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C5orf47 Gene

protein-coding   GIFtS: 33
GCID: GC05P173400

Chromosome 5 Open Reading Frame 47

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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 5 Open Reading Frame 471 2
Uncharacterized Protein C5orf472

External Ids:    HGNC: 270261   Entrez Gene: 1334912   Ensembl: ENSG000001850567   UniProtKB: Q569G33   
ORGUL members:         

Export aliases for C5orf47 gene to outside databases

Previous GC identifers: GC05P173334 GC05P168512


(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 C5orf47 Gene:
C5orf47 (chromosome 5 open reading frame 47) 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_000005.9  NT_023133.14  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C5orf47 gene promoter:
         Tal-1   Pbx1a   MyoD   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   HNF-3beta   E47   Cart-1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C5orf47

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C5orf47


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

Entrez Gene cytogenetic band: 5q35.2   Ensembl cytogenetic band:  5q35.2   HGNC cytogenetic band: 5q35.2

C5orf47 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C5orf47 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P173400:  view genomic region     (about GC identifiers)

Start:
173,400,782 bp from pter      End:
173,433,143 bp from pter
Size:
32,362 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: CE047_HUMAN, Q569G3 (See protein sequence)
Recommended Name: Uncharacterized protein C5orf47  
Size: 176 amino acids; 19206 Da
Sequence caution: Sequence=AAH34971.1; Type=Erroneous initiation; Sequence=AAH92489.1; Type=Erroneous initiation;
Secondary accessions: Q8IYU7

Explore the universe of human proteins at neXtProt for C5orf47: NX_Q569G3

Explore proteomics data for C5orf47 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C5orf47 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001138426.1  
    ENSEMBL proteins: 
     ENSP00000340887  

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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: Q569G3


    (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 C5orf47

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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
    nucleus2
    cytosol1
    mitochondrion1

    (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 C5orf47
    Interactions:

        Search GeneGlobe Interaction Network for C5orf47

    (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 C5orf47 (CE047)



    (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 C5orf47 gene: 
    NM_001144954.1  

    Unigene Cluster for C5orf47:

    Chromosome 5 open reading frame 47
    Hs.131469  [show with all ESTs]
    Unigene Representative Sequence: NM_001144954
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000522195 ENST00000340147(uc003mcv.3 uc003mcw.4)
    miRNA
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    Additional mRNA sequence: 

    BC034971.1 BC047225.1 BC053953.1 BC057842.1 BC066964.1 BC092489.1 BC121167.1 BC121168.1 

    3 DOTS entries:

    DT.100017501  DT.91801330  DT.97762442 

    23 AceView cDNA sequences:

    BC047225 AL703559 BX116313 AI911393 BC057842 BC066964 AL039664 BC053953 
    BX118847 AI024186 BM172306 AI148022 BG720152 BG717383 AL039665 BC034971 
    BG719508 BG772248 BG773228 BG772939 BG720356 BG717321 BI463178 

    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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    C5orf47 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGAATGAA
    C5orf47 Expression
    About this image

    C5orf47 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C5orf47 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.131469
        Custom PCR Arrays for C5orf47
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    In Situ
    Assay Products:
     

     
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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 human and mouse.

    Orthologs for C5orf47 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 4930524B15Rik1 , 5 RIKEN cDNA 4930524B15 gene1, 5 66.25(n)1
    54.72(a)1
      11 (18.71 cM)5
    675921  NM_026262.11  NP_080538.11 
     319655925 


    ENSEMBL Gene Tree for C5orf47 (if available)
    TreeFam Gene Tree for C5orf47 (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 C5orf47 (see all 359)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1406726381,2
    --173414187(+) GGCCAC/TTGATG 1 -- us2k10--------
    rs738083291,2
    C--173414245(+) CATGAG/AGTGCT 1 -- us2k12Minor allele frequency- A:0.07WA 120
    rs670841331,2
    C--173414621(+) ATTAGC/TCAGGC 1 -- us2k14Minor allele frequency- T:0.21WA NA EA 360
    rs340816571,2
    C,F--173414643(+) TGGGCG/ATGGTG 1 -- us2k12Minor allele frequency- A:0.18NA 122
    rs1496859551,2
    C--173414770(+) CTGAC-/AAAAG 
            
    AAAAA
    1 -- us2k10--------
    rs603867511,2
    C,F--173414826(+) TAAAGA/CAATTA 1 -- us2k14Minor allele frequency- C:0.15WA CSA NA 242
    rs360764541,2
    C,F--173414926(+) CTCACA/GACTCA 1 -- us2k16Minor allele frequency- G:0.24NA WA CSA EA 364
    rs623786831,2
    F--173415213(+) AGATCG/ACACCA 1 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1508445141,2
    --173415330(+) CTAACA/CAGCTT 1 -- us2k10--------
    rs117445841,2
    C,F,H--173415407(+) GCCAGG/ACCAAG 1 -- us2k123Minor allele frequency- A:0.09NS EA NA 3000

    HapMap Linkage Disequilibrium report for C5orf47 (173400782 - 173433143 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for C5orf47:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2497414CNV Deletion19546169

    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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      --

    (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 C5orf47 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C5orf47)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (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)

    (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: 133491 HGNC: 27026 AceView: LOC133491 Ensembl:ENSG00000185056 euGenes: HUgn133491
    ECgene: C5orf47 H-InvDB: C5orf47

    (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 C5orf47 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 C5orf47 gene:
    Search GeneIP for patents involving C5orf47

    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
    Advanced Cell Diagnostics, Animal models from genOway)
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     genOway: Develop your customized and physiologically relevant rodent model for C5orf47
      Search antibodies-online for antibodies for C5orf47
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     antibodies-online proteins for C5orf47
           
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