FB2008_02 Release Notes

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General FlyBase FB2008_02 Statistics
	Number of references in FlyBase 187261 Number of research papers 79366 Number of abstracts 36435 Number of personal communications to FlyBase 3959 Number of fly stocks 85568 Number of fly images 870 Drosophila workers registered with FlyBase 7418
Drosophila melanogaster (R5.5)
Statistics	Gene records 30965 Genes located to the genome 15186 Genes not located to the genome 15779 Alleles 101739 Alleles of located genes 83174 Alleles of unlocated genes 18565 Aberrations 30209 Deficiencies 19722 Deficiencies with mapped endpoints 13479 Transposable element insertions 89724 Insertions mapped to the sequence 42049
Annotation Release 5.5
Summary of changes from previous release	New Gene Models 1 Restored Gene Models 5 Deleted Gene Models 0 Merged Gene Models 2 -> 1 Split Gene Models 0
Annotated Gene Models
	Annotated Gene Models Count Avg. size Longest Shortest Change Genes 15186 5381 258567 19 5 Protein coding genes 14146 5727 258567 132 5 Protein coding transcripts 20925 2331 69571 132 101 Exons 68268 477 27725 1 129 Introns 50648 1351 166135 11 91 5' untranslated regions 18755 183 3391 1 73 3' untranslated regions 13065 374 5684 1 84 Unique polypeptides 18055 574 23015 25 94 rRNA genes 161 504 6026 123 0 rRNA 161 504 6026 123 0 tRNA genes 314 75 186 61 0 tRNA 314 73 87 61 0 snRNA genes 47 115 275 36 0 snRNA 47 115 275 36 0 snoRNA genes 249 113 316 46 0 snoRNA 249 113 316 46 0 miRNA genes 90 24 100 19 0 miRNA 90 24 100 19 0 Miscellaneous non-coding RNA genes 88 3015 31065 31 0 Miscellaneous non-coding RNA 105 1182 14084 31 0 Pseudogenes 88 3218 179585 53 0 Transposable elements present in the sequenced strain 5552 1507 66001 23 0 Annotated repeat regions 10159
Other Annotated Gene Features
Mapped Nucleotide Changes
	Annotated Gene Features Count Change total mapped nucleotide changes 3583 162 aberration junction 193 3 complex substitution 52 4 deletion 225 12 insertion site 48 2 point mutation 2804 140 sequence variant 204 1 TE target site duplication 40 0 uncharacterized change in nucleotide sequence 17 0
Mapped Regulatory Elements
	Annotated Gene Features Count Change total mapped regulatory elements 2319 58 enhancer 22 0 poly A site 98 -1 protein binding site 1396 0 regulatory region 240 0 rescue fragment 563 59
Mapped Reagent Features
	Annotated Gene Features Count Change transposable element insertion site 42049 927 microarray amplicons 14095 0 dsRNA amplicons 67381 0 BAC 973 15 oligonucleotide 583294 0
Aligned Evidence Features
Nucleotide Alignments
	Annotated Gene Features Algorithm Count Change D. melanogaster cDNA inserts sim4tandem,splign 15980 0 D. melanogaster EST sim4,splign 503590 0 Other melanogaster DNA sequences sim4tandem,splign 12673 0
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 6133 0 Other insect proteins WU-blastx 2.0 5195 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 13046 0 Other vertebrate proteins WU-blastx 2.0 10443 0 Other proteins Prosplign 10672 0
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 5 Sequence Assembly
	The release 5 sequence by BDGP (see the BDGP release notes) contains some major improvements to the assembly of the major chromosome arm scaffolds as well as improvements to the assembly of those portions of the centric heterochromatin that cannot currently be attached to the major arms. The improvements to the arms include the major differences noted below plus an additional 4.7 Mbp of heterochromatic sequence attached to the proximal ends of the arms. Further, Release_5 is the first non-redundant assembly of the D. melanogaster genome, unifying the previously separate assemblies of the largely euchromatic arm scaffolds and the heterochromatic scaffolds. The entire Release_5 assembly can be downloaded from the BDGP web site. The Release 5.5 annotation update is a collaboration between FlyBase, BDGP and DHGP, and includes a full set of annotated gene models for the D. melanogaster euchromatin and heterochromatin assemblies. At present, we are working with NCBI on the submission of the Release_5.5 data used in to GenBank, but until that is completed, the latest GenBank version of the D. melanogaster genome is Release_5.1. The table describing Release_5.1 is presented here. We will update this table once the GenBank submission is completed and we have the relevant accession numbers and versions. TABLE 1: Release_5 Assembly (from BDGP) and Release_5.1 Accessions Scaffold Length (bp) Gaps Release 5.1 GenBank Accession Major Difference Compared to Release 4 ArmX 22,422,827 3 AE014298.4 8kb added to the distal end, gaps filled in regions 1-11 Arm2L 23,011,544 2 AE014134.5 591kb added to the proximal end of the arm Arm2R 21,146,708 1 AE013599.4 380kb added to the proximal end Arm3L 24,543,557 1 AE014296.4 16kb added on distal end, 718kb added to proximal end, other gaps filled Arm3R 27,905,053 0 AE014297.2 None Arm4 1,351,857 1 AE014135.3 70kbp added to the distal end XHet 204,112 n.a. n.a. n.a. YHet 347,038 n.a. n.a. n.a. 2LHet 368,872 n.a. n.a. n.a. 2RHet 3,288,761 n.a. n.a. n.a. 3LHet 2,555,491 n.a. n.a. n.a. 3RHet 2,517,507 n.a. n.a. n.a. ArmU 10,049,037 n.a. n.a. n.a. Release 5 of the euchromatic sequence contains eight (known) gaps. There are two gaps on the X that have estimates for their size and 6 other gaps in the genome which are not sized. (Gaps of unknown size are denoted by 100 N's in the fasta files.). The gap 21485539..21485638 of scaffold Arm2L is the Histone gene cluster which reputedly contains ca. 100 copies of a ca. 5kb repeat unit containing the His1, His2A, His2B, His3 and His4 genes. TABLE 2: Known Gaps in the Release 5 Assembly Scaffold GenBank Accession Gaps Notes ArmX AE014298.4 111523..129522 sized 21684450..21684549 unsized 21687344..21759343 sized Arm2L AE014134.5 21485539..21485638 unsized 22420242..22420341 unsized Arm2R AE013599.4 16668213..16668312 unsized Arm3L AE014296.4 5107767..5107866 Arm3R AE014297.2 None Arm4 AE014135.3 1221289..1221388
Location of Heterochromatin
	Chr/Arm Sequence coordinates X