FB2008_09 Release Notes

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General FlyBase FB2008_09 Statistics
	Number of references in FlyBase 189959 Number of research papers 79969 Number of abstracts 37393 Number of personal communications to FlyBase 4260 Number of fly stocks 87902 Number of fly images 981 Drosophila workers registered with FlyBase 7465
Drosophila melanogaster (R5.12)
Statistics	Gene records 30835 Genes located to the genome 15140 Genes not located to the genome 15695 Alleles 106651 Alleles of located genes 87784 Alleles of unlocated genes 18867 Aberrations 18260 Deficiencies 7722 Deficiencies with mapped endpoints 1491 Transposable element insertions 102723 Insertions mapped to the sequence 43181
Annotation Release 5.12
Summary of changes from previous release	New Gene Models 33 Restored Gene Models 0 Deleted Gene Models 2 Merged Gene Models 2 -> 1 Split Gene Models 0 Complex combinations 0
Annotated Gene Models
	Annotated Gene Models Count Avg. size Longest Shortest Change Genes 15140 5494 395988 19 31 Protein coding genes 14058 5863 395988 132 29 Protein coding transcripts 21243 2376 69439 132 116 Exons 68784 480 27725 1 216 Introns 51110 1393 166135 29 158 5' untranslated regions 19324 184 3391 1 133 3' untranslated regions 13734 373 5684 1 184 Unique polypeptides 18199 584 22971 11 59 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 131 2411 31065 31 1 Miscellaneous non-coding RNA 154 1100 14084 31 2 Pseudogenes 89 3196 179585 53 1 Transposable elements present in the sequenced strain 5580 1513 66001 15 26 Annotated repeat regions 10159
Other Annotated Gene Features
Mapped Nucleotide Changes
	Annotated Gene Features Count Change total mapped nucleotide changes 6751 3168 aberration junction 3354 3168 complex substitution 54 0 deletion 229 0 insertion site 48 0 point mutation 2804 0 sequence variant 204 0 TE target site duplication 40 0 uncharacterized change in nucleotide sequence 18 0
Mapped Regulatory Elements
	Annotated Gene Features Count Change total mapped regulatory elements 2319 0 enhancer 22 0 poly A site 98 0 protein binding site 1396 0 regulatory region 240 0 rescue fragment 563 0
Mapped Reagent Features
	Annotated Gene Features Count Change transposable element insertion site 43181 231 microarray amplicons 14095 0 dsRNA amplicons 67381 0 BAC 973 0 oligonucleotide 583294 0
Aligned Evidence Features
Nucleotide Alignments
	Annotated Gene Features Algorithm Count Change D. melanogaster cDNA inserts sim4tandem,splign 16547 0 D. melanogaster EST sim4,splign 495232 -8969 Other melanogaster DNA sequences sim4tandem,splign 12738 25
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 30944 28 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 29289 498
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
	Date updated: 12-FEB-2008 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 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 Heterochromatin Scaffold GenBank Accessions & Seq. Coordinates