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C12orf42 Gene

protein-coding   GIFtS: 42
GCID: GC12M103631

Chromosome 12 Open Reading Frame 42

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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 12 Open Reading Frame 421 2
Uncharacterized Protein C12orf422

External Ids:    HGNC: 247291   Entrez Gene: 3744702   Ensembl: ENSG000001790887   UniProtKB: Q96LP63   
ORGUL members:         

Export aliases for C12orf42 gene to outside databases

Previous GC identifers: GC12M102199 GC12M100754


(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 C12orf42 Gene:
C12orf42 (chromosome 12 open reading frame 42) 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_000012.11  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C12orf42 gene promoter:
         MEF-2A   Bach1   HNF-1   aMEF-2   HNF-1A   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C12orf42

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C12orf42


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

Entrez Gene cytogenetic band: 12q23.2   Ensembl cytogenetic band:  12q23.3   HGNC cytogenetic band: 12q23.2

C12orf42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C12orf42 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M103631:  view genomic region     (about GC identifiers)

Start:
103,631,369 bp from pter      End:
103,889,749 bp from pter
Size:
258,381 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: CL042_HUMAN, Q96LP6 (See protein sequence)
Recommended Name: Uncharacterized protein C12orf42  
Size: 360 amino acids; 39738 Da
Secondary accessions: Q49A64 Q4G0S2
Alternative splicing: 3 isoforms:  Q96LP6-1   Q96LP6-2   Q96LP6-3   (No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for C12orf42: NX_Q96LP6

Explore proteomics data for C12orf42 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C12orf42 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001092806.1  NP_001265348.1  NP_001265349.1  NP_940923.2  

    ENSEMBL proteins: 
     ENSP00000446908   ENSP00000447908   ENSP00000449362   ENSP00000449447   ENSP00000447795  
     ENSP00000324984   ENSP00000367353  

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    antibodies-online peptides for C12orf42

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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: Q96LP6


    (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 C12orf42

    miRNA
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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

    (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 C12orf42
    Interactions:

        Search GeneGlobe Interaction Network for C12orf42

    (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 C12orf42 (CL042)



    (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 C12orf42 gene (4 alternative transcripts): 
    NM_001099336.2  NM_001278419.1  NM_001278420.1  NM_198521.3  

    Unigene Cluster for C12orf42:

    Chromosome 12 open reading frame 42
    Hs.534649  [show with all ESTs]
    Unigene Representative Sequence: BC044617
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000547347(uc001tjs.3) ENST00000547470 ENST00000549927 ENST00000551303
    ENST00000550650 ENST00000546526 ENST00000552977 ENST00000548883(uc001tjt.2)
    ENST00000548048 ENST00000551134(uc001tju.2) ENST00000548789 ENST00000552578
    ENST00000550497 ENST00000552372 ENST00000548196 ENST00000315192 ENST00000378113(uc009zuf.1)

    miRNA
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    6 qRT-PCR Assays for microRNAs that regulate C12orf42:
    hsa-miR-4261 hsa-miR-3200-5p hsa-miR-514 hsa-miR-489 hsa-miR-514b-3p hsa-miR-3190
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Additional mRNA sequence: 

    AK058052.1 BC044617.1 BC117392.1 BC117394.1 

    6 DOTS entries:

    DT.206949  DT.95155904  DT.121192907  DT.121192918  DT.40124719  DT.95308551 

    21 AceView cDNA sequences:

    AK058052 BC039352 NM_198521 BM559576 BI460188 AI479330 BI464411 AA405093 
    BI830750 AI027657 AA399053 AI638494 AA397714 BE246180 AI688816 AA913933 
    BE244095 AA992269 AA758779 AI001900 AI797464 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for C12orf42    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b
    SP1:                                                                  
    SP2:              -                       -                           
    SP3:                                      -                           


    ECgene alternative splicing isoforms for C12orf42

    (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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    C12orf42 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAATCTGGC
    C12orf42 Expression
    About this image

    C12orf42 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C12orf42 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.534649
        Custom PCR Arrays for C12orf42
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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 human and mouse.

    Orthologs for C12orf42 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1700113H08Rik1 , 5 RIKEN cDNA 1700113H08 gene1, 5 65.73(n)1
    48.28(a)1
      10 (43.50 cM)5
    766401  NM_029685.11  NP_083961.11 
     870580465 


    ENSEMBL Gene Tree for C12orf42 (if available)
    TreeFam Gene Tree for C12orf42 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for C12orf42 gene

    Find genes that share paralogs with C12orf42           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for C12orf42
    PGOHUM00000233791


    (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 C12orf42 (see all 3786)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs581571401,2
    C--100874624(+) AAATA-/AATAA 
     ATAAATA
    TCAGC
    2 -- int11Minor allele frequency- AATAAATAAATA:0.00NA 2
    rs347575551,2
    C,F--103695378(+) CTGACA/CTTAAA 2 -- int13Minor allele frequency- C:0.33NA 6
    rs1386760931,2
    --103695506(+) AGGCCC/GTTAGA 2 -- int10--------
    rs1413050121,2
    --103695561(+) ACCTGC/TGAAAG 2 -- int10--------
    rs1884880901,2
    --103695675(+) GACACC/TGCAGA 2 -- int10--------
    rs1172339711,2
    C,F--103695757(+) TAGGTT/CCAAAA 2 -- ut311Minor allele frequency- C:0.03EA 120
    rs1818842031,2
    --103695833(+) CTGAGA/CAGGCA 2 -- ut310--------
    rs1508023941,2
    C--103695862(+) GCACTC/TGCCGA 2 -- ut310--------
    rs1852733501,2
    --103695893(+) AATGTA/CAGTGA 4 * L stg10--------
    rs1904002011,2
    C--103695896(+) GTAAGA/TGAGCA 4 H L mis10--------

    HapMap Linkage Disequilibrium report for C12orf42 (103631369 - 103881369 bp, first 250kb of C12orf42)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for C12orf42:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv309e199CNV Deletion23128226
    esv269933CNV Insertion20981092
    nsv521147CNV Loss19592680
    esv22217CNV Loss19812545
    nsv826506CNV Loss20364138
    dgv1485n71CNV Gain21882294

    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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    Find genes that share disorders with C12orf42           About GenesLikeMe

    Genetic Association Database (GAD): C12orf42
    Human Genome Epidemiology (HuGE) Navigator: C12orf42 (1 document)

    Export disorders for C12orf42 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 C12orf42 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C12orf42)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention. (PubMed id 21878436)1, 4 Sampietro M.L....Jukema J.W. (Hum. Mol. Genet. 2011)
    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. Molecular characterization of a novel chromosomal translocation t(12;14)(q23;q11.2) in T-lymphoblastic lymphoma between the T-cell receptor delta-deleting elements (TRDREC and TRAJ61) and the hypothetical gene C12orf42. (PubMed id 20659153)1 Przybylski G.K....Schmidt C.A. (Eur. J. Haematol. 2010)
    5. 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)
    6. Framingham Heart Study genome-wide association: results for pulmonary function measures. (PubMed id 17903307)4 Wilk J.B....O'Connor G.T. (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 finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)
    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: 374470 HGNC: 24729 AceView: FLJ25323 Ensembl:ENSG00000179088 euGenes: HUgn374470
    ECgene: C12orf42 H-InvDB: C12orf42

    (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 C12orf42 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 C12orf42 gene:
    Search GeneIP for patents involving C12orf42

    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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