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Platform GPL87 Query DataSets for GPL87
Status Public on Mar 11, 2002
Title [RG_U34C] Affymetrix Rat Genome U34 Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Rattus norvegicus
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site

The RG-U34 set includes 3 arrays with a total of 26379 entries and was indexed 29-Jan-2002.
The set includes ~7,000 known genes and >17,000 EST clusters.
The A array contains probes derived from all full-length or annotated genes as well as thousands of EST clusters.
The B and C arrays contain only EST clusters.

 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/projects/geo/info/geo_affy.html

June 03, 2009: annotation table updated with netaffx build 28
June 21, 2012: annotation table updated with netaffx build 32
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=rgu34
http://www.affymetrix.com/analysis/index.affx
Submission date Feb 19, 2002
Last update date Jun 21, 2012
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (441) GSM5016, GSM5017, GSM5018, GSM5019, GSM5020, GSM5021 
Series (10)
GSE353 Effect of age on skeletal muscle
GSE413 Kidneys of Dahl salt sensitive rats
GSE464 CNS Regeneration

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
SPOT_ID identifies controls
Species Scientific Name The genus and species of the organism represented by the probe set.
Annotation Date The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type
Sequence Source The database from which the sequence used to design this probe set was taken.
Target Description
Representative Public ID The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID Entrez Gene Database UID
RefSeq Transcript ID References to multiple sequences in RefSeq. The field contains the ID and Description for each entry, and there can be multiple entries per ProbeSet.
Gene Ontology Biological Process Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".

Data table
ID GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type Sequence Source Target Description Representative Public ID Gene Title Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
AA012646_i_at AA012646 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012646 RPU0102AC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012646 /gi=1473712 /ug=Rn.17509 /len=118 AA012646
AA012646_r_at AA012646 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012646 RPU0102AC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012646 /gi=1473712 /ug=Rn.17509 /len=118 AA012646
AA012654_at AA012654 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012654 RPU0303CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012654 /gi=1473780 /ug=Rn.17604 /len=189 AA012654
AA012693_at AA012693 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012693 RPU0901AC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012693 /gi=1473743 /ug=Rn.934 /len=359 AA012693
AA012699_at AA012699 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012699 RPU1102CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012699 /gi=1473749 /ug=Rn.17560 /len=153 AA012699
AA012708_f_at AA012708 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012708 RPU1504CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012708 /gi=1473758 /ug=Rn.17571 /len=123 AA012708 glioma tumor suppressor candidate region gene 2 Gltscr2 292624 NM_207591
AA012709_at AA012709 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012709 RPU1601CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012709 /gi=1473759 /ug=Rn.17573 /len=233 AA012709 Splicing factor 3b, subunit 1 Sf3b1 84486 NM_053426 0008380 // RNA splicing // not recorded /// 0009952 // anterior/posterior pattern formation // inferred from electronic annotation /// 0009952 // anterior/posterior pattern formation // not recorded 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // not recorded 0003682 // chromatin binding // inferred from electronic annotation /// 0003682 // chromatin binding // not recorded /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // not recorded
AA012719_at AA012719 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012719 RPU2101CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012719 /gi=1473769 /ug=Rn.17580 /len=470 AA012719 Tropomyosin 2, beta Tpm2 500450 NM_001024345 0006936 // muscle contraction // not recorded /// 0043462 // regulation of ATPase activity // not recorded 0005737 // cytoplasm // inferred from electronic annotation /// 0005856 // cytoskeleton // inferred from electronic annotation 0003779 // actin binding // inferred from electronic annotation /// 0003779 // actin binding // not recorded /// 0005515 // protein binding // not recorded
AA012727_at AA012727 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012727 RPU2401CG Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012727 /gi=1473777 /ug=Rn.17595 /len=327 AA012727 Colony stimulating factor 1 (macrophage) Csf1 78965 NM_023981 0001503 // ossification // inferred from mutant phenotype /// 0001954 // positive regulation of cell-matrix adhesion // inferred from electronic annotation /// 0001954 // positive regulation of cell-matrix adhesion // not recorded /// 0003006 // developmental process involved in reproduction // inferred from electronic annotation /// 0003006 // developmental process involved in reproduction // not recorded /// 0007275 // multicellular organismal development // traceable author statement /// 0008284 // positive regulation of cell proliferation // inferred from electronic annotation /// 0008284 // positive regulation of cell proliferation // not recorded /// 0010628 // positive regulation of gene expression // inferred from electronic annotation /// 0010628 // positive regulation of gene expression // not recorded /// 0010744 // positive regulation of macrophage derived foam cell differentiation // inferred from electronic annotation /// 0010744 // positive regulation of macrophage derived foam cell differentiation // not recorded /// 0030225 // macrophage differentiation // inferred from expression pattern /// 0030278 // regulation of ossification // inferred from electronic annotation /// 0030278 // regulation of ossification // not recorded /// 0030316 // osteoclast differentiation // inferred from mutant phenotype /// 0030316 // osteoclast differentiation // not recorded /// 0030316 // osteoclast differentiation // traceable author statement /// 0030335 // positive regulation of cell migration // inferred from electronic annotation /// 0030335 // positive regulation of cell migration // not recorded /// 0032270 // positive regulation of cellular protein metabolic process // inferred from electronic annotation /// 0032270 // positive regulation of cellular protein metabolic process // not recorded /// 0032946 // positive regulation of mononuclear cell proliferation // inferred from electronic annotation /// 0032946 // positive regulation of mononuclear cell proliferation // not recorded /// 0040018 // positive regulation of multicellular organism growth // inferred from electronic annotation /// 0040018 // positive regulation of multicellular organism growth // not recorded /// 0042476 // odontogenesis // inferred from mutant phenotype /// 0042488 // positive regulation of odontogenesis of dentine-containing tooth // inferred from electronic annotation /// 0042488 // positive regulation of odontogenesis of dentine-containing tooth // not recorded /// 0045651 // positive regulation of macrophage differentiation // inferred from electronic annotation /// 0045651 // positive regulation of macrophage differentiation // not recorded /// 0045657 // positive regulation of monocyte differentiation // inferred from electronic annotation /// 0045657 // positive regulation of monocyte differentiation // not recorded /// 0045672 // positive regulation of osteoclast differentiation // inferred from electronic annotation /// 0045672 // positive regulation of osteoclast differentiation // not recorded /// 0045860 // positive regulation of protein kinase activity // inferred from electronic annotation /// 0045860 // positive regulation of protein kinase activity // not recorded /// 0046579 // positive regulation of Ras protein signal transduction // inferred from electronic annotation /// 0046579 // positive regulation of Ras protein signal transduction // not recorded /// 0048873 // homeostasis of number of cells within a tissue // inferred from electronic annotation /// 0048873 // homeostasis of number of cells within a tissue // not recorded /// 0060444 // branching involved in mammary gland duct morphogenesis // inferred from electronic annotation /// 0060444 // branching involved in mammary gland duct morphogenesis // not recorded /// 0060611 // mammary gland fat development // inferred from electronic annotation /// 0060611 // mammary gland fat development // not recorded /// 0060763 // mammary duct terminal end bud growth // inferred from electronic annotation /// 0060763 // mammary duct terminal end bud growth // not recorded 0005576 // extracellular region // inferred from electronic annotation /// 0005615 // extracellular space // inferred from electronic annotation /// 0005615 // extracellular space // not recorded /// 0005886 // plasma membrane // inferred from electronic annotation /// 0005887 // integral to plasma membrane // traceable author statement /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation /// 0043235 // receptor complex // inferred from electronic annotation /// 0043235 // receptor complex // not recorded /// 0048471 // perinuclear region of cytoplasm // inferred from electronic annotation /// 0048471 // perinuclear region of cytoplasm // not recorded 0005125 // cytokine activity // inferred from electronic annotation /// 0005125 // cytokine activity // not recorded /// 0005157 // macrophage colony-stimulating factor receptor binding // inferred from electronic annotation /// 0005157 // macrophage colony-stimulating factor receptor binding // not recorded /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // not recorded /// 0008083 // growth factor activity // inferred from electronic annotation /// 0008083 // growth factor activity // not recorded /// 0042803 // protein homodimerization activity // inferred from direct assay /// 0042803 // protein homodimerization activity // not recorded /// 0042803 // protein homodimerization activity // inferred from electronic annotation
AA012785_at AA012785 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012785 RPU0302GC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012785 /gi=1473847 /ug=Rn.17607 /len=203 AA012785 TNFAIP3 interacting protein 2 Tnip2 305451 NM_001024771 0007249 // I-kappaB kinase/NF-kappaB cascade // inferred from electronic annotation /// 0007249 // I-kappaB kinase/NF-kappaB cascade // not recorded 0005737 // cytoplasm // inferred from electronic annotation /// 0005737 // cytoplasm // not recorded 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // not recorded
AA012807_at AA012807 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012807 RPU2301AC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012807 /gi=1473869 /ug=Rn.17501 /len=539 AA012807
AA012808_at AA012808 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA012808 RPU0401AC Rattus norvegicus cDNA, 5' end /clone_end=5' /gb=AA012808 /gi=1473870 /ug=Rn.19191 /len=296 AA012808 Chaperonin containing Tcp1, subunit 8 (theta) Cct8 288305 NM_001105897 0006457 // protein folding // inferred from electronic annotation /// 0044267 // cellular protein metabolic process // inferred from electronic annotation 0005634 // nucleus // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005737 // cytoplasm // not recorded /// 0005829 // cytosol // not recorded 0000166 // nucleotide binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0051082 // unfolded protein binding // inferred from electronic annotation
AA108284_at AA108284 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA108284 EST0027 Rattus norvegicus cDNA, 5' end /clone=pCO136 /clone_end=5' /gb=AA108284 /gi=1659752 /ug=Rn.22519 /len=205 AA108284 carbonic anhydrase 3 Car3 54232 NM_019292 0006730 // one-carbon metabolic process // inferred from electronic annotation /// 0006979 // response to oxidative stress // inferred from mutant phenotype 0005737 // cytoplasm // inferred from electronic annotation 0004089 // carbonate dehydratase activity // traceable author statement /// 0004089 // carbonate dehydratase activity // inferred from electronic annotation /// 0008270 // zinc ion binding // inferred from electronic annotation /// 0016151 // nickel ion binding // inferred from electronic annotation /// 0016151 // nickel ion binding // not recorded /// 0016829 // lyase activity // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation
AA684857_s_at AA684857 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA684857 EST105587 Rattus norvegicus cDNA, 5' end /clone=RPCAL77 /clone_end=5' /gb=AA684857 /gi=2671455 /ug=Rn.23245 /len=276 AA684857 heterogeneous nuclear ribonucleoprotein K Hnrnpk 117282 NM_057141 0006397 // mRNA processing // inferred from electronic annotation /// 0008380 // RNA splicing // inferred from electronic annotation /// 0008380 // RNA splicing // not recorded 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // not recorded /// 0005654 // nucleoplasm // inferred from electronic annotation /// 0005681 // spliceosomal complex // inferred from electronic annotation /// 0005730 // nucleolus // not recorded /// 0005737 // cytoplasm // inferred from electronic annotation /// 0030529 // ribonucleoprotein complex // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0003697 // single-stranded DNA binding // inferred from direct assay /// 0003723 // RNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0005515 // protein binding // not recorded
AA684879_at AA684879 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA684879 EST105661 Rattus norvegicus cDNA, 5' end /clone=RPCAP25 /clone_end=5' /gb=AA684879 /gi=2671477 /ug=Rn.870 /len=326 AA684879 death-domain associated protein Daxx 140926 NM_080891 0000281 // cytokinesis after mitosis // inferred from electronic annotation /// 0000281 // cytokinesis after mitosis // not recorded /// 0006350 // transcription // inferred from electronic annotation /// 0006915 // apoptosis // inferred from electronic annotation /// 0016481 // negative regulation of transcription // not recorded /// 0016481 // negative regulation of transcription // inferred from sequence or structural similarity /// 0016481 // negative regulation of transcription // inferred from electronic annotation /// 0030521 // androgen receptor signaling pathway // inferred from electronic annotation /// 0030521 // androgen receptor signaling pathway // not recorded /// 0031396 // regulation of protein ubiquitination // not recorded /// 0031396 // regulation of protein ubiquitination // inferred from sequence or structural similarity /// 0045449 // regulation of transcription // not recorded /// 0045449 // regulation of transcription // inferred from electronic annotation /// 0045892 // negative regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0045892 // negative regulation of transcription, DNA-dependent // not recorded 0000792 // heterochromatin // inferred from electronic annotation /// 0000792 // heterochromatin // not recorded /// 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // not recorded /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005634 // nucleus // inferred from electronic annotation /// 0005654 // nucleoplasm // inferred from electronic annotation /// 0005730 // nucleolus // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005938 // cell cortex // inferred from direct assay /// 0016605 // PML body // inferred from electronic annotation /// 0016605 // PML body // not recorded /// 0016605 // PML body // inferred from sequence or structural similarity /// 0043005 // neuron projection // inferred from direct assay /// 0044297 // cell body // inferred from direct assay 0002039 // p53 binding // not recorded /// 0005515 // protein binding // inferred from physical interaction /// 0005515 // protein binding // not recorded /// 0005515 // protein binding // inferred from electronic annotation /// 0008134 // transcription factor binding // inferred from electronic annotation /// 0008134 // transcription factor binding // not recorded /// 0008134 // transcription factor binding // inferred from sequence or structural similarity /// 0016564 // transcription repressor activity // inferred from electronic annotation /// 0016564 // transcription repressor activity // not recorded /// 0019899 // enzyme binding // not recorded /// 0031625 // ubiquitin protein ligase binding // not recorded /// 0042802 // identical protein binding // not recorded /// 0042802 // identical protein binding // inferred from electronic annotation /// 0042803 // protein homodimerization activity // inferred from electronic annotation /// 0042803 // protein homodimerization activity // not recorded /// 0042803 // protein homodimerization activity // inferred from sequence or structural similarity /// 0047485 // protein N-terminus binding // inferred from electronic annotation /// 0047485 // protein N-terminus binding // not recorded /// 0050681 // androgen receptor binding // inferred from electronic annotation /// 0050681 // androgen receptor binding // not recorded
AA684961_at AA684961 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA684961 EST105868 Rattus norvegicus cDNA, 5' end /clone=RPCAT95 /clone_end=5' /gb=AA684961 /gi=2671559 /ug=Rn.19935 /len=252 AA684961
AA685015_at AA685015 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA685015 EST106003 Rattus norvegicus cDNA, 5' end /clone=RPCAW26 /clone_end=5' /gb=AA685015 /gi=2671613 /ug=Rn.14670 /len=338 AA685015 similar to Hypothetical UPF0327 protein RGD1560187 362641 NM_001173556 /// XM_001071412 /// XM_002726642 /// XM_002729554 /// XM_342957 0005739 // mitochondrion // not recorded
AA685212_at AA685212 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA685212 EST106606 Rattus norvegicus cDNA, 5' end /clone=RPCBE32 /clone_end=5' /gb=AA685212 /gi=2671810 /ug=Rn.21423 /len=318 AA685212
AA685258_at AA685258 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA685258 EST106705 Rattus norvegicus cDNA, 5' end /clone=RPCBF28 /clone_end=5' /gb=AA685258 /gi=2671856 /ug=Rn.12929 /len=298 AA685258 enhancer of zeste homolog 1 (Drosophila) Ezh1 303547 NM_001107051 0005634 // nucleus // not recorded /// 0005730 // nucleolus // not recorded /// 0035098 // ESC/E(Z) complex // not recorded 0003677 // DNA binding // inferred from electronic annotation /// 0005515 // protein binding // not recorded
AA685760_at AA685760 Rattus norvegicus Jun 9, 2011 Exemplar sequence GenBank AA685760 EST108080 Rattus norvegicus cDNA, 5' end /clone=RPCCH39 /clone_end=5' /gb=AA685760 /gi=2672358 /ug=Rn.11514 /len=321 AA685760

Total number of rows: 8789

Table truncated, full table size 6981 Kbytes.






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