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

SAA3P Gene

pseudogene   GIFtS: 27
GCID: GC11M018090

Serum Amyloid A3 Pseudogene


(Previous symbol: SAA3)
  See related diseases
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 8

Aliases
Serum Amyloid A3 Pseudogene1 2
SAA31 2

External Ids:    HGNC: 105151   Entrez Gene: 62902   Ensembl: ENSG000001667877   
ORGUL members:         
NONCODE14:n372406      

Export aliases for SAA3P gene to outside databases

Previous GC identifers: GC11M019254 GC11M019076 GC11M018174 GC11M018098 GC11M017816


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

GeneCards Summary for SAA3P Gene: 
SAA3P (serum amyloid A3 pseudogene) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with SAA3P include hyperglycemia, and atherosclerosis.


(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_000011.9  NC_018922.2  NT_009237.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SAA3P gene promoter:
         Max1   TBP   FOXD3   POU2F1a   POU2F1b   FOXJ2 (long isoform)   HOXA5   FOXJ2   POU2F1c   c-Myc   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SAA3P

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SAA3P


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

Entrez Gene cytogenetic band: 11p15.1   Ensembl cytogenetic band:  11p15.1   HGNC cytogenetic band: 11p15.1

SAA3P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SAA3P gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M018090:  view genomic region     (about GC identifiers)

Start:
18,134,019 bp from pter      End:
18,137,679 bp from pter
Size:
3,661 bases      Orientation:
minus 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

Molecular Function:
     Genatlas biochemistry entry for SAA3P:
serum amyloid A3,pseudogene,constitutively expressed

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

SuperPaths for SAA3P About                                                                                                See pathways by source

SuperPathContained pathways About
1Selenium Pathway
Selenium Pathway


1 BioSystems Pathway for SAA3P
    Selenium Pathway


Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SAA3P

(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
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for SAA3P

Search CenterWatch for drugs/clinical trials and news about SAA3P

(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 SAA3P:

Serum amyloid A3 pseudogene
Hs.454496
Unigene Representative Sequence: AY209188
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000534768(uc001mnt.3) ENST00000533267
miRNA
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Additional mRNA sequence: 

AY209188.1 NR_026576.1 

1 AceView cDNA sequence:

AY209188 

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

SAA3P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAGAGGATTC
SAA3P Expression
About this image


Genevestigator expression for SAA3P

SOURCE GeneReport for Unigene cluster: Hs.454496
    SABiosciences Custom PCR Arrays for SAA3P
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SAA3P

(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 SAA3P (if available)
TreeFam Gene Tree for SAA3P (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

10/128 SNPs in SAA3P are shown (see all 128)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1845907591,2
--18133712(+) TATTTG/TTCTAT 1 -- ds50010--------
rs1474184201,2
--18133855(+) GTGGTC/TCATGT 1 -- ds50010--------
rs105008321,2
C,F,H--18133858(+) GTCCAT/CGTATA 1 -- ds500185Minor allele frequency- C:0.01NS EA PA EU CA WA NA 4460
rs728631531,2
C,F--18133882(+) CCCCAA/GTTCCC 1 -- ds50012Minor allele frequency- G:0.07WA NA 238
rs1881397831,2
--18133929(+) AAACAC/GTGATG 1 -- ds50010--------
rs1167541001,2
C,F--18134041(+) TATTAA/CGCATT 1 -- nc-transcript-variant1Minor allele frequency- C:0.03WA 118
rs618825331,2
C,F--18134192(+) CAGGTC/TGGAAG 1 -- nc-transcript-variant8Minor allele frequency- T:0.17WA NA CSA EA EU 957
rs1139603221,2
C--18134219(+) CACTCA/C/TGGCCC 2 -- nc-transcript-variant1CSA 1
rs1820070241,2
--18134408(+) GGAAGA/GCCAAG 1 -- int10--------
rs734320091,2
C,F--18134531(+) TTCTAC/GCATCC 1 -- int14Minor allele frequency- G:0.40WA CSA 123

HapMap Linkage Disequilibrium report for SAA3P (18134019 - 18137679 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SAA3P: --
SABiosciences Cancer Mutation PCR Assays
SeqTarget long-range PCR primers for resequencing SAA3P
DNA2.0 Custom Variant and Variant Library Synthesis for SAA3P

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
4 diseases for SAA3P:    About MalaCards
hyperglycemia    atherosclerosis    rheumatoid arthritis    arthritis


SAA3P for disorders           About GeneDecksing

1 Novoseek inferred disease relationship for SAA3P gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
atherosclerosis 13.3 1 15590982 (1)


Export disorders for SAA3P 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 SAA3P gene, integrated from 9 sources (see all 18):
(articles sorted by number of sources associating them with SAA3P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Localization of four human serum amyloid A (SAA) protein superfamily genes to chromosome 11p: characterization of a fifth SAA-related gene sequence. (PubMed id 8325654)1, 3 Sellar G.C. and Whitehead A.S. (1993)
  2. The human serum amyloid A (SAA)-encoding gene GSAA1: nucleotide sequence and possible autocrine-collagenase-inducer function. (PubMed id 2558975)1, 3 Sack G.H. Jr. and Talbot C.C. Jr. (1989)
  3. Induction of human mammary-associated serum amyloid A3 expression by prolactin or lipopolysaccharide. (PubMed id 12589816)1, 9 Larson M.A....McDonald T.L. (2003)
  4. The human plasma proteome: a nonredundant list developed by combination of four separate sources. (PubMed id 14718574)1 Anderson N.L....Lobley A. (2004)
  5. Nonexpression of the human serum amyloid A three (SAA3) gene. (PubMed id 1755958)1 Kluve-Beckerman B.... Benson M.D. (1991)
  6. The fifth serum amyloid A-related gene sequence, GSAA4, is SAA3. (PubMed id 8047850)9 Watson G....Woo P. (1994)
  7. The acute phase reactant serum amyloid A (SAA3) is a novel substrate for degradation by the metalloproteinases collagenase and stromelysin. (PubMed id 8461313)9 Mitchell T.I....Brinckerhoff C.E. (1993)
  8. Serum amyloid A3 expression is stimulated by dexamethasone and interleukin-6 in 3T3-L1 adipocytes. (PubMed id 15590982)9 Fasshauer M....Paschke R. (2004)
  9. Purification and characterization of the serum amyloid A3 enhancer factor. (PubMed id 10455131)9 Bing Z.... Liao W.S.-L. (1999)
  10. Adipose tissue depots of Holstein cows are immune res ponsive: inflammatory gene expression in vitro. (PubMed id 19914024)9 Mukesh M....Loor J.J. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Disorders
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: 6290 HGNC: 10515 AceView: SAA3P Ensembl:ENSG00000166787 euGenes: HUgn6290
ECgene: SAA3P H-InvDB: SAA3P

(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 SAA3P 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 SAA3P gene:
Search GeneIP for patents involving SAA3P

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
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