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C15orf48 Gene

protein-coding   GIFtS: 43
GCID: GC15P045722

Chromosome 15 Open Reading Frame 48

  See C15orf48-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 15 Open Reading Frame 481 2
Normal Mucosa Of Esophagus Specific 11 2
NMES12 5
FOAP-112
Normal Mucosa Of Esophagus-Specific Gene 1 Protein2
Protein FOAP-113

External Ids:    HGNC: 298981   Entrez Gene: 844192   Ensembl: ENSG000001669207   OMIM: 6084095   UniProtKB: Q9C0023   

Export aliases for C15orf48 gene to outside databases

Previous GC identifers: GC15P043511 GC15P022547


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for C15orf48 Gene:
This gene was first identified in a study of human esophageal squamous cell carcinoma tissues. Levels of both the
message and protein are reduced in carcinoma samples. In adult human tissues, this gene is expressed in the the
esophagus, stomach, small intestine, colon and placenta. Alternatively spliced transcript variants that encode
the same protein have been identified. (provided by RefSeq, Jun 2012)

GeneCards Summary for C15orf48 Gene:
C15orf48 (chromosome 15 open reading frame 48) is a protein-coding gene. Diseases associated with C15orf48 include esophageal squamous cell carcinoma.




(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_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the C15orf48 gene promoter:
         STAT1   Bach2   FOXD1   E47   NF-AT   N-Myc   NF-AT4   NF-AT2   NF-AT3   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C15orf48

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C15orf48


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

Entrez Gene cytogenetic band: 15q21.1   Ensembl cytogenetic band:  15q21.1   HGNC cytogenetic band: 15q21.1

C15orf48 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C15orf48 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P045722:  view genomic region     (about GC identifiers)

Start:
45,722,727 bp from pter      End:
45,740,959 bp from pter
Size:
18,233 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NMES1_HUMAN, Q9C002 (See protein sequence)
Recommended Name: Normal mucosa of esophagus-specific gene 1 protein  
Size: 83 amino acids; 9617 Da

Explore the universe of human proteins at neXtProt for C15orf48: NX_Q9C002

Explore proteomics data for C15orf48 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C15orf48 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_115789.1  NP_922946.1  

    ENSEMBL proteins: 
     ENSP00000379887   ENSP00000452967   ENSP00000341610  

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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:
     IPR010530 B12D

    Graphical View of Domain Structure for InterPro Entry Q9C002

    ProtoNet protein and cluster: Q9C002

    UniProtKB/Swiss-Prot: NMES1_HUMAN, Q9C002
    Similarity: Belongs to the complex I NDUFA4 subunit family


    Find genes that share domains with C15orf48           About GenesLikeMe


    (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, 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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    Phenotypes:
         1 GenomeRNAi human phenotype for C15orf48:
     Increased number of cells in m 

    Animal Models:
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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
    NMES1_HUMAN, Q9C002: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    extracellular3
    mitochondrion2
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA12209954
    GO:0005739mitochondrion IEA--

    Find genes that share ontologies with C15orf48           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 C15orf48
    Interactions:

        Search GeneGlobe Interaction Network for C15orf48

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for C15orf48 (ENSP000003416104) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ABL2ENSP000003565954STRING: ENSP00000356595
    TSSK3ENSP000003626344STRING: ENSP00000362634
    About this table

    (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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for C15orf48 (NMES1)



    (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 C15orf48 gene (2 alternative transcripts): 
    NM_032413.3  NM_197955.2  

    Unigene Cluster for C15orf48:

    Chromosome 15 open reading frame 48
    Hs.112242  [show with all ESTs]
    Unigene Representative Sequence: NM_032413
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000396650 ENST00000558435 ENST00000344300(uc001zvg.3 uc001zvh.3)
    ENST00000558632
    miRNA
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    hsa-miR-28-3p hsa-miR-298 hsa-miR-513a-3p hsa-miR-143* hsa-miR-4282 hsa-miR-548c-3p hsa-miR-2113 hsa-miR-3692
    SwitchGear 3'UTR luciferase reporter plasmidC15orf48 3' UTR sequence
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      QuantiFast Probe-based Assays in human, mouse, rat C15orf48

    Additional mRNA sequence: 

    AB026707.1 AF228422.1 AK026298.1 BC021173.2 

    7 DOTS entries:

    DT.100755295  DT.91758671  DT.99958682  DT.100025292  DT.100755294  DT.40131427  DT.95112615 

    Selected AceView cDNA sequences (see all 94):

    AB026707 BM838465 AA298786 AI207367 BU949284 AW176424 BM312626 BM504582 
    AI335741 NM_197955 D20798 AA298773 CA309087 BQ217789 BQ218935 AK026298 
    AA620995 BQ632588 CD641987 BM312802 BQ631958 BQ632294 AW665458 AI625959 

    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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    C15orf48 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTGTGGCGG
    C15orf48 Expression
    About this image

    C15orf48 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C15orf48 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.112242

    UniProtKB/Swiss-Prot: NMES1_HUMAN, Q9C002
    Tissue specificity: Expressed mainly in stomach, placenta, small intestine and colon, as well as in normal mucosa
    of esophagus. Down-regulated in esophageal squamous cell carcinoma

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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 chordates.

    Orthologs for C15orf48 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia AA4671971 , 5 expressed sequence AA4671971, 5 76.71(n)1
    72.29(a)1
      2 (60.64 cM)5
    4334701  NM_001004174.11  NP_001004174.11 
     1226369865 
    chicken
    (Gallus gallus)
    Aves gga-mir-1476
    gga-mir-147
    60(a)
    1 ↔ 1
    10(10168344-10171832)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1533171 zgc:153317 60.57(n)
    58.54(a)
      751757  NM_001198748.1  NP_001185677.1 


    ENSEMBL Gene Tree for C15orf48 (if available)
    TreeFam Gene Tree for C15orf48 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C15orf48 gene
    2 SIMAP similar genes for C15orf48 using alignment to 1 protein entry:     H0YKW5_HUMAN:
    NMES1    NDUFA4L2

    Find genes that share paralogs with C15orf48           About GenesLikeMe



    (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 C15orf48 (see all 49)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs24336121,2
    C,F,H--45721040(+) GAGTCG/TCTTTA 2 -- us2k19Minor allele frequency- T:0.28NS EA NA WA CSA 544
    rs772311011,2
    C--45721073(+) TGAGCC/TGAGAT 2 -- us2k10--------
    rs11538461,2
    C,F--45721111(+) cagagC/Agagac 2 -- us2k12Minor allele frequency- A:0.00NA 4
    rs1433119301,2
    --45721204(+) AGAATA/GCTTTA 2 -- us2k10--------
    rs1388106901,2
    --45721269(+) TGCAGA/GTATAT 2 -- us2k10--------
    rs1826427361,2
    --45721308(+) TTACTC/TAAAGT 2 -- us2k10--------
    rs1869137671,2
    --45721336(+) TATAGC/TAGGGG 2 -- us2k10--------
    rs12888471,2
    C,F,H--45721575(+) ACCTGC/TGTTCT 2 -- us2k113Minor allele frequency- T:0.33NS EA NA WA CSA 1488
    rs1142348521,2
    F--45721626(+) TCTCTG/CAGTCT 2 -- us2k11Minor allele frequency- C:0.03WA 118
    rs1428179621,2
    --45721756(+) TGCTGC/GCTTAG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for C15orf48 (45722727 - 45740959 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for C15orf48:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv469721CNV Complex16826518

    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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    OMIM gene information: 608409    OMIM disorders: --

    1 disease for C15orf48:    
    About MalaCards
    esophageal squamous cell carcinoma


    Find genes that share disorders with C15orf48           About GenesLikeMe

    Human Genome Epidemiology (HuGE) Navigator: C15orf48 (1 document)

    Export disorders for C15orf48 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 C15orf48 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C15orf48)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel gene, NMES1, downregulated in human esophageal squamous cell carcinoma. (PubMed id 12209954)1, 2, 3 Zhou J.... Liu Z. (Int. J. Cancer 2002)
    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. A regulatory dendritic cell signature correlates with the clinical efficacy of allergen-specific sublingual immunotherapy. (PubMed id 22464673)1 Zimmer A....Moingeon P. (J. Allergy Clin. Immunol. 2012)
    4. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    6. Analysis of the methylation status of genes up-regulated by the demethylating agent, 5-aza-2'-deoxycytidine, in esophageal squamous cell carcinoma. (PubMed id 18636205)1 Arai M....Yokosuka O. (Oncol. Rep. 2008)
    7. Discovery of novel methylation biomarkers in cervical carcinoma by global demethylation and microarray analysis. (PubMed id 16434596)1 Sova P....Kiviat N. (amp 2006)
    8. 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: 84419 HGNC: 29898 AceView: NMES1 Ensembl:ENSG00000166920 euGenes: HUgn84419
    ECgene: C15orf48 H-InvDB: C15orf48

    (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 C15orf48 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 C15orf48 gene:
    Search GeneIP for patents involving C15orf48

    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, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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