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C3orf56 Gene

protein-coding   GIFtS: 35
GCID: GC03P126911

Chromosome 3 Open Reading Frame 56

  See 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 3 Open Reading Frame 561 2
Putative Uncharacterized Protein C3orf562

External Ids:    HGNC: 324811   Entrez Gene: 2853112   Ensembl: ENSG000002143247   UniProtKB: Q8N8133   

Export aliases for C3orf56 gene to outside databases

Previous GC identifers: GC03P128396 GC03P124290


(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 C3orf56 Gene:
C3orf56 (chromosome 3 open reading frame 56) is a protein-coding gene. Diseases associated with C3orf56 include alzheimer's disease.


(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:
NC_000003.12  NC_018914.2  NT_005612.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the C3orf56 gene promoter:
         LHX3b/Lhx3b   Pbx1a   FOXD1   Nkx2-5   CUTL1   E47   S8   LHX3a/Lhx3a   Hand1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C3orf56

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C3orf56


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

Entrez Gene cytogenetic band: 3q21.3   Ensembl cytogenetic band:  3q21.3   HGNC cytogenetic band: 3q21.3

C3orf56 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C3orf56 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P126911:  view genomic region     (about GC identifiers)

Start:
126,911,974 bp from pter      End:
126,917,025 bp from pter
Size:
5,052 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CC056_HUMAN, Q8N813 (See protein sequence)
Recommended Name: Putative uncharacterized protein C3orf56  
Size: 242 amino acids; 26007 Da
Secondary accessions: B2RNW5

Explore the universe of human proteins at neXtProt for C3orf56: NX_Q8N813

Explore proteomics data for C3orf56 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C3orf56 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001007535.1  
    ENSEMBL proteins: 
     ENSP00000381182  

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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: Q8N813


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         1 GenomeRNAi human phenotype for C3orf56:
     Decreased p24 protein expressi 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C3orf56
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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
    peroxisome2
    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 C3orf56
    Interactions:

        Search GeneGlobe Interaction Network for C3orf56

    (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 C3orf56 (CC056)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for C3orf56 gene: 
    NM_001007534.2  

    Unigene Cluster for C3orf56:

    Chromosome 3 open reading frame 56
    Hs.591284  [show with all ESTs]
    Unigene Representative Sequence: AK097460
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000398112(uc003eji.1)
    miRNA
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    Additional mRNA sequence: 

    AK097460.1 BC137154.1 BC137155.1 XR_108480.1 XR_112539.1 XR_171405.1 

    1 DOTS entry:

    DT.75171965 

    1 AceView cDNA sequence:

    AK097460 

    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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    C3orf56 expression in normal human tissues (normalized intensities)      C3orf56 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTTTAAAAA
    C3orf56 Expression
    About this image


    C3orf56 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Ovary (Reproductive System)
             Secondary Oocyte Antral Follicle
     
     Gonad
             Secondary Oocyte Antral Follicle
    C3orf56 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C3orf56 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.591284
        Custom PCR Arrays for C3orf56
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C3orf56

    (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 C3orf56 gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia LOC7364731 putative uncharacterized protein C3orf56-like 98.76(n)
    97.93(a)
      736473  XM_001136135.3  XP_001136135.1 


    ENSEMBL Gene Tree for C3orf56 (if available)
    TreeFam Gene Tree for C3orf56 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C3orf56 gene

    C3orf56 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for C3orf56
    PGOHUM00000247157 PGOHUM00000237754


    (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 C3orf56 (see all 163)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1863458691,2
    --126885275(+) CTATGG/TTTTTG 1 -- us2k10--------
    rs1388485681,2
    --126885415(+) AAATTA/GTGTAA 1 -- us2k10--------
    rs1420635241,2
    --126885731(+) AGGCCA/GAGGTG 1 -- us2k10--------
    rs1122892721,2
    C,F--126885792(+) TCCACC/TGCACT 1 -- us2k11Minor allele frequency- T:0.50NA 2
    rs1480825211,2
    --126885822(+) GAAACC/TCTGTC 1 -- us2k10--------
    rs1911457061,2
    --126885938(+) AAGAAA/CCATTC 1 -- us2k10--------
    rs1418600421,2
    --126886020(+) GAATGG/TTAATG 1 -- us2k10--------
    rs1827018101,2
    --126886045(+) AGAGGA/CCTGGG 1 -- us2k10--------
    rs776914781,2
    F--126886136(+) AAGGCG/ACAATG 1 -- us2k11Minor allele frequency- A:0.33NA 6
    rs783005621,2
    F--126886139(+) GCGCAA/CTGTCA 1 -- us2k11Minor allele frequency- C:0.33NA 6

    HapMap Linkage Disequilibrium report for C3orf56 (126911974 - 126917025 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for C3orf56: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C3orf56
    DNA2.0 Custom Variant and Variant Library Synthesis for C3orf56

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    1 disease for C3orf56:    About MalaCards
    alzheimer's disease


    C3orf56 for disorders           About GeneDecksing

    Genetic Association Database (GAD): C3orf56
    Human Genome Epidemiology (HuGE) Navigator: C3orf56 (1 document)

    Export disorders for C3orf56 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 C3orf56 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C3orf56)
        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, 3 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients. (PubMed id 24025145)1 Chung S....Nakamura Y. (Breast Cancer Res. 2013)
    3. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. (PubMed id 21116278)4 Furney S.J.... . (Mol. Psychiatry 2011)
    4. 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)
    5. 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: 285311 HGNC: 32481 AceView: LOC285311 Ensembl:ENSG00000214324 euGenes: HUgn285311
    ECgene: C3orf56 H-InvDB: C3orf56

    (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 C3orf56 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 C3orf56 gene:
    Search GeneIP for patents involving C3orf56

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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