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NetAffx Annotation Release 21 Notes
November 2006

This table lists the Data sources used for NetAffx Annotation Release 21, 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-06
155
All
full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)
RefSeq
mRNA, peptide
11-Jul-06
18
All
mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)
UniProt
protein
22-Aug-06
8.5
All
Protein sequence data from both Swiss-Prot 50.5 and TrEMBL 33.5
Entrez Gene
mRNA
29-Aug-06
All
Gene information database derived from RefSeq, model organism databases, and other NCBI databases
Ensembl
mRNA, peptide
Aug-06
40
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
14-Jul-06
54
Arabidopsis thaliana
15-Jun-06
79
Bos taurus
3-Jul-06
30
Caenorhabditis elegans
16-Jul-06
16
Canis familiaris
12-Jul-05
6
Citrus sinensis
31-Jul-06
93
Danio rerio
16-Jul-06
45
Drosophila melanogaster
2-Aug-05
31
Gallus gallus
6-Aug-05
25
Glycine max
7-May-06
191
Homo sapiens
3-Aug-06
46
Hordeum vulgare
3-Aug-06
25
Lycopersicon esculentum
3-Aug-06
5
Macaca mulatta
7-Aug-06
25
Medicago truncatula
27-Apr-06
153
Mus musculus
15-Jul-06
62
Oryza sativa
27-May-05
1
Populus balsamifera
1-Dec-05
9
Populus tremula x Populus tremuloides
3-Jul-06
1
Populus trichocarpa
19-Jul-06
155
Rattus norvegicus
2-Jul-06
7
Saccharum officinarum
3-Aug-06
25
Solanum tuberosum
30-Jul-06
25
Sus scrofa
31-Jul-06
46
Triticum aestivum
26-Jul-06
19
Vitis vinifera
31-Jul-06
70
Xenopus laevis
4-Aug-06
31
Xenopus tropicalis
8-Aug-06
58
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
BIS_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 exon arrays. Not yet accessible via NetAffx. Contact us if interested.
Mus musculus
Rattus norvegicus
JGI
DNA
Jun-04
1.0
Populus trichocarpa
Nuclear genome assembly, 7.5x coverage
mRNA
13-Feb-06
1.0
Populus trichocarpa
Transcripts from predicted gene models
FlyBase
DNA
17-Apr-06
5.0
Drosophila melanogaster
Nuclear genome assembly
mRNA, peptide
21-Feb-06
4.3
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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