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C9orf172 Gene

protein-coding   GIFtS: 31
GCID: GC09P139738          (predicted)

Chromosome 9 Open Reading Frame 172

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(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 1721 2
Uncharacterized Protein C9orf1722

External Ids:    HGNC: 372841   Entrez Gene: 3898132   Ensembl: ENSG000002324347   UniProtKB: C9J0693   

Export aliases for C9orf172 gene to outside databases

Previous GC identifers: GC09P138859 GC09P109200


(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 C9orf172 Gene:
C9orf172 (chromosome 9 open reading frame 172) 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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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Search for regulatory transcription factor binding sites for C9orf172
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C9orf172

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf172


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

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

C9orf172 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf172 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P139738:  view genomic region     (about GC identifiers)

Start:
139,738,867 bp from pter      End:
139,741,797 bp from pter
Size:
2,931 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CI172_HUMAN, C9J069 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf172  
Size: 976 amino acids; 106650 Da

Explore the universe of human proteins at neXtProt for C9orf172: NX_C9J069

Explore proteomics data for C9orf172 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C9orf172 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001073951.2  
    ENSEMBL proteins: 
     ENSP00000412388  

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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: C9J069


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:
       genOway: Develop your customized and physiologically relevant rodent model for C9orf172

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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
    nucleus3
    cytosol2

    (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 C9orf172
    Interactions:

        Search GeneGlobe Interaction Network for C9orf172

    (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 C9orf172 (CI172)



    (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 C9orf172 gene: 
    NM_001080482.2  

    Unigene Cluster for C9orf172:

    Chromosome 9 open reading frame 172
    Hs.495485  [show with all ESTs]
    Unigene Representative Sequence: NM_001080482
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000436881(uc011meh.2)
    miRNA
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    2 DOTS entries:

    DT.97783503  DT.100708129 

    1 AceView cDNA sequence:

    BQ278870 

    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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    C9orf172 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCGCCTCCG
    C9orf172 Expression
    About this image

    C9orf172 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf172 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.495485
        Custom PCR Arrays for C9orf172
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for C9orf172 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Gm9961 , 5 predicted gene 9961, 5 81.57(n)1
    87.15(a)1
      2 (17.44 cM)5
    3813531  NM_001005424.21  NP_001005424.21 
     255754165 
    chicken
    (Gallus gallus)
    Aves C17H9ORF1721 chromosome 17 open reading frame, human C9orf172 68.91(n)
    62.72(a)
      427779  XM_425350.4  XP_425350.4 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004959301 chromosome unknown open reading frame, human C9orf172 61.09(n)
    59.53(a)
      100495930  XM_002940729.2  XP_002940775.2 
    zebrafish
    (Danio rerio)
    Actinopterygii C5H9orf172 (1 of 2)6
    C5H9orf172 (2 of 2)6
    chromosome 9 open reading frame 172
    47(a)
    40(a)
    many → 1
    many → 1
    5(5493505-5496804) ENSDARG00000076268
    8(32097009-32102411) ENSDARG00000076873
    fruit fly
    (Drosophila melanogaster)
    Insecta CG427486
    --
    10(a)
    1 ↔ 1
    2L(22131221-22166221)
    worm
    (Caenorhabditis elegans)
    Secernentea ajm-16
    Protein AJM-1, isoform b
    10(a)
    1 ↔ 1
    X(9098346-9113618) WBGene00000100


    ENSEMBL Gene Tree for C9orf172 (if available)
    TreeFam Gene Tree for C9orf172 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C9orf172 gene

    Find genes that share paralogs with C9orf172           About GenesLikeMe


    2 Pseudogenes.org Pseudogenes for C9orf172
    PGOHUM00000234886 PGOHUM00000240343


    (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 C9orf172 (see all 50)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1838068401,2
    C--139736917(+) AGCCAG/TGCCAG 1 -- us2k10--------
    rs117934141,2
    C,H--139736942(+) CCTGGA/GAGCTT 1 -- us2k10--------
    rs1911233731,2
    --139737234(+) TCTCCA/GTGGGC 1 -- us2k10--------
    rs562098091,2
    C--139737591(+) CCCCGA/GGAGGC 1 -- us2k10--------
    rs352722401,2
    C--139737720(+) CTGAC-/A/TGAC
            
    GCACC
    1 -- us2k10--------
    rs1828613211,2
    --139737752(+) ATCACA/GGAGGG 1 -- us2k10--------
    rs125542081,2
    C,F,H--139737804(+) GGGGCC/TTAAGA 1 -- us2k14Minor allele frequency- T:0.01NS NA 568
    rs1886599991,2
    --139738012(+) TGTGCA/GTTTAC 1 -- us2k10--------
    rs1932674571,2
    --139738399(+) TTCCAA/CCTGCG 1 -- us2k10--------
    rs1851001111,2
    --139738664(+) CCCGGA/CATGGA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for C9orf172 (139738867 - 139741797 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for C9orf172 (see all 24):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422220CNV Deletion17116639
    nsv894483CNV Loss21882294
    dgv8414n71CNV Loss21882294
    dgv8421n71CNV Loss21882294
    dgv8416n71CNV Loss21882294
    dgv8420n71CNV Loss21882294
    nsv894491CNV Loss21882294
    nsv894469CNV Loss21882294
    dgv8418n71CNV Loss21882294
    esv29973CNV Loss17803354

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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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      --

    (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 article for C9orf172 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C9orf172)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)

    (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: 389813 HGNC: 37284 AceView: LOC389813.1 Ensembl:ENSG00000232434 euGenes: HUgn389813
    ECgene: C9orf172 H-InvDB: C9orf172

    (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 C9orf172 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 C9orf172 gene:
    Search GeneIP for patents involving C9orf172

    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, eBioscience, antibodies-online, 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
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