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RPSAP9 Gene

pseudogene   GIFtS: 20
GCID: GC09P079014

Ribosomal Protein SA Pseudogene 9

(Previous name: laminin receptor 1 pseudogene 9)
(Previous symbol: LAMR1P9)
  Search for RPSAP9
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ribosomal Protein SA Pseudogene 91 2
LAMR1P91 2
Laminin Receptor 1 Pseudogene 91
RPSA_20_9862

External Ids:    HGNC: 314631   Entrez Gene: 6531622   Ensembl: ENSG000002346187   

Export aliases for RPSAP9 gene to outside databases

Previous GC identifers: GC09U900700 GC09P078204


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RPSAP9 Gene:
RPSAP9 (ribosomal protein SA pseudogene 9) is a pseudogene.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000009.12  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the RPSAP9 gene promoter:
         TBP   USF1   AML1a   GR-beta   ATF-2   MIF-1   C/EBPalpha   USF-1   TFIID   Sox9   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPSAP9


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q21.13   Ensembl cytogenetic band:  9q21.13   HGNC cytogenetic band: 9q21.13

RPSAP9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPSAP9 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P079014:  view genomic region     (about GC identifiers)

Start:
79,013,515 bp from pter      End:
79,014,954 bp from pter
Size:
1,440 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for RPSAP9 About    
See pathways by source

SuperPathSelected contained pathways About (see all per SuperPath)
1Influenza Viral RNA Transcription and Replication
Viral mRNA Translation0.94
Eukaryotic Translation Initiation0.89
Peptide chain elongation0.94
Cap-dependent Translation Initiation0.89
Nonsense Mediated Decay Independent of the Exon Junction Complex0.94
Nonsense Mediated Decay Enhanced by the Exon Junction Complex0.89
Formation of a pool of free 40S subunits0.94
Nonsense-Mediated Decay0.89
2Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
Translation initiation complex formation0.91
Ribosomal scanning and start codon recognition0.91
Formation of the ternary complex, and subsequently, the 43S complex0.91
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S0.90
3Gene Expression
Gene Expression0.40
4Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Metabolism of proteins0.30
5Disease
Disease



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Interactions:

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for RPSAP9



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for RPSAP9:

Ribosomal protein SA pseudogene 9
Hs.655646  [show with all ESTs]
Unigene Representative Sequence: NR_026890
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000418207(uc011lsj.1)
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Additional mRNA sequence: NR_026890.1 

16 DOTS entries:

DT.100811553  DT.100865110  DT.91786760  DT.95378151  DT.100742475  DT.100742502  DT.100742512  DT.100860380 
DT.120682871  DT.121205784  DT.121322796  DT.121395645  DT.91786421  DT.92068647  DT.92394644  DT.95377954 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RPSAP9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RPSAP9 Expression
About this image

RPSAP9 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.655646
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for RPSAP9 (if available)
TreeFam Gene Tree for RPSAP9 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for RPSAP9 (see all 78)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs123462171,2
C,F--48840440(+) gcacaG/Ctggct 1 -- us2k12Minor allele frequency- C:0.50WA NA 6
rs715098701,2
C,F--48840449(+) CTCATT/GCCTGT 1 -- us2k12Minor allele frequency- G:0.25NA 4
rs1858747191,2
--79011527(+) CTGAGA/GCCGGT 1 -- us2k10--------
rs65605131,2
C,F,A--79011666(+) ggcacA/Gagagt 1 -- us2k14Minor allele frequency- G:0.19CSA WA NA EA 360
rs25019211,2
C,F,H--79011728(-) gccccG/Atatgg 1 -- us2k118Minor allele frequency- A:0.04NS EA NA WA CSA 779
rs353635701,2
F--79011830(+) CCCCAG/TAATTT 1 -- us2k12Minor allele frequency- T:0.09NA 122
rs1428316141,2
--79011920(+) AGGCCA/GGGCGC 1 -- us2k10--------
rs24905851,2
C,F,A,H--79012090(+) ctactT/Cgggag 1 -- us2k112Minor allele frequency- C:0.04NS WA NA CSA EA 376
rs1907279281,2
--79012138(+) GGTTGC/GTATGA 1 -- us2k10--------
rs1396694701,2
--79012192(+) GATTCC/TTTCTC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for RPSAP9 (79013515 - 79014954 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for RPSAP9:    About this table    
Variant IDTypeSubtypePubMed ID
nsv6570CNV Insertion18451855
nsv893479CNV Gain21882294
nsv893478CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing RPSAP9
DNA2.0 Custom Variant and Variant Library Synthesis for RPSAP9

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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RPSAP9 for disorders           About GeneDecksing

Genetic Association Database (GAD): RPSAP9

Export disorders for RPSAP9 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RPSAP9 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RPSAP9)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. (PubMed id 21546767)1, 4 Murea M....Freedman B.I. (Am. J. Nephrol. 2011)
  2. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. (PubMed id 19123937)1, 3 Balasubramanian S....Gerstein M. (Genome Biol. 2009)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 653162 HGNC: 31463 Ensembl:ENSG00000234618 euGenes: HUgn653162 ECgene: RPSAP9
H-InvDB: RPSAP9

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RPSAP9 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RPSAP9 gene:
Search GeneIP for patents involving RPSAP9

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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