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NetAffx Annotation Release 24 Notes
November 2007

This table lists the Data sources used for NetAffx Annotation Release 24, 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-Aug-07
161
All
full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)  
RefSeq
mRNA, peptide
10-Jul-07
24
All
mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)  
UniProt
protein
21-Aug-07
12.1
All
Protein sequence data from both Swiss-Prot 54.1 and TrEMBL 37.1  
Entrez Gene
mRNA
22-Aug-07
All
Gene information database derived from RefSeq, model organism databases, and other NCBI databases  
Ensembl
mRNA, peptide
Aug-07
46
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
UniGene
mRNA
29-Jun-07
36
Anopheles gambiae
EST-based non-redundant gene-oriented clusters  
24-Jul-07
61
Arabidopsis thaliana
01-Aug-07
85
Bos taurus
15-Jun-07
35
Caenorhabditis elegans
29-Jun-07
19
Canis familiaris
15-May-07
9
Citrus sinensis
01-Aug-07
105
Danio rerio
23-May-07
50
Drosophila melanogaster
29-Jun-07
34
Gallus gallus
20-Jun-07
29
Glycine max
10-Jul-07
204
Homo sapiens
18-Jul-07
50
Hordeum vulgare
23-Feb-07
27
Lycopersicon esculentum
19-Jun-07
8
Macaca mulatta
04-Jun-07
26
Medicago truncatula
10-Jul-07
165
Mus musculus
03-Jul-07
68
Oryza sativa
27-May-05
1
Populus balsamifera
31-Jan-07
12
Populus tremula x Populus tremuloides
23-May-07
4
Populus trichocarpa
28-Jul-07
165
Rattus norvegicus
18-Jul-07
11
Saccharum officinarum
26-Jul-07
29
Solanum tuberosum
05-Aug-07
30
Sus scrofa
23-Apr-07
48
Triticum aestivum
20-Jul-07
3
Vitis vinifera
03-Aug-07
78
Xenopus laevis
22-Jun-07
38
Xenopus tropicalis
05-Aug-07
65
Zea mays
UCSC
DNA
Feb-03
anoGam1
Anopheles gambiae
Nuclear and mitochondrial genome assemblies  
Aug-07
bosTau3
Bos taurus
Mar-04
ce2
Caenorhabditis elegans
May-05
canFam2
Canis familiaris
Mar-06
danRer4
Danio rerio
Apr-06
dm3
Drosophila melanogaster
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
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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