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C9orf139 Gene

protein-coding   GIFtS: 32
GCID: GC09P139921          (predicted)

Chromosome 9 Open Reading Frame 139

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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 1391 2
Uncharacterized Protein C9orf1392

External Ids:    HGNC: 314261   Entrez Gene: 4015632   Ensembl: ENSG000001805397   UniProtKB: Q6ZV773   

Export aliases for C9orf139 gene to outside databases

Previous GC identifers: GC09P139041 GC09P109381


(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 C9orf139 Gene:
C9orf139 (chromosome 9 open reading frame 139) 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:
   Regulatory transcription factor binding sites in the C9orf139 gene promoter:
         Elk-1   Sp1   HTF   Olf-1   Tal-1beta   ITF-2   GATA-2   c-Ets-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C9orf139

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C9orf139


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

C9orf139 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf139 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P139921:  view genomic region     (about GC identifiers)

Start:
139,921,916 bp from pter      End:
139,931,234 bp from pter
Size:
9,319 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: CI139_HUMAN, Q6ZV77 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf139  
Size: 190 amino acids; 20001 Da
Sequence caution: Sequence=BAC04202.1; Type=Erroneous initiation;
Secondary accessions: A2RUA3 B9EGW2 Q5SPY0 Q8N224

Explore the universe of human proteins at neXtProt for C9orf139: NX_Q6ZV77

Explore proteomics data for C9orf139 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C9orf139 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_997394.1  
    ENSEMBL proteins: 
     ENSP00000318119  

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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: Q6ZV77


    (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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    Phenotypes:
         1 GenomeRNAi human phenotype for C9orf139:
     Increased cell number in G2M,  

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for C9orf139

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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
    extracellular2
    cytosol1
    mitochondrion1
    nucleus1

    (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 C9orf139
    Interactions:

        Search GeneGlobe Interaction Network for C9orf139

    (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
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    Browse Tocris compounds for C9orf139 (CI139)



    (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 C9orf139 gene: 
    NM_207511.1  

    Unigene Cluster for C9orf139:

    Chromosome 9 open reading frame 139
    Hs.522509  [show with all ESTs]
    Unigene Representative Sequence: AK124899
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000314330(uc004ckp.1)
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    Additional mRNA sequence: 

    AK093587.1 AK124899.1 BC132809.1 BC136839.1 

    2 DOTS entries:

    DT.95292875  DT.409730 

    4 AceView cDNA sequences:

    AK124899 AK093587 NM_207511 AX748216 

    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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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    C9orf139 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C9orf139 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.522509
        Custom PCR Arrays for C9orf139
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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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      --

    ENSEMBL Gene Tree for C9orf139 (if available)
    TreeFam Gene Tree for C9orf139 (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 C9orf139 (see all 303)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1164553831,2
    F--139956744(+) GGGCCG/AAGTCC 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1459001571,2
    C--139956900(+) GGGTTA/CGCCAA 1 -- us2k10--------
    rs736683831,2
    C,F--139957046(+) GGCCCG/AGCTGC 1 -- us2k12Minor allele frequency- A:0.09WA 120
    rs1130181591,2
    C,F--139957047(+) GCCCGG/CCTGCC 1 -- us2k12Minor allele frequency- C:0.08WA 120
    rs1930399751,2
    --139957217(+) CCTCCA/GTCCCT 1 -- us2k10--------
    rs1835748891,2
    --139957311(+) TGTGTC/TGGGGG 1 -- us2k10--------
    rs1387074251,2
    C--139957312(+) GTGTCA/GGGGGG 1 -- us2k10--------
    rs1427074121,2
    --139957465(+) ACAGAC/GAGGGA 1 -- us2k10--------
    rs1502867491,2
    --139957496(+) AGGAGC/TCTGCT 1 -- us2k10--------
    rs1383287741,2
    --139957594(+) CAGGGC/TGCATG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for C9orf139 (139921916 - 139931234 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for C9orf139 (see all 28):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422220CNV Deletion17116639
    nsv513004CNV Insertion21212237
    nsv894483CNV Loss21882294
    nsv894567CNV Loss21882294
    dgv8416n71CNV Loss21882294
    dgv8439n71CNV Loss21882294
    dgv8440n71CNV Loss21882294
    dgv8428n71CNV Loss21882294
    nsv894521CNV Loss21882294
    nsv894503CNV Loss21882294

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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 articles for C9orf139 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C9orf139)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 401563 HGNC: 31426 AceView: FLJ36268 Ensembl:ENSG00000180539 euGenes: HUgn401563
    ECgene: C9orf139 H-InvDB: C9orf139

    (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 C9orf139 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 C9orf139 gene:
    Search GeneIP for patents involving C9orf139

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



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