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C6orf47 Gene

protein-coding   GIFtS: 46
GCID: GC06M031685

Chromosome 6 Open Reading Frame 47

  See C6orf47-related disease
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 6 Open Reading Frame 471 2
Protein G42 3
G42 3
D6S53E2
NG342
Uncharacterized Protein C6orf472

External Ids:    HGNC: 190761   Entrez Gene: 578272   Ensembl: ENSG000002044397   UniProtKB: O958733   

Export aliases for C6orf47 gene to outside databases

Previous GC identifers: GC06M031689 GC06M031396 GC06M031730 GC06M031735 GC06M031627 GC06M031630 GC06M031634 GC06M031637 GC06M031641 GC06M031646 GC06M031650


(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 C6orf47 Gene:
C6orf47 (chromosome 6 open reading frame 47) is a protein-coding gene. Diseases associated with C6orf47 include human t-cell leukemia virus type 1.


(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_000006.11  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167246.2  NT_167247.2  NT_167248.2  
NT_167249.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C6orf47 gene promoter:
         PPAR-gamma1   Pax-5   HTF   Hand1   HNF-4alpha2   PPAR-gamma2   E47   HNF-4alpha1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C6orf47

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C6orf47


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

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.3

C6orf47 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf47 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M031685:  view genomic region     (about GC identifiers)

Start:
31,626,075 bp from pter      End:
31,628,549 bp from pter
Size:
2,475 bases      Orientation:
minus strand

6 alternative locations:
Chr6-,NT_113891.2 3,135,693-3,138,168      Chr6-,NT_167247 3,005,755-3,008,229      Chr6-,NT_167245 2,911,654-2,914,128     
Chr6-,NT_167249 2,956,873-2,959,347      Chr6-,NT_167248 2,919,712-2,922,186      Chr6-,NT_167246 2,968,964-2,971,439     

(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: CF047_HUMAN, O95873 (See protein sequence)
Recommended Name: Uncharacterized protein C6orf47  
Size: 294 amino acids; 31710 Da
Secondary accessions: B0UXA1 B0UZ50 Q5SSS6 Q95IG0

Explore the universe of human proteins at neXtProt for C6orf47: NX_O95873

Explore proteomics data for C6orf47 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys147, Lys153
  • Modification sites at PhosphoSitePlus

  • See C6orf47 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_067007.3  
    ENSEMBL proteins: 
     ENSP00000365076  

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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: O95873


    (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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    Phenotypes:
         1 GenomeRNAi human phenotype for C6orf47:
     Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C6orf47
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    miRNA
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    miRTarBase miRNAs that target C6orf47:
    hsa-mir-26a-5p (MIRT050157)

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    hsa-miR-142-3p hsa-miR-140-5p hsa-miR-125a-5p hsa-miR-137 hsa-miR-4299 hsa-miR-544b hsa-miR-149 hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidC6orf47 3' UTR sequence
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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
    plasma membrane3
    mitochondrion2
    cytosol1
    golgi apparatus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--

    Find genes that share ontologies with C6orf47           About GenesLikeMe


    (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 C6orf47
    Interactions:

        Search GeneGlobe Interaction Network for C6orf47

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    3 Interacting proteins for C6orf47 (O958733 ENSP000003650764) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FGFR3P226073, ENSP000002607954I2D: score=2 STRING: ENSP00000260795
    ENO2P091043I2D: score=3 
    --Q6FHV63I2D: score=1 
    About this table

    (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 C6orf47 (CF047)



    (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 C6orf47 gene: 
    NM_021184.3  

    Unigene Cluster for C6orf47:

    Chromosome 6 open reading frame 47
    Hs.247323  [show with all ESTs]
    Unigene Representative Sequence: NM_021184
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000375911(uc003nvm.1)
    miRNA
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    hsa-miR-142-3p hsa-miR-140-5p hsa-miR-125a-5p hsa-miR-137 hsa-miR-4299 hsa-miR-544b hsa-miR-149 hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidC6orf47 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat C6orf47
      QuantiFast Probe-based Assays in human, mouse, rat C6orf47

    Additional mRNA sequence: 

    AJ245433.1 AK315349.1 BC012950.1 BC063584.1 

    6 DOTS entries:

    DT.121312702  DT.452848  DT.91768636  DT.121312771  DT.91768626  DT.91700705 

    Selected AceView cDNA sequences (see all 94):

    AA455884 BI820798 AI278956 AI703075 BC063584 AV725733 AI272171 BE549642 
    AA236884 BM808745 BC012950 AA447094 BM915324 BM550864 BM852996 BE782965 
    BE797248 AA282852 AI873461 BU600253 AI160778 AA324267 BI258524 AW189292 

    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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    C6orf47 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAGCCAGAG
    C6orf47 Expression
    About this image

    C6orf47 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C6orf47 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.247323
        Custom PCR Arrays for C6orf47
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C6orf47

    (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 chordates.

    Orthologs for C6orf47 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia D17H6S53E1 , 5 DNA segment, Chr 17, human D6S53E1, 5 79.29(n)1
    76.11(a)1
      17 (18.59 cM)5
    1145851  NM_033477.21  NP_258438.11 
     351263735 
    zebrafish
    (Danio rerio)
    Actinopterygii C19H6orf476
    chromosome 6 open reading frame 47
    23(a)
    1 ↔ 1
    19(27939892-27948447) ENSDARG00000091932


    ENSEMBL Gene Tree for C6orf47 (if available)
    TreeFam Gene Tree for C6orf47 (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 C6orf47 (see all 58)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs92815461,2
    C--31626546(+) TTTTT-/T/T   
       T
    /TTT
    GCTTT
    3 -- ut31 cds10--------
    rs351313581,2
    C--31626580(+) GGTGG-/AAAAAA 1 -- ut310--------
    rs2003196801,2
    C--31626598(-) CACCTC/TCAGTT 1 -- ut310--------
    rs77565031,2
    C--31626634(+) AGCTGA/GTGAAT 1 -- ut31 ese30--------
    rs1448857331,2
    F--31626894(+) AACCCC/TTCACT 2 E syn11Minor allele frequency- T:0.00NA 4542
    rs1449370931,2
    C,F--31626904(+) TCTCCC/GAGTCA 2 S W mis11Minor allele frequency- G:0.01NA 4542
    rs1140795721,2
    C,F--31626938(+) CTCCCG/AGAGGC 2 /R /W mis12Minor allele frequency- A:0.00WA NA 4650
    rs1887248541,2
    --31627017(+) AGGCTC/TAGAAC 2 L syn10--------
    rs1456951131,2
    C,F--31627091(+) TCCACG/ACAGGC 2 /R /C mis12Minor allele frequency- A:0.00NA EU 5315
    rs2004092131,2
    C--31627234(+) AGGGAA/GCTCCT 2 A V mis10--------

    HapMap Linkage Disequilibrium report for C6orf47 (31626075 - 31628549 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for C6orf47:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830627CNV Loss17160897
    dgv6581n71CNV Loss21882294
    nsv462871CNV Loss19166990
    nsv884418CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C6orf47
    DNA2.0 Custom Variant and Variant Library Synthesis for C6orf47

    (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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    1 disease for C6orf47:    
    About MalaCards
    human t-cell leukemia virus type 1


    Find genes that share disorders with C6orf47           About GenesLikeMe

    Genetic Association Database (GAD): C6orf47
    Human Genome Epidemiology (HuGE) Navigator: C6orf47 (7 documents)

    Export disorders for C6orf47 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 C6orf47 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with C6orf47)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    3. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. (PubMed id 14656967)1, 2 Xie T.... Hood L. (Genome Res. 2003)
    4. Identification of multiple HTF-island associated genes in the human major histocompatibility complex class III region. (PubMed id 2477242)1, 3 Sargent C.A.... Campbell R.D. (EMBO J. 1989)
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    6. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (Diabetes Care 2010)
    7. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    8. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1 Barcellos L.F....Criswell L.A. (PLoS Genet. 2009)
    9. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. (PubMed id 19143821)1 McKinnon E....James I. (amp 2009)
    10. Fine mapping of the MHC Class III region demonstrates association of AIF1 and rheumatoid arthritis. (PubMed id 18835879)1 Harney S.M....Brown M.A. (Rheumatology (Oxford) 2008)

    (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: 57827 HGNC: 19076 AceView: C6orf47 Ensembl:ENSG00000204439 euGenes: HUgn57827
    ECgene: C6orf47 H-InvDB: C6orf47

    (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 C6orf47 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 C6orf47 gene:
    Search GeneIP for patents involving C6orf47

    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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