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NetAffx Annotation Release 23 Notes
July 2007

This table lists the Data sources used for NetAffx Annotation Release 23, 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-Feb-07
158
All
full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)
 
RefSeq
mRNA, peptide
05-Mar-07
22
All
mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)
 
UniProt
peptide
12-Jun-07
11.1
All
Protein sequence data from both Swiss-Prot 53.1 and TrEMBL 36.1
 
Entrez Gene
mRNA
5-Jun-07
 
All
Gene information database derived from RefSeq, model organism databases, and other NCBI databases
Release date is the date downloaded
Ensembl
mRNA, peptide
Apr-07
44
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
23-Feb-07
35
Anopheles gambiae
EST-based non-redundant gene-oriented clusters
 
04-Mar-07
58
Arabidopsis thaliana
25-Feb-07
83
Bos taurus
23-Feb-07
34
Caenorhabditis elegans
15-Feb-07
18
Canis familiaris
30-Jan-07
8
Citrus sinensis
23-Feb-07
101
Danio rerio
05-Jan-07
47
Drosophila melanogaster
27-Feb-07
33
Gallus gallus
06-Feb-07
28
Glycine max
01-Mar-07
201
Homo sapiens
16-Feb-07
48
Hordeum vulgare
23-Feb-07
27
Lycopersicon esculentum
27-Feb-07
7
Macaca mulatta
07-Aug-06
25
Medicago truncatula
07-Feb-07
162
Mus musculus
03-Mar-07
67
Oryza sativa
27-May-05
1
Populus balsamifera
31-Jan-07
11
Populus tremula x Populus tremuloides
31-Jan-07
3
Populus trichocarpa
27-Feb-07
161
Rattus norvegicus
02-Feb-07
9
Saccharum officinarum
22-Feb-07
28
Solanum tuberosum
27-Feb-07
28
Sus scrofa
16-Feb-07
47
Triticum aestivum
07-Feb-07
20
Vitis vinifera
22-Feb-07
74
Xenopus laevis
27-Jan-07
35
Xenopus tropicalis
22-Feb-07
62
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)
Release date is the date downloaded
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
GOA
peptide
31-May-07
 
Arabidopsis thaliana
Gene Ontology Annotations for proteins in UniProt
Release date is the date downloaded
Bos taurus
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

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