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NetAffx Annotation Release 31 Notes
August 2010

This table lists the Data sources used for NetAffx Annotation Release 31, including the date of release and version number, if available. Data sources that cover multiple species are listed first, followed by species-specific sources.

Data source Mol Type Release Date Version Species Description Notes
GenBank mRNA, peptide 24-May-10 177 All full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)  
RefSeq mRNA, peptide 01-Jun-10 41 All mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)  
UniProt protein 22-May-10 2010_06 All Protein sequence data from both Swiss-Prot and TrEMBL  
IPI protein 26-May-10   All Protein cross references from the International Protein Index Used for annotating Ensembl transcripts
Entrez Gene mRNA 22-May-10   All Gene information database derived from RefSeq, model organism databases, and other NCBI databases Release date is the date downloaded
dbSNP DNA 25-Mar-10 131 Homo sapiens SNP annotations  
HapMap 3 DNA May-10 Draft 1 Homo sapiens SNP genotypes  
DGV DNA Mar-10 9 Homo sapiens CNV annotations Database of Genomic Variants
Ensembl mRNA, peptide Jul-10 57 Anopheles gambiae cDNA, ncRNA, and peptide sequence including non-hypothetical, ab initio and EST-based transcripts For D. melanogaster and S. cerevisiae, we use predicted transcripts from Ensembl and other annotated transcripts from Flybase and SGD, respectively
Bos taurus
Caenorhabditis elegans
Canis familiaris
Danio rerio
Drosophila melanogaster
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Saccharomyces cerevisiae
Xenopus tropicalis
DNA Oct-07 47 (AgamP3) Anopheles gambiae Nuclear genome assembly Excluded unassembled contigs.
UniGene mRNA 18-Jul-08 41 Anopheles gambiae EST-based non-redundant gene-oriented clusters  
13-May-09 70 Arabidopsis thaliana
07-Dec-09 95 Bos taurus
16-Mar-10 47 Caenorhabditis elegans
18-Sep-08 23 Canis familiaris
28-Dec-08 11 Citrus sinensis
07-Oct-09 118 Danio rerio
27-Jan-10 67 Drosophila melanogaster
23-Nov-09 42 Gallus gallus
01-Sep-09 38 Glycine max
16-Oct-08 10 Gossypium hirsutum
24-Apr-08 7 Gossypium raimondii
14-Apr-09 223 Homo sapiens
03-Apr-09 56 Hordeum vulgare
23-Feb-07 27 Lycopersicon esculentum
08-Sep-08 13 Macaca mulatta
21-Dec-08 35 Medicago truncatula
27-Jan-10 183 Mus musculus
03-Sep-09 80 Oryza sativa
27-May-05 1 Populus balsamifera
03-Jun-07 15 Populus tremula x Populus tremuloides
28-May-08 9 Populus trichocarpa
09-Mar-10 182 Rattus norvegicus
22-Jan-10 14 Saccharum officinarum
25-Nov-09 34 Solanum tuberosum
01-Aug-09 38 Sus scrofa
23-Dec-09 56 Triticum aestivum
21-Jan-09 10 Vitis vinifera
14-Apr-09 87 Xenopus laevis
24-Mar-09 49 Xenopus tropicalis
27-Jan-10 77 Zea mays
UCSC DNA Oct-07 bosTau4 Bos taurus Nuclear and mitochondrial genome assemblies  
May-08 ce6 Caenorhabditis elegans
May-05 canFam2 Canis familiaris
Jul-07 danRer5 Danio rerio
Feb-09 hg19 Homo sapiens
Jul-07 mm9 Mus musculus
May-06 galGal3 Gallus gallus
Jan-06 rheMac2 Macaca mulatta
Nov-04 rn4 Rattus norvegicus
Oct-03 sacCer1 Saccharomyces cerevisiae
RefSeq (bacterial) DNA, RNA, peptide Jun-06   Escherichia coli Strains: MG1655, EDL933, CFT073, EcoRIMD CDS and peptides extracted from the RefSeq genome assembly record.
May-06   Staphyloccus aureus Strains: N315, MU50, COL
May-06   Bacillus subtilis  
TAIR DNA, mitochondrial, chloroplast 19-Jun-09 TAIR9 Arabidopsis thaliana Nuclear and organellar genome assemblies  
mRNA 19-Jun-09 TAIR9 Genome transcript annotations based on the TAIR9 assembly
TIGR mRNA 6-Oct-05   Medicago truncatula Predicted CDS sequences from IMGAG  
DNA, mRNA 1-Aug-04 pfa1 Plasmodium falciparum Nuclear genome assembly and cDNA sequences
mRNA 05-Jun-06 2 Triticum aestivum TIGR Plant Transcript Assemblies
miRBase miRNA Sep-10 16.0 Homo sapiens Precursor miRNA stem-loop sequences Used only for annotating exon arrays.
Mus musculus
Rattus norvegicus
RGAP DNA, mitochondrial, chloroplast, mRNA, peptide 03-Jun-09 6.1 Oryza sativa Rice pseudomolecules and genome annotation Transcripts and peptides from predicted gene models based on the pseudomolecule assemblies.
RAP mRNA, peptide 15-May-07 2 Oryza sativa Rice Annotation Project annotations  
BGI_RIS mRNA, peptide 1-Aug-04   Oryza sativa Fgene-based predictions (Syngenta)  
BDGP DNA 29-Mar-06 5 Drosophila melanogaster Nuclear genome assembly Same assembly used by UCSC dm3. Equivalent to FlyBase 5.3
FlyBase Mitochondrial DNA, RNA, peptide 08-Dec-06 5.1 Drosophila melanogaster Mitochondrial genome assembly  
all RNA, peptide Sep-10 5.31 Drosophila melanogaster Genome sequence annotations
JGI DNA, mitochondrial, chloroplast, mRNA Nov-10 1.09 Glycine max Nuclear and organellar genome assemblies and transcripts from predicted gene models based on this genome Glycine_max_Williams_82 8x Release
DNA Jan-10 v2 Populus trichocarpa  
mRNA, peptide 13-Sep-06 1.1 Transcripts and proteins from predicted gene models
Pasteur Institute mRNA, peptide 09-Jul-04 SLR 16.1 Bacillus subtilis    
PseudoCAP mRNA, peptide 12-Jul-06   Pseudomonas aeruginosa Pseudomonas community annotation project Release date is the date downloaded
Sanger DNA 4-Jul-05   Schizosaccharomyces pombe Nuclear genome assembly  
mRNA, peptide 17-May-06   All ORF CDS
SGD mRNA, peptide 12-May-06   Saccharomyces cerevisiae All ORF CDS  

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