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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C16orf54 Gene

protein-coding   GIFtS: 39
GCID: GC16M029753

chromosome 16 open reading frame 54
  Search for C16orf54
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C16orf54    

Aliases
for C16orf54 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 16 Open Reading Frame 541 2
FLJ356811
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


Summaries
for C16orf54 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
  --

Genomic Views
for C16orf54 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010393.16  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for C16orf54

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for C16orf54 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CP054_HUMAN, Q6UWD8 (See protein sequence)
Recommended Name: Transmembrane protein C16orf54  
Size: 224 amino acids; 24360 Da
Subcellular location: Membrane; Single-pass membrane protein (Potential)
Secondary accessions: A6NJR6 Q8NAB0

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

Post-translational modifications:

  • O-glycosylated with core 1 or possibly core 8 glycans1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6UWD8

    • C16orf54 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_787096.2  
    ENSEMBL proteins: 
     ENSP00000327506  

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    Uscn Proteins for C16orf54

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    C16orf54 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for C16orf54

    Protein Domains /
    Families
    for C16orf54 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q6UWD8


    Function
    for C16orf54 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    1 GenomeRNAi human phenotype for C16orf54:
     Increased gamma-H2AX phosphory 


    Pathways & Interactions
    for C16orf54 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C16orf54

    Drugs & Compounds
    for C16orf54 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for C16orf54
    Search CenterWatch for drugs/clinical trials and news about C16orf54 / CP054 

    Transcripts
    for C16orf54 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    About This Section
    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)

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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 plasmid: C16orf54 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for C16orf54 (see all 4)
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    Primer
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    Additional cDNA sequence: 

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

    2 DOTS entries:

    DT.91673445  DT.120697258 

    11 AceView cDNA sequences:

    BC025741 AK093000 NM_175900 AX747848 AY358833 AU185083 R54004 AV743116 
    CD688583 BI834039 BF894950 

    GeneLoc Exon Structure


    Expression
    for C16orf54 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C16orf54 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAAATAAATA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C16orf54 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Extraembryonic MesodermExtraembryonic Capillary PlexusExtraembryonic AngioblastsEndothelium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C16orf54 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C16orf54

    SOURCE GeneReport for Unigene cluster: Hs.331095
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    In Situ
    Assay Products:     
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    Orthologs
    for C16orf54 gene

    (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)
    About This Section
    This gene was present in the common ancestor of human and mouse.

    Orthologs for C16orf54 gene from 1/7 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
    for C16orf54 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for C16orf54 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/88 NCBI SNPs in C16orf54 are shown (see all 88)     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
    		--29753634(+) AACCCG/AGAGGC 1 -- int12Minor allele frequency- A:0.33CSA 3
    rs1508658401,2
    		--29753664(+) GATCGC/TGCCAT 1 -- int10--------
    rs1817320401,2
    		--29753671(+) CCATCA/GCACTG 1 -- int10--------

    HapMap Linkage Disequilibrium report for C16orf54 (29753784 - 29757340 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for C16orf54
         2 CNVs: 4939 35383

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    Disorders / Diseases
    for C16orf54 gene

    (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.)
    About This Section
    		   --

    Publications
    for C16orf54 gene

    (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)
    About This Section

    PubMed articles for C16orf54 gene integrated from 9 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. (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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (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. (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. (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. (2002)
    8. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (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. (1999)

    External Searches for C16orf54 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing C16orf54 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 283897 HGNC: 26649 AceView: FLJ35681 Ensembl:ENSG00000185905 euGenes: HUgn283897
    ECgene: C16orf54 H-InvDB: C16orf54

    Other Databases showing C16orf54 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C16orf54 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C16orf54 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C16orf54 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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



    Products
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    About This Section

     
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