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NetAffx Annotation Release 22 Notes
March 2007

This table lists the Data sources used for NetAffx Annotation Release 22, including the Version number, if there is one, and the date of the release. Data sources that cover multiple species are listed first, followed by more species-specific sources.

Data source
Mol Type
Release Date
Version
Species
Description
Notes
GenBank mRNA, peptide 15-Oct-06 156 All full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)  
RefSeq mRNA, peptide 05-Nov-06 20 All mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)  
UniProt protein 12-Dec-06 9.3 All Protein sequence data from both Swiss-Prot 51.3 and TrEMBL 34.4  
Entrez Gene mRNA 4-Jan-07   All Gene information database derived from RefSeq, model organism databases, and other NCBI databases  
Ensembl mRNA, peptide Dec-06 42 Anopheles gambiae cDNA 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
UniGene mRNA 13-Jun-06 33 Anopheles gambiae EST-based non-redundant gene-oriented clusters  
29-Oct-06 55 Arabidopsis thaliana
29-Nov-06 81 Bos taurus
09-Nov-06 32 Caenorhabditis elegans
16-Jul-06 16 Canis familiaris
12-Jul-06 6 Citrus sinensis
13-Nov-06 98 Danio rerio
24-Oct-06 46 Drosophila melanogaster
25-Jan-07 32 Gallus gallus
12-Oct-05 26 Glycine max
26-Nov-06 198 Homo sapiens
06-Nov-06 48 Hordeum vulgare
12-Nov-06 26 Lycopersicon esculentum
03-Aug-06 5 Macaca mulatta
07-Aug-06 25 Medicago truncatula
23-Nov-06 160 Mus musculus
18-Jan-07 65 Oryza sativa
27-May-05 1 Populus balsamifera
01-Dec-05 10 Populus tremula x Populus tremuloides
03-Jul-06 1 Populus trichocarpa
29-Nov-06 159 Rattus norvegicus
13-Sep-06 8 Saccharum officinarum
31-Oct-06 27 Solanum tuberosum
22-Oct-06 27 Sus scrofa
31-Jul-06 46 Triticum aestivum
26-Jul-06 19 Vitis vinifera
13-Nov-06 72 Xenopus laevis
07-Nov-06 34 Xenopus tropicalis
18-Jan-07 61 Zea mays
UCSC DNA Feb-03 anoGam1 Anopheles gambiae Nuclear and mitochondrial genome assemblies  
May-05 bosTau2 Bos taurus
Mar-04 ce2 Caenorhabditis elegans
May-05 canFam2 Canis familiaris
Mar-06 danRer4 Danio rerio
Mar-06 hg18 Homo sapiens
Mar-06 mm8 Mus musculus
May-06 galGal3 Gallus gallus
Jan-06 rheMac2 Macaca mulatta
Nov-04 rn4 Rattus norvegicus
Oct-03 sacCer1 Saccharomyces cerevisiae
RefSeq Mitochondrial DNA, mRNA, peptide Oct-05   Arabidopsis thaliana Organellar genome assembly Gene, CDS, and peptide sequences were extracted from the RefSeq genome records.
Nov-05   Oryza sativa
Chloroplast DNA, mRNA, peptide Oct-05   Arabidopsis thaliana
Nov-05   Oryza sativa
Sanger DNA 4-Jul-05   Schizosaccharomyces pombe Nuclear genome assembly  
mRNA, peptide 17-May-06   Schizosaccharomyces pombe All ORF CDS
SGD mRNA, peptide 12-May-06   Saccharomyces cerevisiae All ORF CDS  
TIGR DNA 13-May-04   Arabidopsis thaliana Nuclear genome assembly  
mRNA 6-Oct-05   Medicago truncatula Predicted CDS sequences from IMGAG  
DNA 12-Jan-06 4 Oryza sativa Rice pseudomolecules - nuclear genome assembly  
mRNA 12-Jan-06 4 Oryza sativa Rice pseudomolecules - transcripts  
DNA 1-Aug-04 pfa1 Plasmodium falciparum Nuclear genome assembly  
mRNA 1-Aug-04 pfa1 Plasmodium falciparum cDNA sequences  
BGI_RIS mRNA 1-Aug-04   Oryza sativa Fgene-based predictions (Syngenta)  
miRBase miRNA Sep-06 9.0 Homo sapiens Precursor miRNA stem-loop sequences Used only for annotating exon arrays.
Mus musculus
Rattus norvegicus
JGI DNA Jun-04 1.0 Populus trichocarpa Nuclear genome assembly, 7.5x coverage  
mRNA 13-Sep-06 1.1 Populus trichocarpa Transcripts from predicted gene models
FlyBase DNA 08-Dec-06 5.1 Drosophila melanogaster Nuclear genome assembly  
mRNA, peptide 08-Dec-06 5.1 Drosophila melanogaster Genome sequence annotations
PseudoCAP mRNA, peptide 12-Jul-06   Pseudomonas aeruginosa Pseudomonas community annotation project Release date is the date downloaded

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