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C16orf46 Gene

protein-coding   GIFtS: 45
GCID: GC16M081087

Chromosome 16 Open Reading Frame 46

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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 16 Open Reading Frame 461 2
Uncharacterized Protein C16orf462

External Ids:    HGNC: 265251   Entrez Gene: 1237752   Ensembl: ENSG000001664557   UniProtKB: Q6P3873   
ORGUL members:         

Export aliases for C16orf46 gene to outside databases

Previous GC identifers: GC16M079653 GC16M066843


(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 C16orf46 Gene:
C16orf46 (chromosome 16 open reading frame 46) 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_000016.9  NT_010498.16  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C16orf46 gene promoter:
         ATF-2   FOXD1   CBF-C   CBF-A   FOXO4   FOXJ2 (long isoform)   FOXJ2   NF-kappaB1   MRF-2   CBF(2)   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C16orf46

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C16orf46


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

Entrez Gene cytogenetic band: 16q23.2   Ensembl cytogenetic band:  16q23.2   HGNC cytogenetic band: 16q23.2

C16orf46 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C16orf46 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M081087:  view genomic region     (about GC identifiers)

Start:
81,087,102 bp from pter      End:
81,110,872 bp from pter
Size:
23,771 bases      Orientation:
minus 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: CP046_HUMAN, Q6P387 (See protein sequence)
Recommended Name: Uncharacterized protein C16orf46  
Size: 395 amino acids; 43418 Da
Secondary accessions: Q96MA7
Alternative splicing: 2 isoforms:  Q6P387-1   Q6P387-2   

Explore the universe of human proteins at neXtProt for C16orf46: NX_Q6P387

Explore proteomics data for C16orf46 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C16orf46 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001094343.1  NP_689550.2  

    ENSEMBL proteins: 
     ENSP00000367874   ENSP00000299578   ENSP00000455877  

    C16orf46 Human Recombinant Protein Products:

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    antibodies-online peptides for C16orf46

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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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    1 InterPro protein domain:
     IPR027836 DUF4529

    Graphical View of Domain Structure for InterPro Entry Q6P387

    ProtoNet protein and cluster: Q6P387


    Find genes that share domains with C16orf46           About GenesLikeMe


    (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 C16orf46

    miRNA
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    miRTarBase miRNAs that target C16orf46:
    hsa-mir-192-5p (MIRT026811), hsa-mir-335-5p (MIRT018553)

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    3 qRT-PCR Assays for microRNAs that regulate C16orf46:
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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
    cytosol4
    nucleus4

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--

    Find genes that share ontologies with C16orf46           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 C16orf46
    Interactions:

        Search GeneGlobe Interaction Network for C16orf46

    (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 C16orf46 (CP046)



    (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 C16orf46 gene (2 alternative transcripts): 
    NM_001100873.1  NM_152337.2  

    Unigene Cluster for C16orf46:

    Chromosome 16 open reading frame 46
    Hs.658684  [show with all ESTs]
    Unigene Representative Sequence: AK128467
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378611(uc010chf.3) ENST00000299578(uc002fgc.4 uc010vno.2)
    ENST00000444657 ENST00000565253
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    hsa-miR-3117-3p hsa-miR-3662 hsa-miR-4299
    SwitchGear 3'UTR luciferase reporter plasmidC16orf46 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat C16orf46

    Additional mRNA sequence: 

    AK057264.1 AK128467.1 AK295411.1 BC064143.1 

    7 DOTS entries:

    DT.99944493  DT.40229554  DT.100775253  DT.99990752  DT.92009263  DT.40268560  DT.95272855 

    Selected AceView cDNA sequences (see all 237):

    N72768 BX111930 CR601763 BG528603 CA777840 BI091245 AA304964 N63246 
    BM756167 AI952820 AI650884 BF448093 BG576993 BC000790 CR606547 AI432670 
    AA307978 CR603013 NM_004483 CR603107 AW194585 AA905107 BI093591 AY533031 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for C16orf46    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5
    SP1:              -                           
    SP2:                                          
    SP3:              -     -     -     -         


    ECgene alternative splicing isoforms for C16orf46

    (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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    C16orf46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTCTCCCAAA
    C16orf46 Expression
    About this image

    C16orf46 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C16orf46 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.658684
        Custom PCR Arrays for C16orf46
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C16orf46

    (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 C16orf46 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1700030J22Rik1 , 5 RIKEN cDNA 1700030J22 gene1, 5 69.29(n)1
    56.6(a)1
      8 (63.41 cM)5
    695281  NM_027103.21  NP_081379.11 
     1169695995 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004870551 chromosome unknown open reading frame, human C16orf46 43.34(n)
    30.65(a)
      100487055  XM_002938143.2  XP_002938189.1 


    ENSEMBL Gene Tree for C16orf46 (if available)
    TreeFam Gene Tree for C16orf46 (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 C16orf46 (see all 803)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1136459441,2
    C,F--81086667(+) TACAGG/ATGTGA 1 -- int11Minor allele frequency- A:0.50WA 2
    rs1866249251,2
    --81086688(+) CTAGCC/TATGAA 1 -- int10--------
    rs1490605011,2
    C--81086705(+) TCTAGA/TTTGTT 1 -- int10--------
    rs1899544301,2
    --81086880(+) AGGGAC/TGGCTC 1 -- int10--------
    rs2015339321,2
    --81087134(+) TTTAC-/TAAT  
            
    TAATA
    1 -- ut310--------
    rs121491101,2
    C,H--81087197(+) TTGACC/GTATCA 1 -- ut31 ese34Minor allele frequency- G:0.00NS EA 418
    rs1421387641,2
    C--81087239(+) TTCATA/G/TCTTTA 2 -- ut310--------
    rs1511408741,2
    C--81087274(+) AACATC/TAGGCT 1 -- ut310--------
    rs1402495381,2
    --81087280(+) AGGCTC/GCAAAA 1 -- ut310--------
    rs1125181151,2
    C,F--81087345(+) GTCCAG/ATGTAT 1 -- ut312Minor allele frequency- A:0.50CSA 4

    HapMap Linkage Disequilibrium report for C16orf46 (81087102 - 81110872 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for C16orf46:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422360CNV Duplication17116639
    nsv1897CNV Loss18451855
    dgv356n27CNV Loss19166990
    esv2751615CNV Gain17911159

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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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    Find genes that share disorders with C16orf46           About GenesLikeMe

    Genetic Association Database (GAD): C16orf46
    Human Genome Epidemiology (HuGE) Navigator: C16orf46 (1 document)

    Export disorders for C16orf46 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 C16orf46 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C16orf46)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. (PubMed id 18951430)1, 4 Anney R.J....Gill M. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement. (PubMed id 20235792)4 Uhl G.R....MunafA^ M.R. (Pharmacogenomics 2010)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    6. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
    7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    8. 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)
    9. 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: 123775 HGNC: 26525 AceView: GCSHandFLJ32702 Ensembl:ENSG00000166455 euGenes: HUgn123775
    ECgene: C16orf46 H-InvDB: C16orf46

    (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 C16orf46 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 C16orf46 gene:
    Search GeneIP for patents involving C16orf46

    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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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