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Platform GPL16493 Query DataSets for GPL16493
Status Public on Jan 11, 2013
Title [PorGene-1_0-st] Porcine Gene 1.0 ST Array [transcript (gene) version]
Technology type in situ oligonucleotide
Distribution commercial
Organism Sus scrofa
Manufacturer Affymetrix
Manufacture protocol See manufacturer's web site
 
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

Jan 11, 2013: annotation table updated with netaffx build 33
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=modelorg_1_1_array
http://www.affymetrix.com/support/technical/libraryfilesmain.affx
Submission date Jan 11, 2013
Last update date Oct 06, 2016
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 (358) GSM1078874, GSM1078875, GSM1078876, GSM1078877, GSM1078878, GSM1078879 
Series (26)
GSE44096 Deletion of DMD exon 52 in the pig results in fulminant muscular dystrophy
GSE45554 Resistant starch induces catabolic but suppresses immune and cell division pathways and changes the microbiome in proximal colon of male pigs
GSE56427 Pharmacodynamic effects of GLP-1 agonist liraglutide in adolescent, prediabetic pigs
Relations
Alternative to GPL22530 ([porgene10st_Ss_ENTREZG_17.0.0])

Data table header descriptions
ID transcript_cluster_id
probeset_id Unique identifier for the probe set.
SPOT_ID genomic location of the transcript cluster in the version of the genome assembly used at annotation time. Coordinates are standard 1-based (length=stop-start+1).
seqname chromosome number
strand (+|-)
start (integer). Coordinates are standard 1-based (length=stop-start+1).
stop (integer). Coordinates are standard 1-based (length=stop-start+1).
total_probes Total number of probes contained by this transcript cluster.
gene_assignment Gene name(s) for each assigned mRNA for mRNAs that corresponds to known genes. (multipart)
mrna_assignment Public mRNAs that should be detected by this probe set based on sequence alignment determined at the time of the current NetAffx annotation update. (multipart).
swissprot
unigene
GO_biological_process
GO_cellular_component
GO_molecular_function
pathway
protein_domains
crosshyb_type
category Array design category of the transcript cluster

Data table
ID probeset_id SPOT_ID seqname strand start stop total_probes gene_assignment mrna_assignment swissprot unigene GO_biological_process GO_cellular_component GO_molecular_function pathway protein_domains crosshyb_type category
15183074 15183074 chr1(+):349788-389816 chr1 + 349788 389816 33 ENSSSCT00000004429 // LOC100511482 // PHD finger protein 10-like // --- // 100511482 /// ENSSSCT00000004429 // LOC100511109 // PHD finger protein 10-like // --- // 100511109 /// ENSSSCT00000004435 // LOC100511482 // PHD finger protein 10-like // --- // 100511482 /// ENSSSCT00000004435 // LOC100511109 // PHD finger protein 10-like // --- // 100511109 /// XM_003121078 // LOC100511482 // PHD finger protein 10-like // --- // 100511482 AK346362 // GenBank HTC // Sus scrofa mRNA, clone:LVRM10153G04, expressed in liver. // chr1 // 100 // 97 // 33 // 32 // 0 /// ENSSSCT00000004429 // ENSEMBL // cdna:novel chromosome:Sscrofa10.2:1:1130103:1148947:-1 gene:ENSSSCG00000027750 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 33 // 33 // 0 /// ENSSSCT00000004435 // ENSEMBL // cdna:novel chromosome:Sscrofa10.2:1:935012:955845:1 gene:ENSSSCG00000030155 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 33 // 33 // 0 /// XM_003121078 // RefSeq // PREDICTED: Sus scrofa PHD finger protein 10-like (LOC100511482), mRNA. // chr1 // 100 // 88 // 30 // 29 // 0 /// GENSCAN00000042760 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:1132903:1151681:-1 transcript_biotype:protein_coding // chr1 // 100 // 91 // 30 // 30 // 0 /// GENSCAN00000010652 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:868589:953047:1 transcript_biotype:protein_coding // chr1 // 100 // 91 // 30 // 30 // 0 --- --- --- --- --- --- ENSSSCT00000004429 // Pfam // IPR019787 // Zinc finger, PHD-finger /// ENSSSCT00000004435 // Pfam // IPR019787 // Zinc finger, PHD-finger 3 main
15183086 15183086 chr1(+):399819-708754 chr1 + 399819 708754 22 XM_003480212 // LOC100736968 // WD repeat-containing protein 27-like // --- // 100736968 ENSSSCT00000004431 // ENSEMBL // cdna:novel chromosome:Sscrofa10.2:1:987441:1175801:1 gene:ENSSSCG00000004008 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 27 // 6 // 6 // 0 /// XM_003480212 // RefSeq // PREDICTED: Sus scrofa WD repeat-containing protein 27-like (LOC100736968), mRNA. // chr1 // 100 // 50 // 11 // 11 // 0 /// GENSCAN00000010683 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:959662:997437:1 transcript_biotype:protein_coding // chr1 // 100 // 32 // 7 // 7 // 0 --- --- --- --- --- --- ENSSSCT00000004431 // Pfam // IPR001680 // WD40 repeat 1 main
15183109 15183109 chr1(+):440195-666100 chr1 + 440195 666100 25 --- ENSSSCT00000004433 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:927952:930239:1 gene:ENSSSCG00000004009 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 40 // 10 // 10 // 0 --- --- --- --- --- --- ENSSSCT00000004433 // Pfam // IPR005334 // Tctex-1 1 main
15183114 15183114 chr1(+):926901-949670 chr1 + 926901 949670 29 --- GENSCAN00000042743 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:1591881:1652001:-1 transcript_biotype:protein_coding // chr1 // 100 // 93 // 27 // 27 // 0 --- --- --- --- --- --- --- 1 main
15183133 15183133 chr1(+):1155336-1155422 chr1 + 1155336 1155422 13 --- ENSSSCT00000020209 // ENSEMBL // ncrna:miRNA chromosome:Sscrofa10.2:1:1952604:1952690:1 gene:ENSSSCG00000018614 gene_biotype:miRNA transcript_biotype:miRNA // chr1 // 100 // 100 // 13 // 13 // 0 --- --- --- --- --- --- --- 1 main
15183135 15183135 chr1(+):1880137-1889243 chr1 + 1880137 1889243 25 ENSSSCT00000004439 // LOC100512933 // dapper homolog 2-like // --- // 100512933 /// XM_003121086 // LOC100512933 // dapper homolog 2-like // --- // 100512933 ENSSSCT00000004439 // ENSEMBL // cdna:novel chromosome:Sscrofa10.2:1:2447572:2457750:1 gene:ENSSSCG00000004014 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 92 // 96 // 22 // 24 // 0 /// XM_003121086 // RefSeq // PREDICTED: Sus scrofa dapper homolog 2-like (LOC100512933), mRNA. // chr1 // 88 // 96 // 21 // 24 // 0 /// GENSCAN00000021288 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:2424550:2457002:1 transcript_biotype:protein_coding // chr1 // 92 // 96 // 22 // 24 // 0 --- --- --- --- --- --- --- 3 main
15183141 15183141 chr1(+):2048144-2057707 chr1 + 2048144 2057707 23 XM_003121090 // LOC100514019 // kinesin-like protein KIF25-like // --- // 100514019 XM_003121090 // RefSeq // PREDICTED: Sus scrofa kinesin-like protein KIF25-like (LOC100514019), mRNA. // chr1 // 100 // 91 // 21 // 21 // 0 --- --- --- --- --- --- --- 1 main
15183149 15183149 chr1(+):3193117-3210650 chr1 + 3193117 3210650 31 XM_001928085 // LOC100157985 // Ribonuclease T2 // 1|1 // 100157985 /// ENSSSCT00000004450 // LOC100157985 // Ribonuclease T2 // 1|1 // 100157985 AK392845 // GenBank HTC // Sus scrofa mRNA, clone: ITT010014D01, expressed in intestine. // chr1 // 100 // 100 // 31 // 31 // 0 /// XM_001928085 // RefSeq // PREDICTED: Sus scrofa Ribonuclease T2, transcript variant 1 (LOC100157985), mRNA. // chr1 // 100 // 100 // 31 // 31 // 0 /// ENSSSCT00000004450 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:3289751:3306795:1 gene:ENSSSCG00000004024 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 94 // 29 // 29 // 0 /// GENSCAN00000049308 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:3290175:3306807:1 transcript_biotype:protein_coding // chr1 // 100 // 58 // 18 // 18 // 0 --- --- --- --- --- --- ENSSSCT00000004450 // Pfam // IPR001568 // Ribonuclease T2-like 1 main
15183162 15183162 chr1(+):3360697-3368706 chr1 + 3360697 3368706 20 U91519 // T // T, brachyury homolog (mouse) // --- // 397450 U91519 // GenBank // Sus scrofa brachyury mRNA, partial cds. // chr1 // 88 // 40 // 7 // 8 // 0 U91519 // O02737 --- --- --- --- --- --- 1 main
15183169 15183169 chr1(+):3682966-3683065 chr1 + 3682966 3683065 10 --- ENSSSCT00000021249 // ENSEMBL // ncrna:snRNA chromosome:Sscrofa10.2:1:4256580:4256679:1 gene:ENSSSCG00000019654 gene_biotype:snRNA transcript_biotype:snRNA // chr1 // 100 // 90 // 10 // 9 // 0 --- --- --- --- --- --- --- 1 main
15183171 15183171 chr1(+):3953692-4177717 chr1 + 3953692 4177717 36 XM_001927443 // PDE10A // phosphodiesterase 10A // 1|1 // 100154378 /// ENSSSCT00000004453 // PDE10A // phosphodiesterase 10A // 1|1 // 100154378 XM_001927443 // RefSeq // PREDICTED: Sus scrofa phosphodiesterase 10A (PDE10A), mRNA. // chr1 // 100 // 89 // 32 // 32 // 0 /// ENSSSCT00000004453 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:4635847:4742048:1 gene:ENSSSCG00000004027 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 89 // 32 // 32 // 0 /// GENSCAN00000018020 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:4645672:4694239:1 transcript_biotype:protein_coding // chr1 // 100 // 42 // 15 // 15 // 0 /// GENSCAN00000018022 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:4699753:4742048:1 transcript_biotype:protein_coding // chr1 // 100 // 19 // 7 // 7 // 0 --- --- --- --- --- --- ENSSSCT00000004453 // Pfam // IPR002073 // 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain /// ENSSSCT00000004453 // Pfam // IPR003018 // GAF domain 1 main
15183193 15183193 chr1(+):4194028-4211691 chr1 + 4194028 4211691 22 XR_130245 // C1H6orf118 // chromosome 6 open reading frame 118, human C6orf118 // 1|1 // 100157121 ENSSSCT00000004454 // ENSEMBL // cdna:novel chromosome:Sscrofa10.2:1:4758551:4776214:1 gene:ENSSSCG00000004028 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 22 // 22 // 0 /// XR_130245 // RefSeq // PREDICTED: Sus scrofa uncharacterized protein C6orf118-like (LOC100157121), miscRNA. // chr1 // 100 // 77 // 17 // 17 // 0 /// GENSCAN00000018036 // ENSEMBL // cdna:genscan chromosome:Sscrofa10.2:1:4757332:4780285:1 transcript_biotype:protein_coding // chr1 // 100 // 73 // 16 // 16 // 0 --- --- --- --- --- --- --- 1 main
15183202 15183202 chr1(+):5962175-5962357 chr1 + 5962175 5962357 23 --- --- --- --- --- --- --- --- --- 1 ---
15183204 15183204 chr1(+):6040267-6040629 chr1 + 6040267 6040629 23 --- --- --- --- --- --- --- --- --- 1 ---
15183206 15183206 chr1(+):6518045-7514266 chr1 + 6518045 7514266 28 NM_001044603 // PARK2 // parkinson protein 2, E3 ubiquitin protein ligase (parkin) // --- // 733673 /// ENSSSCT00000004459 // PARK2 // parkinson protein 2, E3 ubiquitin protein ligase (parkin) // --- // 733673 /// DQ525852 // PARK2 // parkinson protein 2, E3 ubiquitin protein ligase (parkin) // --- // 733673 NM_001044603 // RefSeq // Sus scrofa parkinson protein 2, E3 ubiquitin protein ligase (parkin) (PARK2), mRNA. // chr1 // 94 // 61 // 16 // 17 // 0 /// ENSSSCT00000004459 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:7197035:7812493:1 gene:ENSSSCG00000004032 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 36 // 10 // 10 // 0 /// DQ525852 // GenBank // Sus scrofa parkin splice variant (PARK2) mRNA, complete cds, alternatively spliced. // chr1 // 100 // 64 // 18 // 18 // 0 DQ525852 // Q19K47 --- --- --- --- --- ENSSSCT00000004459 // Pfam // IPR000626 // Ubiquitin /// ENSSSCT00000004459 // Pfam // IPR022617 // Small ubiquitin-related modifier, SUMO 1 main
15183222 15183222 chr1(+):7552878-7674727 chr1 + 7552878 7674727 19 ENSSSCT00000004461 // AGPAT4 // 1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta) // 1|1 // 100156632 /// NM_001143697 // AGPAT4 // 1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta) // 1|1 // 100156632 /// FJ439667 // AGPAT4 // 1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta) // 1|1 // 100156632 ENSSSCT00000004461 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:8330536:8439727:-1 gene:ENSSSCG00000004033 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 84 // 16 // 16 // 0 /// NM_001143697 // RefSeq // Sus scrofa 1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta) (AGPAT4), mRNA. // chr1 // 88 // 84 // 14 // 16 // 0 /// FJ439667 // GenBank // Sus scrofa 1-acylglycerol-3-phosphate O-acyltransferase 4 (AGPAT4) mRNA, complete cds. // chr1 // 88 // 84 // 14 // 16 // 0 FJ439667 // B8XTR2 --- --- --- --- --- ENSSSCT00000004461 // Pfam // IPR002123 // Phospholipid/glycerol acyltransferase 1 main
15183232 15183232 chr1(+):7904496-7904663 chr1 + 7904496 7904663 25 ENSSSCT00000004466 // PLG // plasminogen // 1|1 // 733660 /// NM_001044590 // PLG // plasminogen // 1|1 // 733660 /// DQ530369 // PLG // plasminogen // 1|1 // 733660 ENSSSCT00000004466 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:8739981:8787582:1 gene:ENSSSCG00000004038 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 84 // 21 // 21 // 0 /// NM_001044590 // RefSeq // Sus scrofa plasminogen (PLG), mRNA. // chr1 // 95 // 84 // 20 // 21 // 0 /// DQ530369 // GenBank // Sus scrofa plasminogen mRNA, complete cds. // chr1 // 95 // 84 // 20 // 21 // 0 DQ530369 // P06867 --- --- --- --- --- ENSSSCT00000004466 // Pfam // IPR000001 // Kringle /// ENSSSCT00000004466 // Pfam // IPR001254 // Peptidase S1/S6, chymotrypsin/Hap /// ENSSSCT00000004466 // Pfam // IPR003014 // PAN-1 domain /// ENSSSCT00000004466 // Pfam // IPR015420 // Peptidase S1A, nudel 3 main
15183234 15183234 chr1(+):7990323-8049156 chr1 + 7990323 8049156 18 --- ENSSSCT00000004465 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:8516303:8538374:-1 gene:ENSSSCG00000004037 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 22 // 4 // 4 // 0 --- --- --- --- --- --- --- 1 main
15183244 15183244 chr1(+):8079895-8127335 chr1 + 8079895 8127335 23 ENSSSCT00000004466 // PLG // plasminogen // 1|1 // 733660 /// NM_001044590 // PLG // plasminogen // 1|1 // 733660 /// DQ530369 // PLG // plasminogen // 1|1 // 733660 ENSSSCT00000004466 // ENSEMBL // cdna:known chromosome:Sscrofa10.2:1:8739981:8787582:1 gene:ENSSSCG00000004038 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 23 // 23 // 0 /// NM_001044590 // RefSeq // Sus scrofa plasminogen (PLG), mRNA. // chr1 // 95 // 91 // 20 // 21 // 0 /// DQ530369 // GenBank // Sus scrofa plasminogen mRNA, complete cds. // chr1 // 95 // 91 // 20 // 21 // 0 DQ530369 // P06867 --- --- --- --- --- ENSSSCT00000004466 // Pfam // IPR000001 // Kringle /// ENSSSCT00000004466 // Pfam // IPR001254 // Peptidase S1/S6, chymotrypsin/Hap /// ENSSSCT00000004466 // Pfam // IPR003014 // PAN-1 domain /// ENSSSCT00000004466 // Pfam // IPR015420 // Peptidase S1A, nudel 1 main
15183263 15183263 chr1(+):8248175-8248301 chr1 + 8248175 8248301 17 --- ENSSSCT00000020364 // ENSEMBL // ncrna:snoRNA chromosome:Sscrofa10.2:1:8908400:8908526:1 gene:ENSSSCG00000018769 gene_biotype:snoRNA transcript_biotype:snoRNA // chr1 // 100 // 100 // 17 // 17 // 0 --- --- --- --- --- --- --- 1 main

Total number of rows: 27558

Table truncated, full table size 16495 Kbytes.




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