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C12orf40 Gene

protein-coding   GIFtS: 40
GCID: GC12P040019

Chromosome 12 Open Reading Frame 40

  Search for C12orf40
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 12 Open Reading Frame 401 2
HEL-2062
Epididymis Luminal Protein 2062
Uncharacterized Protein C12orf402

External Ids:    HGNC: 268461   Entrez Gene: 2834612   Ensembl: ENSG000001801167   UniProtKB: Q86WS43   

Export aliases for C12orf40 gene to outside databases

Previous GC identifers: GC12P038307 GC12P037046


(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 C12orf40 Gene:
C12orf40 (chromosome 12 open reading frame 40) 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:
NC_000012.12  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C12orf40 gene promoter:
         COUP-TF1   COUP   HNF-4alpha1   Evi-1   POU2F1   COUP-TF   POU2F1a   HSF2   Chx10   c-Myb   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C12orf40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C12orf40


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

Entrez Gene cytogenetic band: 12q12   Ensembl cytogenetic band:  12q12   HGNC cytogenetic band: 12q12

C12orf40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C12orf40 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P040019:  view genomic region     (about GC identifiers)

Start:
40,019,969 bp from pter      End:
40,302,102 bp from pter
Size:
282,134 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CL040_HUMAN, Q86WS4 (See protein sequence)
Recommended Name: Uncharacterized protein C12orf40  
Size: 652 amino acids; 74505 Da
Sequence caution: Sequence=AAH38754.2; Type=Erroneous initiation;
Secondary accessions: B7WNU1 Q8IXY6 Q8N818
Alternative splicing: 3 isoforms:  Q86WS4-1   Q86WS4-2   Q86WS4-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C12orf40: NX_Q86WS4

Explore proteomics data for C12orf40 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C12orf40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001026918.2  
    ENSEMBL proteins: 
     ENSP00000383897   ENSP00000317671   ENSP00000473371   ENSP00000381701  

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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:
     IPR027883 DUF4552

    Graphical View of Domain Structure for InterPro Entry Q86WS4

    ProtoNet protein and cluster: Q86WS4


    C12orf40 for domains           About GeneDecksing


    (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 C12orf40:
     Proliferating cells 

    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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    plasma membrane1

    (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 C12orf40
    Interactions:

        Search GeneGlobe Interaction Network for C12orf40

    (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 C12orf40 (CL040)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for C12orf40 gene (2 alternative transcripts): 
    NM_173599.1  NM_001031748.2  

    Unigene Cluster for C12orf40:

    Chromosome 12 open reading frame 40
    Hs.648205  [show with all ESTs]
    Unigene Representative Sequence: BC048120
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000405531 ENST00000324616(uc001rmc.3) ENST00000468200(uc009zjv.1)
    ENST00000398716
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    Additional mRNA sequence: 

    BC038754.1 BC048120.1 

    4 DOTS entries:

    DT.91663247  DT.99934975  DT.75185693  DT.100014187 

    13 AceView cDNA sequences:

    AL705293 BC038754 BC048120 AW628770 AK097445 BI459303 BI461967 BG772324 
    NM_173599 AW183224 BG724290 AW661998 BE972784 

    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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    C12orf40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTAAAACATT
    C12orf40 Expression
    About this image

    C12orf40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C12orf40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.648205
        Custom PCR Arrays for C12orf40
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    In Situ
    Assay Products:
     

     
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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 C12orf40 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia CN7254255 cDNA sequence CN725425   --   15 (46.04 cM) 91231578 
    chicken
    (Gallus gallus)
    Aves C1H12orf401 chromosome 1 open reading frame, human C12orf40 51.43(n)
    34.36(a)
      101748677  XM_004934757.1  XP_004934814.1 


    ENSEMBL Gene Tree for C12orf40 (if available)
    TreeFam Gene Tree for C12orf40 (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 C12orf40 (see all 2172)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs558734221,2
    C--37074743(+) CCTCA-/TAGAAAA 1 -- int11Minor allele frequency- TA:0.00NA 2
    rs730965831,2
    C,F--40018078(+) CTTAGC/ACTAAT 1 -- us2k12Minor allele frequency- A:0.04WA NA 238
    rs1891581351,2
    --40018104(+) GACTGC/GAAGGA 1 -- us2k10--------
    rs796856961,2
    F--40018121(+) TGACTC/ATAGTA 1 -- us2k11Minor allele frequency- A:0.33NA 6
    rs1815686041,2
    --40018636(+) AAAAAA/GAGTTA 1 -- us2k10--------
    rs1857335751,2
    C--40018888(+) ACAAGA/GTATCT 1 -- us2k10--------
    rs1151500061,2
    C,F--40018941(+) CTTAAC/TAAAAA 1 -- us2k10--------
    rs1381871981,2
    --40019116(+) ATATAC/GAAACT 1 -- us2k10--------
    rs1816724861,2
    --40019149(+) ATTCAA/GTTTTT 1 -- us2k10--------
    rs2009299711,2
    --40019163(+) TGAGA-/TTTTTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for C12orf40 (40019969 - 40269969 bp, first 250kb of C12orf40)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for C12orf40 (see all 14):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2745778CNV Deletion23290073
    esv2745777CNV Deletion23290073
    esv2745776CNV Deletion23290073
    esv271024CNV Insertion20981092
    esv1444745CNV Insertion17803354
    esv1277090CNV Insertion17803354
    esv2452886CNV Loss19546169
    dgv1412n71CNV Loss21882294
    nsv899024CNV Loss21882294
    nsv899022CNV Loss21882294

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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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      --

    (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 C12orf40 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C12orf40)
        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 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)
    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)

    (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: 283461 HGNC: 26846 AceView: FLJ40126 Ensembl:ENSG00000180116 euGenes: HUgn283461
    ECgene: C12orf40 H-InvDB: C12orf40

    (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 C12orf40 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 C12orf40 gene:
    Search GeneIP for patents involving C12orf40

    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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     SwitchGear 3'UTR luciferase reporter plasmids for C12orf40
     Browse SwitchGear Promoter luciferase reporter plasmids for C12orf40
     Search ThermoFisher Antibodies for C12orf40
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C12orf40
     inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C12orf40
     inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for C12orf40
     LSBio Antibodies in human, mouse, rat for C12orf40
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