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Platform GPL1355 Query DataSets for GPL1355
Status Public on Jul 20, 2004
Title [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Rattus norvegicus
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site

The GeneChip Rat Genome 230 2.0 Array is a powerful tool for toxicology, neurobiology, and other applications using rat as a model organism.

- Provides comprehensive coverage of the transcribed rat genome on a single array
- Comprised of more than 31,000 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 well-substantiated rat genes
- The publicly available draft of the rat genome and leading public rat databases were used to refine sequences and provide a higher quality of data output

All probe sets represented on the GeneChip Rat Expression Set 230 are included on the GeneChip Rat Genome 230 2.0 Array. Sequences used in the design of the GeneChip Rat Genome 230 2.0 Array were selected from GenBank, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 99, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the rat genome from the Baylor College of Medicine Human Genome Sequencing Center (June 2002).

The GeneChip Rat Genome 230 2.0 Array includes representation of the RefSeq database sequences and probe sets related to sequences and refined EST clusters previously represented on the GeneChip Rat Genome U34 Set.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Eleven pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Rat Genome 230 2.0 Array.
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

June 03, 2009: annotation table updated with netaffx build 28
June 07, 2012: annotation table updated with netaffx build 32
June 27, 2016: annotation table updated with netaffx build 35
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=rat230-20
http://www.affymetrix.com/analysis/index.affx
Submission date Jul 20, 2004
Last update date Jul 31, 2017
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 (23030) GSM42161, GSM42162, GSM42163, GSM42164, GSM42165, GSM42166 
Series (746)
GSE2275 A Bioinformatic Analysis of Arginine-Sensitive Regulation of rat Hepatic Gene Expression
GSE2547 Olanzapine vs. Saline rat pfc
GSE2690 H_Alessio_05: sedentary and active lifestyles
Relations
Alternative to GPL6872 (Alternative CDF)
Alternative to GPL7598 (Alternative CDF)
Alternative to GPL8201 (Alternative CDF)
Alternative to GPL8597 (Alternative CDF)
Alternative to GPL9199 (Alternative CDF)
Alternative to GPL10226 (Alternative CDF)
Alternative to GPL14123 (Alternative CDF)
Alternative to GPL14976 (Alternative CDF:Rn230_Rn_UG_v9)
Alternative to GPL16251 (Alternative CDF [Brain Array Version 13.0.0, ENSG])
Alternative to GPL17780 (Alternative CDF:Rat2302_Rn_ENTREZG.cdf version 14.1.0)
Alternative to GPL18813 (alternative)
Alternative to GPL19144 (Alternative CDF [Rat2302_Rn_ENTREZG_18.0.0])
Alternative to GPL22499 (Alternative CDF [Rat2302_Rn_ENTREZG_19.0.0])

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
SPOT_ID identifies controls
Species Scientific Name
Annotation Date
Sequence Type
Sequence Source The database from which the sequence used to design this probe set was taken.
Target Description GenBank description associated with the representative public identifier. Blank for some probe sets.
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
1367452_at NM_133594 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_133594.1 /DB_XREF=gi:19424297 /GEN=Smt3h2 /FEA=FLmRNA /CNT=51 /TID=Rn.5958.1 /TIER=FL+Stack /STK=35 /UG=Rn.5958 /DEF=Rattus norvegicus SMT3 suppressor of mif two 3 homolog 2 (yeast) (Smt3h2), mRNA. /PROD=SMT3 suppressor of mif two 3 homolog 2 (yeast) /FL=gb:NM_133594.1 gb:L79949.1 NM_133594 small ubiquitin-like modifier 2 Sumo2 690244 NM_133594 0016925 // protein sumoylation // inferred from direct assay /// 0016925 // protein sumoylation // inferred from electronic annotation /// 0016925 // protein sumoylation // not recorded /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // not recorded /// 0034613 // cellular protein localization // inferred from direct assay /// 0045892 // negative regulation of transcription, DNA-templated // inferred from mutant phenotype /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // not recorded 0005634 // nucleus // inferred from electronic annotation /// 0016605 // PML body // not recorded /// 0016605 // PML body // inferred from sequence or structural similarity 0005515 // protein binding // inferred from physical interaction /// 0019789 // SUMO ligase activity // not recorded /// 0031625 // ubiquitin protein ligase binding // not recorded /// 0031625 // ubiquitin protein ligase binding // inferred from sequence or structural similarity /// 0044822 // poly(A) RNA binding // not recorded
1367453_at NM_053743 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_053743.1 /DB_XREF=gi:16758569 /GEN=Cdc37 /FEA=FLmRNA /CNT=31 /TID=Rn.17982.1 /TIER=FL+Stack /STK=25 /UG=Rn.17982 /LL=114562 /DEF=Rattus norvegicus CDC37 (cell division cycle 37, S. cerevisiae, homolog) (Cdc37), mRNA. /PROD=CDC37 (cell division cycle 37, S. cerevisiae,homolog) /FL=gb:D26564.1 gb:NM_053743.1 NM_053743 cell division cycle 37 Cdc37 114562 NM_053743 0051726 // regulation of cell cycle // inferred from expression pattern /// 0060334 // regulation of interferon-gamma-mediated signaling pathway // inferred from electronic annotation /// 0060334 // regulation of interferon-gamma-mediated signaling pathway // not recorded /// 0060338 // regulation of type I interferon-mediated signaling pathway // inferred from electronic annotation /// 0060338 // regulation of type I interferon-mediated signaling pathway // not recorded 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded /// 0032587 // ruffle membrane // inferred from direct assay /// 0043234 // protein complex // inferred from direct assay /// 0070062 // extracellular vesicular exosome // not recorded 0005515 // protein binding // inferred from electronic annotation /// 0019901 // protein kinase binding // inferred from physical interaction /// 0031072 // heat shock protein binding // not recorded /// 0031435 // mitogen-activated protein kinase kinase kinase binding // inferred from physical interaction /// 0043422 // protein kinase B binding // inferred from physical interaction /// 0051087 // chaperone binding // inferred from physical interaction /// 0051879 // Hsp90 protein binding // inferred from electronic annotation /// 0051879 // Hsp90 protein binding // not recorded
1367454_at NM_021765 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_021765.1 /DB_XREF=gi:11120715 /GEN=Copb /FEA=FLmRNA /CNT=22 /TID=Rn.37178.1 /TIER=FL+Stack /STK=17 /UG=Rn.37178 /LL=60384 /DEF=Rattus norvegicus beta prime COP (Copb), mRNA. /PROD=beta prime COP /FL=gb:NM_021765.1 gb:AF002705.1 NM_021765 coatomer protein complex, subunit beta 2 (beta prime) Copb2 60384 NM_021765 0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006891 // intra-Golgi vesicle-mediated transport // inferred from electronic annotation /// 0006891 // intra-Golgi vesicle-mediated transport // not recorded /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation 0000139 // Golgi membrane // inferred from direct assay /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from direct assay /// 0005794 // Golgi apparatus // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0015629 // actin cytoskeleton // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // not recorded /// 0030663 // COPI-coated vesicle membrane // inferred from electronic annotation /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation 0005080 // protein kinase C binding // inferred from physical interaction /// 0005198 // structural molecule activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction
1367455_at NM_053864 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_053864.1 /DB_XREF=gi:17865350 /GEN=Vcp /FEA=FLmRNA /CNT=53 /TID=Rn.3820.1 /TIER=FL+Stack /STK=16 /UG=Rn.3820 /LL=116643 /DEF=Rattus norvegicus valosin-containing protein (Vcp), mRNA. /PROD=valosin-containing protein /FL=gb:NM_053864.1 gb:U11760.1 NM_053864 valosin-containing protein Vcp 116643 NM_053864 0006200 // ATP catabolic process // inferred from direct assay /// 0006200 // ATP catabolic process // inferred from mutant phenotype /// 0006281 // DNA repair // inferred from electronic annotation /// 0006302 // double-strand break repair // not recorded /// 0006302 // double-strand break repair // inferred from sequence or structural similarity /// 0006310 // DNA recombination // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // not recorded /// 0006810 // transport // inferred from electronic annotation /// 0006888 // ER to Golgi vesicle-mediated transport // inferred from mutant phenotype /// 0006919 // activation of cysteine-type endopeptidase activity involved in apoptotic process // inferred from electronic annotation /// 0006919 // activation of cysteine-type endopeptidase activity involved in apoptotic process // not recorded /// 0006974 // cellular response to DNA damage stimulus // not recorded /// 0006974 // cellular response to DNA damage stimulus // inferred from sequence or structural similarity /// 0016567 // protein ubiquitination // not recorded /// 0016567 // protein ubiquitination // inferred from sequence or structural similarity /// 0018279 // protein N-linked glycosylation via asparagine // not recorded /// 0018279 // protein N-linked glycosylation via asparagine // inferred from sequence or structural similarity /// 0019985 // translesion synthesis // not recorded /// 0019985 // translesion synthesis // inferred from sequence or structural similarity /// 0030433 // ER-associated ubiquitin-dependent protein catabolic process // not recorded /// 0030433 // ER-associated ubiquitin-dependent protein catabolic process // inferred from sequence or structural similarity /// 0030970 // retrograde protein transport, ER to cytosol // inferred from electronic annotation /// 0030970 // retrograde protein transport, ER to cytosol // not recorded /// 0031334 // positive regulation of protein complex assembly // inferred from electronic annotation /// 0031334 // positive regulation of protein complex assembly // not recorded /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // inferred from mutant phenotype /// 0032436 // positive regulation of proteasomal ubiquitin-dependent protein catabolic process // not recorded /// 0034214 // protein hexamerization // inferred from direct assay /// 0045732 // positive regulation of protein catabolic process // not recorded /// 0051260 // protein homooligomerization // inferred from direct assay /// 0070842 // aggresome assembly // inferred from electronic annotation /// 0070842 // aggresome assembly // not recorded /// 1903006 // positive regulation of protein K63-linked deubiquitination // not recorded /// 1903007 // positive regulation of Lys63-specific deubiquitinase activity // not recorded 0000502 // proteasome complex // inferred from electronic annotation /// 0000502 // proteasome complex // not recorded /// 0000836 // Hrd1p ubiquitin ligase complex // not recorded /// 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // not recorded /// 0005730 // nucleolus // not recorded /// 0005737 // cytoplasm // not recorded /// 0005783 // endoplasmic reticulum // inferred from direct assay /// 0005783 // endoplasmic reticulum // not recorded /// 0005789 // endoplasmic reticulum membrane // not recorded /// 0005811 // lipid particle // inferred from electronic annotation /// 0005811 // lipid particle // not recorded /// 0005829 // cytosol // inferred from direct assay /// 0005829 // cytosol // not recorded /// 0035861 // site of double-strand break // not recorded /// 0035861 // site of double-strand break // inferred from sequence or structural similarity /// 0043231 // intracellular membrane-bounded organelle // inferred from direct assay /// 0043234 // protein complex // not recorded /// 0048471 // perinuclear region of cytoplasm // not recorded /// 0070062 // extracellular vesicular exosome // not recorded 0000166 // nucleotide binding // inferred from electronic annotation /// 0005102 // receptor binding // inferred from direct assay /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from direct assay /// 0005524 // ATP binding // inferred from mutant phenotype /// 0008289 // lipid binding // inferred from electronic annotation /// 0009378 // four-way junction helicase activity // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016887 // ATPase activity // inferred from direct assay /// 0016887 // ATPase activity // inferred from mutant phenotype /// 0017111 // nucleoside-triphosphatase activity // inferred from electronic annotation /// 0019903 // protein phosphatase binding // inferred from electronic annotation /// 0019903 // protein phosphatase binding // not recorded /// 0019904 // protein domain specific binding // inferred from electronic annotation /// 0019904 // protein domain specific binding // not recorded /// 0031593 // polyubiquitin binding // inferred from electronic annotation /// 0031593 // polyubiquitin binding // not recorded /// 0032403 // protein complex binding // inferred from physical interaction /// 0035800 // deubiquitinase activator activity // not recorded /// 0042802 // identical protein binding // inferred from direct assay /// 0043531 // ADP binding // inferred from mutant phenotype /// 0044822 // poly(A) RNA binding // not recorded /// 1990381 // ubiquitin-specific protease binding // not recorded
1367456_at NM_031237 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_031237.1 /DB_XREF=gi:13676842 /GEN=Ube2d3 /FEA=FLmRNA /CNT=47 /TID=Rn.2778.1 /TIER=FL+Stack /STK=11 /UG=Rn.2778 /LL=81920 /DEF=Rattus norvegicus ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC45) (Ube2d3), mRNA. /PROD=ubiquitin-conjugating enzyme E2D 3 (homologousto yeast UBC45) /FL=gb:NM_031237.1 gb:AB006852.1 gb:U13175.1 NM_031237 ubiquitin-conjugating enzyme E2D 2 /// ubiquitin-conjugating enzyme E2D 3 Ube2d2 /// Ube2d3 81920 641452 NM_001037292 /// NM_031237 /// XM_006233333 /// XM_006233334 /// XM_006233335 /// XM_006233336 /// XM_006233337 /// XM_006233338 0000209 // protein polyubiquitination // not recorded /// 0000209 // protein polyubiquitination // inferred from sequence or structural similarity /// 0006281 // DNA repair // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from direct assay /// 0006513 // protein monoubiquitination // inferred from electronic annotation /// 0006513 // protein monoubiquitination // not recorded /// 0006915 // apoptotic process // inferred from electronic annotation /// 0006974 // cellular response to DNA damage stimulus // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 0016567 // protein ubiquitination // not recorded /// 0043161 // proteasome-mediated ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0043161 // proteasome-mediated ubiquitin-dependent protein catabolic process // not recorded /// 0043161 // proteasome-mediated ubiquitin-dependent protein catabolic process // inferred from sequence or structural similarity /// 0070936 // protein K48-linked ubiquitination // inferred from electronic annotation /// 0070936 // protein K48-linked ubiquitination // not recorded /// 0070936 // protein K48-linked ubiquitination // inferred from sequence or structural similarity /// 0070979 // protein K11-linked ubiquitination // inferred from electronic annotation /// 0070979 // protein K11-linked ubiquitination // not recorded /// 0070979 // protein K11-linked ubiquitination // inferred from sequence or structural similarity 0000151 // ubiquitin ligase complex // not recorded /// 0005768 // endosome // inferred from electronic annotation /// 0005886 // plasma membrane // inferred from electronic annotation /// 0010008 // endosome membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0043234 // protein complex // not recorded 0000166 // nucleotide binding // inferred from electronic annotation /// 0004842 // ubiquitin-protein transferase activity // inferred from direct assay /// 0004842 // ubiquitin-protein transferase activity // inferred from electronic annotation /// 0004842 // ubiquitin-protein transferase activity // not recorded /// 0004842 // ubiquitin-protein transferase activity // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016874 // ligase activity // inferred from electronic annotation /// 0016881 // acid-amino acid ligase activity // inferred from electronic annotation
1367457_at NM_053739 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_053739.1 /DB_XREF=gi:16758561 /GEN=Becn1 /FEA=FLmRNA /CNT=20 /TID=Rn.2776.1 /TIER=FL+Stack /STK=10 /UG=Rn.2776 /LL=114558 /DEF=Rattus norvegicus beclin 1 (coiled-coil, myosin-like BCL2-interacting protein) (Becn1), mRNA. /PROD=beclin 1 (coiled-coil, myosin-likeBCL2-interacting protein) /FL=gb:AY033824.1 gb:NM_053739.1 NM_053739 beclin 1, autophagy related Becn1 114558 NM_001034117 /// NM_053739 0000045 // autophagic vacuole assembly // inferred from mutant phenotype /// 0000910 // cytokinesis // inferred from electronic annotation /// 0000910 // cytokinesis // inferred from sequence or structural similarity /// 0001666 // response to hypoxia // inferred from expression pattern /// 0006914 // autophagy // inferred from expression pattern /// 0006914 // autophagy // inferred from mutant phenotype /// 0006914 // autophagy // not recorded /// 0007040 // lysosome organization // inferred from electronic annotation /// 0007040 // lysosome organization // not recorded /// 0007049 // cell cycle // inferred from electronic annotation /// 0008285 // negative regulation of cell proliferation // inferred from electronic annotation /// 0008285 // negative regulation of cell proliferation // not recorded /// 0016239 // positive regulation of macroautophagy // inferred from electronic annotation /// 0016239 // positive regulation of macroautophagy // not recorded /// 0033197 // response to vitamin E // inferred from expression pattern /// 0042493 // response to drug // inferred from expression pattern /// 0048666 // neuron development // inferred from electronic annotation /// 0048666 // neuron development // not recorded /// 0050435 // beta-amyloid metabolic process // inferred from electronic annotation /// 0050435 // beta-amyloid metabolic process // not recorded /// 0050790 // regulation of catalytic activity // not recorded /// 0051301 // cell division // inferred from electronic annotation /// 0051607 // defense response to virus // inferred from electronic annotation /// 0051707 // response to other organism // not recorded /// 0060548 // negative regulation of cell death // inferred from mutant phenotype /// 0071275 // cellular response to aluminum ion // inferred from expression pattern /// 0071364 // cellular response to epidermal growth factor stimulus // inferred from expression pattern 0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005802 // trans-Golgi network // inferred from electronic annotation /// 0005802 // trans-Golgi network // not recorded /// 0016020 // membrane // inferred from electronic annotation /// 0016023 // cytoplasmic membrane-bounded vesicle // inferred from electronic annotation /// 0016023 // cytoplasmic membrane-bounded vesicle // not recorded /// 0030425 // dendrite // inferred from direct assay /// 0043234 // protein complex // inferred from electronic annotation /// 0043234 // protein complex // not recorded /// 0045335 // phagocytic vesicle // not recorded 0005515 // protein binding // inferred from electronic annotation /// 0043565 // sequence-specific DNA binding // inferred from electronic annotation
1367458_at NM_031342 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_031342.1 /DB_XREF=gi:13786177 /GEN=Lypla2 /FEA=FLmRNA /CNT=14 /TID=Rn.8586.1 /TIER=FL /STK=4 /UG=Rn.8586 /LL=83510 /DEF=Rattus norvegicus lysophospholipase II (Lypla2), mRNA. /PROD=lysophospholipase II /FL=gb:NM_031342.1 gb:AB021645.1 NM_031342 lysophospholipase II Lypla2 83510 NM_031342 0006629 // lipid metabolic process // inferred from electronic annotation /// 0006631 // fatty acid metabolic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation /// 0070062 // extracellular vesicular exosome // not recorded 0016787 // hydrolase activity // inferred from electronic annotation
1367459_at BE329198 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BE329198 /DB_XREF=gi:9202974 /DB_XREF=hq38b08.x1 /CLONE=IMAGE:3121623 /FEA=FLmRNA /CNT=82 /TID=Rn.1391.1 /TIER=Stack /STK=9 /UG=Rn.1391 /LL=64310 /UG_GENE=Arf1 /UG_TITLE=ADP-ribosylation factor 1 /FL=gb:NM_022518.1 gb:L12380.1 BE329198 ADP-ribosylation factor 1 Arf1 64310 NM_022518 /// XM_006246524 /// XM_006246525 0002090 // regulation of receptor internalization // inferred from direct assay /// 0006810 // transport // inferred from electronic annotation /// 0006878 // cellular copper ion homeostasis // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0007186 // G-protein coupled receptor signaling pathway // inferred from electronic annotation /// 0007264 // small GTPase mediated signal transduction // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // not recorded /// 0034315 // regulation of Arp2/3 complex-mediated actin nucleation // inferred from direct assay /// 0060292 // long term synaptic depression // inferred from direct assay /// 0097061 // dendritic spine organization // inferred from mutant phenotype 0005622 // intracellular // inferred from electronic annotation /// 0005634 // nucleus // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded /// 0005886 // plasma membrane // inferred from electronic annotation /// 0012505 // endomembrane system // not recorded /// 0014069 // postsynaptic density // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0030017 // sarcomere // inferred from electronic annotation /// 0030017 // sarcomere // not recorded /// 0030054 // cell junction // inferred from electronic annotation /// 0043005 // neuron projection // inferred from electronic annotation /// 0045202 // synapse // inferred from electronic annotation /// 0045211 // postsynaptic membrane // inferred from electronic annotation /// 0048471 // perinuclear region of cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003924 // GTPase activity // inferred from electronic annotation /// 0004871 // signal transducer activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation /// 0019001 // guanyl nucleotide binding // inferred from electronic annotation /// 0031683 // G-protein beta/gamma-subunit complex binding // inferred from electronic annotation
1367460_at BM387347 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BM387347 /DB_XREF=gi:18187400 /DB_XREF=UI-R-CN1-cjj-c-19-0-UI.s1 /CLONE=UI-R-CN1-cjj-c-19-0-UI /FEA=FLmRNA /CNT=36 /TID=Rn.1441.1 /TIER=Stack /STK=20 /UG=Rn.1441 /LL=29661 /UG_GENE=Gdi2 /UG_TITLE=guanosine diphosphate (GDP) dissociation inhibitor 2 /FL=gb:NM_017276.1 BM387347 GDP dissociation inhibitor 2 Gdi2 29662 NM_017276 0007264 // small GTPase mediated signal transduction // not recorded /// 0015031 // protein transport // traceable author statement /// 0016192 // vesicle-mediated transport // inferred from expression pattern /// 0032851 // positive regulation of Rab GTPase activity // not recorded /// 0043547 // positive regulation of GTPase activity // inferred from electronic annotation /// 0050790 // regulation of catalytic activity // inferred from direct assay 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0005829 // cytosol // traceable author statement /// 0016020 // membrane // inferred from electronic annotation /// 0070062 // extracellular vesicular exosome // not recorded 0005093 // Rab GDP-dissociation inhibitor activity // inferred from direct assay /// 0005096 // GTPase activator activity // inferred from electronic annotation /// 0005097 // Rab GTPase activator activity // not recorded /// 0031267 // small GTPase binding // inferred from direct assay /// 0044822 // poly(A) RNA binding // not recorded
1367461_at NM_080781 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:NM_080781.1 /DB_XREF=gi:18158448 /GEN=Copb1 /FEA=FLmRNA /CNT=30 /TID=Rn.4327.1 /TIER=FL+Stack /STK=14 /UG=Rn.4327 /LL=114023 /DEF=Rattus norvegicus coatomer protein complex, subunit beta 1 (Copb1), mRNA. /PROD=coatomer protein complex, subunit beta 1 /FL=gb:NM_080781.1 NM_080781 coatomer protein complex, subunit beta 1 Copb1 114023 NM_080781 /// XM_006230073 /// XM_006230074 0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // traceable author statement /// 0006891 // intra-Golgi vesicle-mediated transport // inferred from direct assay /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation 0000139 // Golgi membrane // inferred from electronic annotation /// 0005737 // cytoplasm // not recorded /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005793 // endoplasmic reticulum-Golgi intermediate compartment // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from direct assay /// 0005794 // Golgi apparatus // not recorded /// 0005798 // Golgi-associated vesicle // inferred from direct assay /// 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // inferred from direct assay /// 0030137 // COPI-coated vesicle // not recorded /// 0030663 // COPI-coated vesicle membrane // inferred from electronic annotation /// 0031090 // organelle membrane // inferred from electronic annotation /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation /// 0043231 // intracellular membrane-bounded organelle // not recorded 0005198 // structural molecule activity // inferred from electronic annotation /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction
1367462_at U10861 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:U10861.1 /DB_XREF=gi:505657 /FEA=FLmRNA /CNT=39 /TID=Rn.3430.1 /TIER=FL+Stack /STK=7 /UG=Rn.3430 /LL=29156 /UG_GENE=Capns1 /DEF=Rattus norvegicus calpain small subunit mRNA, complete cds. /PROD=calpain small subunit /FL=gb:U10861.1 U10861 calpain, small subunit 1 Capns1 29156 NM_017118 0006508 // proteolysis // inferred from mutant phenotype /// 0006508 // proteolysis // not recorded 0005737 // cytoplasm // not recorded /// 0005829 // cytosol // not recorded /// 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // not recorded /// 0070062 // extracellular vesicular exosome // not recorded 0004198 // calcium-dependent cysteine-type endopeptidase activity // inferred from direct assay /// 0004198 // calcium-dependent cysteine-type endopeptidase activity // not recorded /// 0005509 // calcium ion binding // inferred from electronic annotation /// 0005509 // calcium ion binding // traceable author statement /// 0046872 // metal ion binding // inferred from electronic annotation /// 0046982 // protein heterodimerization activity // inferred from physical interaction
1367463_at AI235510 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:AI235510 /DB_XREF=gi:3829016 /DB_XREF=EST232072 /CLONE=ROVCS86 /FEA=mRNA /CNT=29 /TID=Rn.3235.1 /TIER=Stack /STK=23 /UG=Rn.3235 /UG_TITLE=B-cell receptor associated protein 37 (BAP-37) mRNA, partial cds and 3 untranslated sequence AI235510 prohibitin 2 Phb2 114766 NM_001013035 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0033147 // negative regulation of intracellular estrogen receptor signaling pathway // inferred from electronic annotation /// 0033147 // negative regulation of intracellular estrogen receptor signaling pathway // not recorded /// 0033600 // negative regulation of mammary gland epithelial cell proliferation // inferred from electronic annotation /// 0033600 // negative regulation of mammary gland epithelial cell proliferation // not recorded /// 0045892 // negative regulation of transcription, DNA-templated // not recorded /// 0045892 // negative regulation of transcription, DNA-templated // inferred from sequence or structural similarity /// 0060744 // mammary gland branching involved in thelarche // inferred from electronic annotation /// 0060744 // mammary gland branching involved in thelarche // not recorded /// 0060749 // mammary gland alveolus development // inferred from electronic annotation /// 0060749 // mammary gland alveolus development // not recorded /// 0060762 // regulation of branching involved in mammary gland duct morphogenesis // inferred from electronic annotation /// 0060762 // regulation of branching involved in mammary gland duct morphogenesis // not recorded 0005634 // nucleus // not recorded /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005739 // mitochondrion // not recorded /// 0005743 // mitochondrial inner membrane // not recorded /// 0005743 // mitochondrial inner membrane // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0016363 // nuclear matrix // not recorded /// 0016363 // nuclear matrix // inferred from sequence or structural similarity /// 0043234 // protein complex // not recorded /// 0043234 // protein complex // inferred from sequence or structural similarity /// 0070062 // extracellular vesicular exosome // not recorded
1367464_at AI598391 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:AI598391 /DB_XREF=gi:4607439 /DB_XREF=EST250094 /CLONE=REMDQ63 /FEA=mRNA /CNT=15 /TID=Rn.21553.1 /TIER=Stack /STK=11 /UG=Rn.21553 /LL=84401 /UG_GENE=Siahbp1 /UG_TITLE=siah binding protein 1; FBP interacting repressor; pyrimidine tract binding splicing factor; Ro ribonucleoprotein-binding protein 1 AI598391 poly-U binding splicing factor 60 Puf60 84401 NM_001191880 /// XM_006241894 /// XM_006241895 /// XM_006241896 /// XM_006241897 /// XM_006241898 /// XM_006241899 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0006397 // mRNA processing // inferred from electronic annotation /// 0006915 // apoptotic process // inferred from electronic annotation /// 0008380 // RNA splicing // inferred from electronic annotation 0005634 // nucleus // inferred from electronic annotation /// 0019907 // cyclin-dependent protein kinase activating kinase holoenzyme complex // inferred from electronic annotation /// 0019907 // cyclin-dependent protein kinase activating kinase holoenzyme complex // not recorded /// 0030529 // ribonucleoprotein complex // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003676 // nucleic acid binding // inferred from electronic annotation /// 0003677 // DNA binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0042802 // identical protein binding // inferred from electronic annotation /// 0042802 // identical protein binding // not recorded /// 0044822 // poly(A) RNA binding // not recorded
1367465_at AI013627 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:AI013627 /DB_XREF=gi:3227683 /DB_XREF=EST208302 /CLONE=RSPBP78 /FEA=DNA /CNT=22 /TID=Rn.7262.1 /TIER=Stack /STK=19 /UG=Rn.7262 /UG_TITLE=Rattus norvegicus DAD-1 gene AI013627 defender against cell death 1 Dad1 192275 NM_138910 0001824 // blastocyst development // inferred from electronic annotation /// 0001824 // blastocyst development // not recorded /// 0006486 // protein glycosylation // inferred from electronic annotation /// 0006486 // protein glycosylation // inferred from sequence or structural similarity /// 0006915 // apoptotic process // inferred from electronic annotation /// 0007584 // response to nutrient // inferred from expression pattern /// 0042493 // response to drug // inferred from expression pattern /// 0043066 // negative regulation of apoptotic process // inferred from electronic annotation /// 0043066 // negative regulation of apoptotic process // not recorded 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005789 // endoplasmic reticulum membrane // inferred from electronic annotation /// 0008250 // oligosaccharyltransferase complex // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0070062 // extracellular vesicular exosome // not recorded 0004576 // oligosaccharyl transferase activity // inferred from sequence or structural similarity /// 0004579 // dolichyl-diphosphooligosaccharide-protein glycotransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016757 // transferase activity, transferring glycosyl groups // inferred from electronic annotation
1367466_at AI406518 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:AI406518 /DB_XREF=gi:4250022 /DB_XREF=EST234804 /CLONE=RBRDL35 /FEA=EST /CNT=49 /TID=Rn.897.1 /TIER=Stack /STK=47 /UG=Rn.897 /UG_TITLE=ESTs, Moderately similar to C50C3.6.p (Caenorhabditis elegans) (C.elegans) AI406518 pre-mRNA processing factor 8 Prpf8 287530 NM_001191590 /// XM_006246892 0000398 // mRNA splicing, via spliceosome // inferred from electronic annotation 0005634 // nucleus // not recorded /// 0005681 // spliceosomal complex // inferred from electronic annotation /// 0071013 // catalytic step 2 spliceosome // inferred from electronic annotation /// 0071013 // catalytic step 2 spliceosome // not recorded 0003676 // nucleic acid binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0017070 // U6 snRNA binding // inferred from electronic annotation /// 0030623 // U5 snRNA binding // inferred from electronic annotation /// 0044822 // poly(A) RNA binding // not recorded /// 0046982 // protein heterodimerization activity // inferred from electronic annotation
1367467_at BG380638 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BG380638 /DB_XREF=gi:13305110 /DB_XREF=UI-R-CT0-btz-f-07-0-UI.s1 /CLONE=UI-R-CT0-btz-f-07-0-UI /FEA=EST /CNT=56 /TID=Rn.121.1 /TIER=Stack /STK=45 /UG=Rn.121 /UG_TITLE=ESTs, Weakly similar to T26931 hypothetical protein Y45F10D.4 - Caenorhabditis elegans (C.elegans) BG380638 iron-sulfur cluster assembly enzyme Iscu 288740 NM_001105936 0016226 // iron-sulfur cluster assembly // inferred from electronic annotation 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // not recorded /// 0005829 // cytosol // inferred from electronic annotation /// 0005829 // cytosol // not recorded 0005506 // iron ion binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0032947 // protein complex scaffold // inferred from electronic annotation /// 0032947 // protein complex scaffold // not recorded /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation
1367468_at BM386654 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BM386654 /DB_XREF=gi:18186707 /DB_XREF=UI-R-CN1-cjg-j-09-0-UI.s1 /CLONE=UI-R-CN1-cjg-j-09-0-UI /FEA=EST /CNT=43 /TID=Rn.1095.1 /TIER=Stack /STK=38 /UG=Rn.1095 /UG_TITLE=ESTs, Weakly similar to ZF94_RAT ZINC FINGER PROTEIN 94 (ZFP-94) (ZINC FINGER PROTEIN Y1) (RLZF-Y) (R.norvegicus) BM386654 SCAN domain-containing 1 Scand1 362252 NM_001108599 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0006357 // regulation of transcription from RNA polymerase II promoter // not recorded /// 0006366 // transcription from RNA polymerase II promoter // not recorded /// 2001141 // regulation of RNA biosynthetic process // not recorded 0005634 // nucleus // not recorded 0000981 // sequence-specific DNA binding RNA polymerase II transcription factor activity // not recorded /// 0003700 // sequence-specific DNA binding transcription factor activity // inferred from electronic annotation /// 0003713 // transcription coactivator activity // not recorded
1367469_at BG667162 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BG667162 /DB_XREF=gi:13889084 /DB_XREF=DRA07E03 /CLONE=DRA07E03 /FEA=EST /CNT=59 /TID=Rn.3992.1 /TIER=Stack /STK=32 /UG=Rn.3992 /UG_TITLE=ESTs, Weakly similar to S49172 translation initiation factor eIF-4 gamma (H.sapiens) BG667162 eukaryotic translation initiation factor 4, gamma 2 Eif4g2 361628 NM_001017374 0006446 // regulation of translational initiation // not recorded /// 0016070 // RNA metabolic process // inferred from electronic annotation 0005737 // cytoplasm // not recorded /// 0016281 // eukaryotic translation initiation factor 4F complex // not recorded 0003677 // DNA binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from electronic annotation /// 0003743 // translation initiation factor activity // not recorded /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0008135 // translation factor activity, nucleic acid binding // not recorded /// 0044822 // poly(A) RNA binding // not recorded
1367470_at AA851321 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:AA851321 /DB_XREF=gi:2938861 /DB_XREF=EST194089 /CLONE=RPLAF21 /FEA=EST /CNT=34 /TID=Rn.15760.1 /TIER=Stack /STK=31 /UG=Rn.15760 /UG_TITLE=ESTs, Weakly similar to ARF6_HUMAN ADP-RIBOSYLATION FACTOR 6 (R.norvegicus) AA851321 secretion associated, Ras related GTPase 1A Sar1a 361842 NM_001007739 /// XM_006256450 /// XM_006256451 0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0007186 // G-protein coupled receptor signaling pathway // inferred from electronic annotation /// 0007264 // small GTPase mediated signal transduction // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // not recorded /// 1901301 // regulation of cargo loading into COPII-coated vesicle // not recorded /// 1901303 // negative regulation of cargo loading into COPII-coated vesicle // not recorded 0005622 // intracellular // inferred from electronic annotation /// 0005634 // nucleus // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // not recorded /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005794 // Golgi apparatus // not recorded /// 0016529 // sarcoplasmic reticulum // inferred from electronic annotation /// 0016529 // sarcoplasmic reticulum // not recorded /// 0070062 // extracellular vesicular exosome // not recorded 0000166 // nucleotide binding // inferred from electronic annotation /// 0003924 // GTPase activity // inferred from electronic annotation /// 0004871 // signal transducer activity // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation /// 0019001 // guanyl nucleotide binding // inferred from electronic annotation /// 0031683 // G-protein beta/gamma-subunit complex binding // inferred from electronic annotation
1367471_at BI279090 Rattus norvegicus Oct 6, 2014 Consensus sequence GenBank gb:BI279090 /DB_XREF=gi:14926572 /DB_XREF=UI-R-DA0-byj-b-03-0-UI.s1 /CLONE=UI-R-DA0-byj-b-03-0-UI /FEA=EST /CNT=38 /TID=Rn.1769.1 /TIER=Stack /STK=30 /UG=Rn.1769 /UG_TITLE=ESTs, Highly similar to RPB5_HUMAN DNA-DIRECTED RNA POLYMERASE II 23 KD POLYPEPTIDE (H.sapiens) BI279090 polymerase (RNA) II (DNA directed) polypeptide E Polr2e 690966 NM_001109614 /// XM_006241009 /// XM_006241010 /// XM_006241011 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006360 // transcription from RNA polymerase I promoter // not recorded /// 0006366 // transcription from RNA polymerase II promoter // not recorded /// 0006366 // transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006383 // transcription from RNA polymerase III promoter // not recorded 0005634 // nucleus // not recorded /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005665 // DNA-directed RNA polymerase II, core complex // not recorded /// 0005665 // DNA-directed RNA polymerase II, core complex // inferred from sequence or structural similarity /// 0005666 // DNA-directed RNA polymerase III complex // not recorded /// 0005736 // DNA-directed RNA polymerase I complex // not recorded 0001054 // RNA polymerase I activity // not recorded /// 0001055 // RNA polymerase II activity // not recorded /// 0001056 // RNA polymerase III activity // not recorded /// 0003677 // DNA binding // inferred from electronic annotation /// 0003899 // DNA-directed RNA polymerase activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation

Total number of rows: 31099

Table truncated, full table size 41255 Kbytes.






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