
70
0
snRNA genes
38
153
274
47
0
snRNA
38
153
274
47
0
snoRNA genes
252
111
316
45
0
snoRNA
252
111
316
45
0
miRNA genes
81
84
127
63
0
miRNA
88
22
29
20
0
Miscellaneous non-coding RNA genes
5
1178
3727
275
0
Miscellaneous non-coding RNA
5
1178
3727
275
0
Pseudogenes
2
72
73
72
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14863
0
BREN N-Scan
N-Scan
16723
0
DGIL snap
SNAP
25198
0
DGIL snap homology
SNAP
24654
0
EISE exonerate
EXONERATE
33587
0
EISE genemapper
GENE MAPPER
28987
0
EISE genewise
Genewise
43127
0
GLEANR consensus
GLEANR
16880
0
NCBI gnomon
GNOMON
18662
0
OXFD exonerate
EXONERATE
13568
0
PACH genemapper
GENE MAPPER
19020
0
RGUI geneid
GENEID 1.2
18654
0
RGUI geneid u12
GENEID 1.2
18866
0
showDrosophila grimshawi (R1.3)
Statistics
Gene records
15904
Genes located to the genome
15585
Genes not located to the genome
319
Alleles
6
Alleles of located genes
5
Alleles of unlocated genes
1
Aberrations
1
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15585
3993
238808
46
0
Protein coding genes
14982
4150
238808
117
0
Protein coding transcripts
14986
1488
26535
117
0
Exons
56795
393
13188
1
0
Introns
41370
965
216011
1
0
5' untranslated regions
1
2
2
2
1
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14741
500
8844
38
0
rRNA genes
70
132
180
97
0
rRNA
70
132
180
97
0
tRNA genes
260
76
191
71
0
tRNA
260
73
86
71
0
snRNA genes
32
155
266
98
0
snRNA
32
155
266
98
0
snoRNA genes
154
110
244
46
0
snoRNA
154
110
244
46
0
miRNA genes
82
83
126
63
0
miRNA
88
22
29
20
0
Miscellaneous non-coding RNA genes
4
308
348
293
0
Miscellaneous non-coding RNA
4
308
348
293
0
Pseudogenes
1
75
75
75
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14003
0
BREN N-Scan
N-Scan
17378
0
DGIL snap
SNAP
34975
0
DGIL snap homology
SNAP
34420
0
EISE exonerate
EXONERATE
34389
0
EISE genemapper
GENE MAPPER
32724
0
EISE genewise
Genewise
19258
0
GLEANR consensus
GLEANR
16901
0
NCBI gnomon
GNOMON
17922
0
OXFD exonerate
EXONERATE
11052
0
PACH genemapper
GENE MAPPER
16572
0
RGUI geneid
GENEID 1.2
29516
0
RGUI geneid u12
GENEID 1.2
30148
0
showDrosophila mojavensis (R1.3)
Statistics
Gene records
15740
Genes located to the genome
15179
Genes not located to the genome
561
Alleles
44
Alleles of located genes
36
Alleles of unlocated genes
8
Aberrations
10
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15179
4262
299059
60
0
Protein coding genes
14594
4429
299059
105
0
Protein coding transcripts
14595
1482
26781
105
0
Exons
55195
392
14595
2
0
Introns
40199
1075
245033
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14512
494
8926
34
0
rRNA genes
75
149
1990
103
0
rRNA
75
149
1990
103
0
tRNA genes
264
75
194
71
0
tRNA
264
73
86
71
0
snRNA genes
30
158
264
98
0
snRNA
30
158
264
98
0
snoRNA genes
139
116
273
60
0
snoRNA
139
116
273
60
0
miRNA genes
71
84
127
62
0
miRNA
78
22
29
20
0
Miscellaneous non-coding RNA genes
3
303
323
294
0
Miscellaneous non-coding RNA
3
303
323
294
0
Pseudogenes
3
78
91
72
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14779
0
BREN N-Scan
N-Scan
18863
0
DGIL snap
SNAP
34235
0
DGIL snap homology
SNAP
39387
0
EISE exonerate
EXONERATE
33573
0
EISE genemapper
GENE MAPPER
31926
0
EISE genewise
Genewise
41625
0
GLEANR consensus
GLEANR
17738
0
NCBI gnomon
GNOMON
17950
0
OXFD exonerate
EXONERATE
10902
0
PACH genemapper
GENE MAPPER
16684
0
RGUI geneid
GENEID 1.2
19994
0
RGUI geneid u12
GENEID 1.2
20482
0
showDrosophila persimilis (R1.3)
Statistics
Gene records
18164
Genes located to the genome
17573
Genes not located to the genome
591
Alleles
37
Alleles of located genes
8
Alleles of unlocated genes
29
Aberrations
32
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
1
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17573
3484
231798
45
-1
Protein coding genes
16874
3624
231798
72
-1
Protein coding transcripts
16878
1284
24363
72
-1
Exons
59145
367
9522
1
-1
Introns
41743
949
160788
1
0
5' untranslated regions
2
1
2
1
2
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
16741
429
8120
23
-1
rRNA genes
85
260
3969
103
0
rRNA
85
260
3969
103
0
tRNA genes
305
75
195
71
0
tRNA
305
74
93
71
0
snRNA genes
31
160
313
97
0
snRNA
31
160
313
97
0
snoRNA genes
199
110
277
45
0
snoRNA
199
110
277
45
0
miRNA genes
75
85
110
62
0
miRNA
81
22
29
20
0
Miscellaneous non-coding RNA genes
3
304
322
296
0
Miscellaneous non-coding RNA
3
304
322
296
0
Pseudogenes
1
75
75
75
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
18611
0
BREN N-Scan
N-Scan
19699
0
DGIL snap
SNAP
38209
0
DGIL snap homology
SNAP
36086
0
EISE exonerate
EXONERATE
35069
0
EISE genemapper
GENE MAPPER
32760
0
EISE genewise
Genewise
25594
0
GLEANR consensus
GLEANR
23029
0
NCBI gnomon
GNOMON
24696
0
OXFD exonerate
EXONERATE
11924
0
PACH genemapper
GENE MAPPER
17011
0
RGUI geneid
GENEID 1.2
28798
0
RGUI geneid u12
GENEID 1.2
28613
0
showDrosophila pseudoobscura pseudoobscura (R2.26)
Statistics
Gene records
19866
Genes located to the genome
16702
Genes not located to the genome
3164
Alleles
327
Alleles of located genes
68
Alleles of unlocated genes
259
Aberrations
61
Deficiencies
1
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 2.26
Summary of changes from previous release
New Gene Models
16
Restored Gene Models
4
Deleted Gene Models
2
Merged Gene Models
0
Split Gene Models
1 → 2
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16702
3445
205154
26
19
Protein coding genes
15984
3586
205154
36
19
Protein coding transcripts
16621
1499
55449
36
12
Exons
58244
407
16920
2
23
Introns
42068
848
168194
0
13
5' untranslated regions
698
133
2871
1
1
3' untranslated regions
624
256
2005
1
1
Unique polypeptides
16516
494
18482
11
11
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
72
84
110
62
0
miRNA
79
22
29
20
0
Miscellaneous non-coding RNA genes
3
841
1905
296
0
Miscellaneous non-coding RNA
3
552
1038
296
0
Pseudogenes
58
2409
68216
75
0
Nucleotide Alignments
Annotated Gene Features
Algorithm
Count
Change
D. pseudoobscura cDNA inserts
splign
11
0
D. pseudoobscura ESTs
splign
25011
0
Other insect cDNAs/mRNAs
splign
31740
64
Aligned Drosophila annotations
splign
245880
43065
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
16158
0
BREN N-Scan
N-Scan
17088
0
DGIL snap
SNAP
23678
0
DGIL snap homology
SNAP
21676
0
EISE exonerate
EXONERATE
34828
0
EISE genemapper
GENE MAPPER
32857
0
EISE genewise
Genewise
42938
0
GLEANR consensus
GLEANR
17328
0
Genewise
Genewise
17882
0
Genscan
Genscan 1.0
16829
0
NCBI gnomon
GNOMON
19259
0
OXFD exonerate
EXONERATE
11690
0
PACH genemapper
GENE MAPPER
17265
0
RGUI geneid
GENEID 1.2
19060
0
RGUI geneid u12
GENEID 1.2
18970
0
Twinscan
Twinscan
18082
0
Proteins Aligned
Annotated Gene Features
Algorithm
Count
Change
Other proteins
Prosplign
169532
4644
D. pseudoobscura proteins
Prosplign
16598
3
showDrosophila sechellia (R1.3)
Statistics
Gene records
17948
Genes located to the genome
17273
Genes not located to the genome
675
Alleles
13
Alleles of located genes
4
Alleles of unlocated genes
9
Aberrations
1
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
17273
3172
215256
27
0
Protein coding genes
16467
3321
215256
27
0
Protein coding transcripts
16471
1305
43656
27
0
Exons
58765
367
11004
1
0
Introns
41665
799
173070
1
0
5' untranslated regions
2
1
1
1
2
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
16125
440
14551
8
0
rRNA genes
139
235
1997
30
0
rRNA
139
235
1997
30
0
tRNA genes
299
75
189
70
-9
tRNA
299
74
86
70
-9
snRNA genes
30
156
273
98
0
snRNA
30
156
273
98
0
snoRNA genes
242
112
315
46
0
snoRNA
242
112
315
46
0
miRNA genes
78
84
127
63
0
miRNA
85
22
29
20
0
Miscellaneous non-coding RNA genes
5
1178
3707
277
0
Miscellaneous non-coding RNA
5
1178
3707
277
0
Pseudogenes
13
74
75
71
9
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
15887
0
BREN N-Scan
N-Scan
18367
0
DGIL snap
SNAP
36782
0
DGIL snap homology
SNAP
31358
0
EISE exonerate
EXONERATE
34854
0
EISE genemapper
GENE MAPPER
28216
0
EISE genewise
Genewise
25095
0
GLEANR consensus
GLEANR
21332
0
NCBI gnomon
GNOMON
25689
0
OXFD exonerate
EXONERATE
14423
0
PACH genemapper
GENE MAPPER
18928
0
RGUI geneid
GENEID 1.2
29159
0
RGUI geneid u12
GENEID 1.2
29186
0
showDrosophila simulans (R1.3)
Statistics
Gene records
17775
Genes located to the genome
16104
Genes not located to the genome
1671
Alleles
413
Alleles of located genes
188
Alleles of unlocated genes
225
Aberrations
33
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
6
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16104
3233
179058
30
0
Protein coding genes
15413
3373
179058
54
0
Protein coding transcripts
15415
1234
25239
54
0
Exons
53950
353
7825
1
0
Introns
37971
869
168520
1
0
5' untranslated regions
3
1
2
1
3
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15346
411
8412
17
0
rRNA genes
72
158
180
30
0
rRNA
72
158
180
30
0
tRNA genes
266
75
189
58
0
tRNA
266
73
86
58
0
snRNA genes
32
156
273
97
0
snRNA
32
156
273
97
0
snoRNA genes
246
111
315
46
0
snoRNA
246
111
315
46
0
miRNA genes
70
84
127
63
0
miRNA
75
22
29
20
0
Miscellaneous non-coding RNA genes
3
1426
3706
277
0
Miscellaneous non-coding RNA
3
1426
3706
277
0
Pseudogenes
2
73
74
73
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
15530
0
BREN N-Scan
N-Scan
18989
0
DGIL snap
SNAP
28265
0
DGIL snap homology
SNAP
24623
0
EISE exonerate
EXONERATE
35213
0
EISE genemapper
GENE MAPPER
27790
0
EISE genewise
Genewise
27426
0
GLEANR consensus
GLEANR
17049
0
NCBI gnomon
GNOMON
19856
0
OXFD exonerate
EXONERATE
12420
0
PACH genemapper
GENE MAPPER
18260
0
RGUI geneid
GENEID 1.2
13797
0
RGUI geneid u12
GENEID 1.2
14128
0
showDrosophila virilis (R1.2)
Statistics
Gene records
16103
Genes located to the genome
15343
Genes not located to the genome
760
Alleles
571
Alleles of located genes
111
Alleles of unlocated genes
460
Aberrations
83
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
5
Annotation Release 1.2
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
15343
4220
565985
49
0
Protein coding genes
14491
4461
565985
93
0
Protein coding transcripts
14491
1500
40500
93
0
Exons
55557
393
23577
1
0
Introns
40386
1071
535952
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
14382
501
13499
30
0
rRNA genes
299
189
1995
49
0
rRNA
299
189
1995
49
0
tRNA genes
277
76
191
71
0
tRNA
277
73
86
71
0
snRNA genes
31
158
261
98
0
snRNA
31
158
261
98
0
snoRNA genes
165
113
282
57
0
snoRNA
165
113
282
57
0
miRNA genes
74
84
126
58
0
miRNA
81
22
29
20
0
Miscellaneous non-coding RNA genes
4
303
330
294
0
Miscellaneous non-coding RNA
4
303
330
294
0
Pseudogenes
2
87
89
85
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
14476
0
BATZ Contrast NA
CONTRAST
14476
0
BREN N-Scan
N-Scan
18350
0
BREN N-Scan
N-Scan
18350
0
DGIL snap
SNAP
35378
0
DGIL snap
SNAP
35378
0
DGIL snap homology
SNAP
35285
0
DGIL snap homology
SNAP
35285
0
EISE exonerate
EXONERATE
33940
0
EISE exonerate
EXONERATE
33940
0
EISE genemapper
GENE MAPPER
32430
0
EISE genemapper
GENE MAPPER
32430
0
EISE genewise
Genewise
19550
0
EISE genewise
Genewise
19550
0
GLEANR consensus
GLEANR
17679
0
GLEANR consensus
GLEANR
17679
0
NCBI gnomon
GNOMON
18636
0
NCBI gnomon
GNOMON
18636
0
OXFD exonerate
EXONERATE
11117
0
OXFD exonerate
EXONERATE
11117
0
PACH genemapper
GENE MAPPER
16744
0
PACH genemapper
GENE MAPPER
16744
0
RGUI geneid
GENEID 1.2
26095
0
RGUI geneid
GENEID 1.2
26095
0
RGUI geneid u12
GENEID 1.2
27145
0
RGUI geneid u12
GENEID 1.2
27145
0
showDrosophila willistoni (R1.3)
Statistics
Gene records
16934
Genes located to the genome
16385
Genes not located to the genome
549
Alleles
203
Alleles of located genes
6
Alleles of unlocated genes
197
Aberrations
57
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16385
4318
683577
30
0
Protein coding genes
15512
4555
683577
90
0
Protein coding transcripts
15513
1462
27624
90
0
Exons
57093
399
21318
2
0
Introns
40896
1203
682464
1
0
5' untranslated regions
0
NA
NA
NA
0
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15434
488
9207
29
0
rRNA genes
80
308
1987
30
0
rRNA
80
308
1987
30
0
tRNA genes
296
76
191
62
0
tRNA
296
73
84
62
0
snRNA genes
37
160
363
97
0
snRNA
37
160
363
97
0
snoRNA genes
216
119
209
57
0
snoRNA
216
119
209
57
0
miRNA genes
77
85
138
63
0
miRNA
83
22
29
20
0
Miscellaneous non-coding RNA genes
3
314
346
298
0
Miscellaneous non-coding RNA
3
314
346
298
0
Pseudogenes
164
72
79
65
0
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
12928
0
BREN N-Scan
N-Scan
16784
0
DGIL snap
SNAP
53474
0
DGIL snap homology
SNAP
50296
0
EISE exonerate
EXONERATE
34660
0
EISE genemapper
GENE MAPPER
32996
0
EISE genewise
Genewise
19279
0
GLEANR consensus
GLEANR
20211
0
NCBI gnomon
GNOMON
24902
0
OXFD exonerate
EXONERATE
10778
0
PACH genemapper
GENE MAPPER
16855
0
RGUI geneid
GENEID 1.2
25184
0
RGUI geneid u12
GENEID 1.2
27260
0
showDrosophila yakuba (R1.3)
Statistics
Gene records
17534
Genes located to the genome
16891
Genes not located to the genome
643
Alleles
7
Alleles of located genes
4
Alleles of unlocated genes
3
Aberrations
0
Deficiencies
0
Deficiencies with mapped endpoints
0
Transposable element insertions
0
Annotation Release 1.3
Summary of changes from previous release
New Gene Models
0
Restored Gene Models
0
Deleted Gene Models
0
Merged Gene Models
0
Split Gene Models
0
Complex combinations
0
Annotated Gene Models
Count
Avg. size
Longest
Shortest
Change
Genes
16891
3422
252576
39
0
Protein coding genes
16077
3590
252576
39
0
Protein coding transcripts
16082
1408
26793
39
0
Exons
59388
382
13188
2
0
Introns
42642
824
161037
1
0
5' untranslated regions
1
1
1
1
1
3' untranslated regions
0
NA
NA
NA
0
Unique polypeptides
15940
471
8930
12
0
rRNA genes
57
242
3981
91
0
rRNA
57
242
3981
91
0
tRNA genes
328
75
191
71
-46
tRNA
328
74
86
71
-46
snRNA genes
37
158
276
98
0
snRNA
37
158
276
98
0
snoRNA genes
255
110
316
45
0
snoRNA
255
110
316
45
0
miRNA genes
80
85
127
63
0
miRNA
87
22
29
20
0
Miscellaneous non-coding RNA genes
5
1169
3705
275
0
Miscellaneous non-coding RNA
5
1169
3705
275
0
Pseudogenes
52
72
76
62
46
Gene Predictions
Annotated Gene Features
Algorithm
Count
Change
BATZ Contrast NA
CONTRAST
16923
0
BREN N-Scan
N-Scan
19482
0
DGIL snap
SNAP
32761
0
DGIL snap homology
SNAP
32029
0
EISE exonerate
EXONERATE
34716
0
EISE genemapper
GENE MAPPER
29982
0
EISE genewise
Genewise
20916
0
GLEANR consensus
GLEANR
18816
0
NCBI gnomon
GNOMON
20302
0
OXFD exonerate
EXONERATE
14290
0
PACH genemapper
GENE MAPPER
18907
0
RGUI geneid
GENEID 1.2
15647
0
RGUI geneid u12
GENEID 1.2
16037
0