Drosophila melanogaster genome annotation release 3.2.2 date 10212004 DATA CONTENTS Feature counts in release 3.2 compared (r322 oct 04, r321 jul04, r320 March 04) Feature 322 321 320 ------------------------------------------------------------ BAC 949 949 949 CDS 18747 18747 18746 DNA_motif 5 5 5 EST 0^ 310718 304257 RNA_motif 1 1 0 aberration_junction 86 86 87 cDNA_clone 0^ 10283 10204 chromosome_arm 7 0 0 chromosome_band 5715 0 0 enhancer 27 27 27 five_prime_UTR 15769$ 18621 13608 gene 13472 13472 13473 insertion_site 457 457 424 intron 16153 16153 16199 mRNA 19302 19307 18810 mRNA_genscan 19189 19052 -- mRNA_piecegenie 13794 13740 -- match_HDP 2448 2448 0 match_RNAiHDP 40 40 0 match_blastx_aa_SP.hyp.dros 354 0 0 match_blastx_aa_SP.real.dros 22163 0 0 match_blastx_aa_SPTR.dros 68846 0 0 match_blastx_aa_SPTR.insect 7492 0 0 match_blastx_aa_SPTR.othinv 12471 0 0 match_blastx_aa_SPTR.othvert 11774 0 0 match_blastx_aa_SPTR.plant 9609 0 0 match_blastx_aa_SPTR.primate 16345 0 0 match_blastx_aa_SPTR.rodent 16081 0 0 match_blastx_aa_SPTR.worm 12679 0 0 match_blastx_aa_SPTR.yeast 5211 0 0 match_blastx_aa_TR.real.dros 43823 0 0 match_blastx_aa_users_i.dros 4633 0 0 match_fgenesh 14837 14838 0 match_sim4_na_DGC.dros 15270 0 0 match_sim4_na_EST.all_nr.dros 267828 0 0 match_sim4_na_adh.cDNAs.dros 51 0 0 match_sim4_na_cDNA.dros 10319 0 0 match_sim4_na_gadfly.dros.RE.. 14389 0 0 match_sim4_na_gb.dros 14977 0 0 match_sim4_na_pe.dros 3201 0 0 match_tblastx_na_dbEST.insect 16818 0 0 match_tblastx_na_unigene.rod.. 11707 0 0 mature_peptide 7 7 8 ncRNA 70 65 65 oligo 197726 197330 193813 orthologous_region 12101+ 0 0 point_mutation 485 485 476 polyA_site 107 107 101 processed_transcript 0^ 15105 16748 protein 0^ 162562 233812 protein_binding_site 90 90 85 pseudogene 40 40 39 rRNA 96 96 85 region 30 30 28 regulatory_region 137 137 136 repeat_region 4652 4051 3390 rescue_fragment 136 136 135 scaffold 437 437 437 sequence_variant 232 232 225 signal_peptide 0 0 1 snRNA 28 28 28 snoRNA 28 28 28 syntenic_region 1230+ 0 0 tRNA 288 288 288 tRNA_trnascan 297 294 -- three_prime_UTR 16777$ 18590 15493 transcription_start_site 35737 35698 16997 transposable_element 1572 1572 1567 transposable_element_inserti.. 3257 3257 4566 transposable_element_pred 1572 1572 -- ------------------------------------------------------------ -- == data not available for this feature + syntenic_region, orthologous_region added from D.pseudoobscura x dmel data. $ empty five_prime_UTR, three_prime_UTR features removed (0 bases) ^ various types split into match (computated analysis) subtypes: EST (310718) -> match_sim4_na_EST.all_nr.dros (267828) + match_sim4_na_DGC.dros (15270) + other cDNA_clone (10283) -> match_sim4_na_cDNA.dros (10319) processed_transcript (15105) -> match:sim4:na_gadfly.dros.RELEASE2 (14389) + other sim4 protein (162562) -> various match_blast types Table of D. mel. genome feature counts per release. Feature 322 321 320 ------------------------------------------------------------ cyto_insertion 16363 16363 21379 cytobreakpoint_inv 4565 4565 4565 cytobreakpoint_other 791 791 791 cytobreakpoint_ttp 6243 6243 6243 cytodeleted_segment 11073 11073 11073 cytoduplicated_segment 880 880 880 cytogene 5671 5671 6683 ------------------------------------------------------------ -- == data not available for this feature ------- Data are from Postgres Chado database, release 3.2, v 26s, 3 Aug 2004 Copy at ftp://flybase.net/genomes/Drosophila_melanogaster/ dmel_r3.2.1_07212004/pgsql/chado_r3_2_26_s.gz BULK FILE SET See ftp://flybase.net/genomes/Drosophila_melanogaster/current/ blast/ - NCBI blast database set for selected fasta/ feature sets. dna/ - contains dna raw format files per chromosome-arm; no change from release 3 data. fasta/ - dna and protein data per chromosome and feature type; chromosome-arm dna in fasta format also now find -all- files which catenate each chromosome set. gff/ - GFF v2 standard feature files per chromosome gnomap/ - Gnomap standard feature files per chromosome (drive genome map views) These two contain chromosome locations of above listed features