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C16orf54 Gene

protein-coding   GIFtS: 41
GCID: GC16M029753

Chromosome 16 Open Reading Frame 54

  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 16 Open Reading Frame 541 2
Transmembrane Protein C16orf542

External Ids:    HGNC: 266491   Entrez Gene: 2838972   Ensembl: ENSG000001859057   UniProtKB: Q6UWD83   

Export aliases for C16orf54 gene to outside databases

Previous GC identifers: GC16M029662 GC16M029663 GC16M027414


(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 C16orf54 Gene:
C16orf54 (chromosome 16 open reading frame 54) is a protein-coding gene. Diseases associated with C16orf54 include pancreatitis.


(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_000016.10  NC_018927.2  NT_187260.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the C16orf54 gene promoter:
         E2F-4   E2F-3a   E2F-5   Tal-1   AML1a   E2F-2   LCR-F1   E47   E2F   E2F-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C16orf54

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C16orf54


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

Entrez Gene cytogenetic band: 16p11.2   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p11.2

C16orf54 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C16orf54 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M029753:  view genomic region     (about GC identifiers)

Start:
29,753,784 bp from pter      End:
29,757,340 bp from pter
Size:
3,557 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, 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: CP054_HUMAN, Q6UWD8 (See protein sequence)
Recommended Name: Transmembrane protein C16orf54  
Size: 224 amino acids; 24360 Da
Secondary accessions: A6NJR6 Q8NAB0

Explore the universe of human proteins at neXtProt for C16orf54: NX_Q6UWD8

Explore proteomics data for C16orf54 at MOPED

Post-translational modifications: 

  • O-glycosylated with core 1 or possibly core 8 glycans1
  • Ubiquitination2 at Lys215
  • Glycosylation2 at Thr4
  • Modification sites at PhosphoSitePlus

  • See C16orf54 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_787096.2  
    ENSEMBL proteins: 
     ENSP00000327506  

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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: Q6UWD8


    (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 C16orf54:
     Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C16orf54
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    SwitchGear 3'UTR luciferase reporter plasmidC16orf54 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 UniProtKB/Swiss-Prot
    CP054_HUMAN, Q6UWD8: Membrane; Single-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1
    golgi apparatus1
    mitochondrion1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    C16orf54 for ontologies           About GeneDecksing


    (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 C16orf54
    Interactions:

        Search GeneGlobe Interaction Network for C16orf54

    (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 C16orf54 (CP054)



    (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 C16orf54 gene: 
    NM_175900.3  

    Unigene Cluster for C16orf54:

    Chromosome 16 open reading frame 54
    Hs.331095  [show with all ESTs]
    Unigene Representative Sequence: NM_175900
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000329410(uc002dtp.2)
    miRNA
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    hsa-miR-3688-3p hsa-miR-330-5p hsa-miR-3065-3p hsa-miR-340 hsa-miR-766 hsa-miR-661 hsa-miR-508-5p hsa-miR-326
    SwitchGear 3'UTR luciferase reporter plasmidC16orf54 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat C16orf54

    Additional mRNA sequence: 

    AK093000.1 AY358833.1 BC025741.1 BC104466.2 BC104467.2 

    2 DOTS entries:

    DT.91673445  DT.120697258 

    11 AceView cDNA sequences:

    BC025741 AX747848 AU185083 NM_175900 AY358833 AK093000 AV743116 R54004 
    CD688583 BI834039 BF894950 

    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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    C16orf54 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAAATAAATA
    C16orf54 Expression
    About this image


    C16orf54 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Pancreas (Endocrine System)    fully expand to see all 2 entries
             Endocrine Progenitor Cells Ventral Pancreatic Bud
     
     Endothelium (Cardiovascular System)
             Extraembryonic Angioblasts Extraembryonic Capillary Plexus
     
     Extraembryonic Mesoderm (Extraembryonic Tissues)
             Extraembryonic Angioblasts Extraembryonic Capillary Plexus
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
    C16orf54 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C16orf54 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.331095
        Custom PCR Arrays for C16orf54
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C16orf54

    (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 C16orf54 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia AI4676061 , 5 expressed sequence AI4676061, 5 76.53(n)1
    72.2(a)1
      7 (69.32 cM)5
    1016021  NM_178901.31  NP_849232.11 
     1270914365 


    ENSEMBL Gene Tree for C16orf54 (if available)
    TreeFam Gene Tree for C16orf54 (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 C16orf54 (see all 114)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1131377731,2
    C--29753314(+) CCCCTG/ATGCGG 1 -- int11Minor allele frequency- A:0.50CSA 2
    rs1848485351,2
    --29753317(+) CTGTGC/TGGGGC 1 -- int10--------
    rs1390099941,2
    --29753357(+) TCTCAC/TTGTGG 1 -- int10--------
    rs1897262161,2
    --29753437(+) CGGGCA/GCGGTG 1 -- int10--------
    rs1817214021,2
    --29753495(+) CATGAA/GGTCAG 1 -- int10--------
    rs1850424211,2
    --29753506(+) GAGTTC/TGAGAC 1 -- int10--------
    rs1889788691,2
    --29753599(+) AGCTAC/TTTGGG 1 -- int10--------
    rs1120822431,2
    C,F--29753634(+) AACCCG/AGAGGC 1 -- int12Minor allele frequency- A:0.33CSA 3
    rs1508658401,2
    C--29753664(+) GATCGC/TGCCAT 1 -- int10--------
    rs1817320401,2
    --29753671(+) CCATCA/GCACTG 1 -- int10--------

    HapMap Linkage Disequilibrium report for C16orf54 (29753784 - 29757340 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for C16orf54:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv34n68CNV Loss17160897
    nsv833186CNV Loss17160897

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    (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 C16orf54:    
    About MalaCards
    pancreatitis


    C16orf54 for disorders           About GeneDecksing


    Export disorders for C16orf54 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 C16orf54 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C16orf54)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    5. Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD. (PubMed id 22171320)2 Halim A.... Larson G. (Mol. Cell. Proteomics 2011)
    6. 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)
    7. 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)
    8. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)
    9. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PubMed id 10493829)1 Loftus B.J.... Adams M.D. (Genomics 1999)

    (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: 283897 HGNC: 26649 AceView: FLJ35681 Ensembl:ENSG00000185905 euGenes: HUgn283897
    ECgene: C16orf54 H-InvDB: C16orf54

    (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 C16orf54 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 C16orf54 gene:
    Search GeneIP for patents involving C16orf54

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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