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C9orf53 Gene

protein-coding   GIFtS: 25
GCID: GC09P021959

Chromosome 9 Open Reading Frame 53

  Search for C9orf53
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
Chromosome 9 Open Reading Frame 531 2
bA149I2.32

External Ids:    HGNC: 238311   Entrez Gene: 511982   Ensembl: ENSG000002248547   UniProtKB: Q9UH643   

Export aliases for C9orf53 gene to outside databases

Previous GC identifer: GC09U900641


(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 C9orf53 Gene:
C9orf53 (chromosome 9 open reading frame 53) is a protein-coding gene.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the C9orf53 gene promoter:
         HOXA9   HOXA9B   Sox5   Pax-5   Sp1   Meis-1b   Evi-1   C/EBPalpha   Meis-1   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf53


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

Entrez Gene cytogenetic band: 9p21.3   Ensembl cytogenetic band:  9p21.3   HGNC cytogenetic band: 9p21.3

C9orf53 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf53 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P021959:  view genomic region     (about GC identifiers)

Start:
21,967,137 bp from pter      End:
21,967,753 bp from pter
Size:
617 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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/Swiss-Prot: NSGX_HUMAN, Q9UH64 (See protein sequence)
Recommended Name: Susceptibility protein NSG-x  
Size: 79 amino acids; 8851 Da
Secondary accessions: Q5VVJ4

Explore the universe of human proteins at neXtProt for C9orf53: NX_Q9UH64

Explore proteomics data for C9orf53 at MOPED


See C9orf53 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000414893  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: Q9UH64


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
extracellular1

(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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for C9orf53
Interactions:

    Search GeneGlobe Interaction Network for C9orf53

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for C9orf53 (NSGX)



(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for C9orf53 gene: 
NM_016349.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000441769(uc011lnm.2)
miRNA
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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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C9orf53 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
C9orf53 Expression
About this image

C9orf53 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C9orf53 Protein Expression
    Custom PCR Arrays for C9orf53
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf53

(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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This gene was present in the common ancestor of human and chimp.

Orthologs for C9orf53 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C9orf536
chromosome 9 open reading frame 53
99(a)
1 ↔ 1
9(22283477-22283716)


ENSEMBL Gene Tree for C9orf53 (if available)
TreeFam Gene Tree for C9orf53 (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 C9orf53 (see all 39)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1131901151,2
C--21965163(+) TGACGC/TGTGCT 1 -- us2k11Minor allele frequency- T:0.50CSA 2
rs21881271,2
C,F--21965232(+) ACAGCC/GCCCGT 1 -- us2k15Minor allele frequency- G:0.10NA WA 244
rs1112686391,2
C,F--21965251(+) GGTTGG/ATTGGG 1 -- us2k11Minor allele frequency- A:0.03NA 120
rs1836787221,2
--21965291(+) TCCCCG/TCCTCC 1 -- us2k10--------
rs736528091,2
C,F--21965337(+) GGCCTC/AGAACA 1 -- us2k13Minor allele frequency- A:0.09WA CSA 122
rs1423420631,2
--21965558(+) AGTGTC/GCTCGG 1 -- us2k10--------
rs1891180031,2
--21965570(+) AAACAC/TGCGTG 1 -- us2k10--------
rs1914710281,2
--21965719(+) GGACTG/TCGAAC 1 -- us2k10--------
rs777776661,2
C,F--21965758(+) GAGGGG/CAATGT 1 -- us2k11Minor allele frequency- C:0.05NA 120
rs1464827911,2
C--21965960(+) ATGTT-/GACA  
        
GACAG
1 -- us2k10--------

HapMap Linkage Disequilibrium report for C9orf53 (21967137 - 21967753 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for C9orf53:    About this table    
Variant IDTypeSubtypePubMed ID
nsv8426CNV Loss18304495
nsv892746CNV Loss21882294
nsv892745CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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(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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Find genes that share disorders with C9orf53           About GenesLikeMe

Human Genome Epidemiology (HuGE) Navigator: C9orf53 (2 documents)

Export disorders for C9orf53 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 C9orf53 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C9orf53)
    Utopia: connect your pdf to the dynamic
world of online information

  1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
  2. The contribution of a 9p21.3 variant, a KIF6 variant, and C-reactive protein to predicting risk of myocardial infarction in a prospective study. (PubMed id 21406102)1 Shiffman D....Psaty B.M. (BMC Cardiovasc Disord 2011)
  3. Six sequence variants on chromosome 9p21.3 are associated with a positive family history of myocardial infarction: a multicenter registry. (PubMed id 21385355)1 Scheffold T....Haltern G. (BMC Cardiovasc Disord 2011)
  4. Chromosome 9p21.3 genotype is associated with vascular dementia and Alzheimer's disease. (PubMed id 19664850)1 Emanuele E....Politi P. (Neurobiol. Aging 2011)
  5. Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph. (PubMed id 21048031)1 Casabonne D....de Sanjose S. (Haematologica 2011)
  6. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1 Olsen J.V....Mann M. (Cell 2006)
  7. (PubMed id )2 

(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: 51198 HGNC: 23831 Ensembl:ENSG00000224854 euGenes: HUgn51198 ECgene: C9orf53
H-InvDB: C9orf53

(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 C9orf53 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 C9orf53 gene:
Search GeneIP for patents involving C9orf53

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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