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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RPSAP9 Gene

pseudogene   GIFtS: 21
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)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

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   
ORGUL members:         
NONCODE14:n407433      

Export aliases for RPSAP9 gene to outside databases

Previous GC identifers: GC09U900700 GC09P078204


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RPSAP9 Gene: 
RPSAP9 (ribosomal protein SA pseudogene 9) is a pseudogene, and is affiliated with the lncRNA class.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.2  NT_008470.19  
Regulatory elements:
   SABiosciences 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

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
  --

(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPSAP9

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Browse Tocris compounds for RPSAP9

Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


SOURCE GeneReport for Unigene cluster: Hs.655646
    SABiosciences Custom PCR Arrays for RPSAP9
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In Situ
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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)
About This Section
  --

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/78 SNPs in RPSAP9 are shown (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

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

RPSAP9 for disorders           About MalaCards

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)
About This Section

PubMed articles for RPSAP9 gene integrated from 9 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. (2011)
  2. Comparative analysis of processed ribosomal protein p seudogenes in four mammalian genomes. (PubMed id 19123937)1, 3 Balasubramanian S....Gerstein M. (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. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 653162 HGNC: 31463 Ensembl:ENSG00000234618 euGenes: HUgn653162 ECgene: RPSAP9
H-InvDB: RPSAP9

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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