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

C12orf42 Gene

protein-coding   GIFtS: 39
GCID: GC12M103631

chromosome 12 open reading frame 42
 Explore 1 disease affiliated with
C12orf42 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C12orf42    

Aliases
for C12orf42 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 12 Open Reading Frame 421 2
FLJ253231
Uncharacterized Protein C12orf422

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

Export aliases for C12orf42 gene to outside databases

Previous GC identifers: GC12M102199 GC12M100754


Summaries
for C12orf42 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 C12orf42 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_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for C12orf42

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for C12orf42 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: 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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96LP6

    • C12orf42 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

    ENSEMBL proteins: 
     ENSP00000446908   ENSP00000447908   ENSP00000449362   ENSP00000449447   ENSP00000447795  
     ENSP00000324984   ENSP00000367353  

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    Protein Domains /
    Families
    for C12orf42 gene

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

    ProtoNet protein and cluster: Q96LP6


    Function
    for C12orf42 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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    Pathways & Interactions
    for C12orf42 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 C12orf42

    Drugs & Compounds
    for C12orf42 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 C12orf42
    Search CenterWatch for drugs/clinical trials and news about C12orf42 / CL042 

    Transcripts
    for C12orf42 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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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for C12orf42 gene (2 alternative transcripts): 
    NM_001099336.1  NM_198521.2  

    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)


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    Additional cDNA 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:

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

    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

    Expression
    for C12orf42 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

    C12orf42 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCAATCTGGC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See C12orf42 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C12orf42

    SOURCE GeneReport for Unigene cluster: Hs.534649
        SABiosciences Custom PCR Arrays for C12orf42
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    In Situ
    Assay Products:     
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    Orthologs
    for C12orf42 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 C12orf42 gene from 1/3 species (see all 3)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia 1700113H08Rik1 , 5 RIKEN cDNA 1700113H08 gene1, 5 66.04(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
    for C12orf42 gene

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

    C12orf42 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for C12orf42
    PGOHUM00000233791


    Genomic Variants
    for C12orf42 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

    10/3292 NCBI SNPs in C12orf42 are shown (see all 3292)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 12 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    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--------
    rs1822341291,2
    		--103695959(+) TTGGGC/TGGGGG 4 H R mis10--------

    HapMap Linkage Disequilibrium report for C12orf42 (103631369 - 103881369 bp, first 250kb of C12orf42)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 4 variations for C12orf42
         4 CNVs: 76139 86545 86546 66316

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    Disorders / Diseases
    for C12orf42 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
    C12orf42 for disorders           About GeneDecksing

    1 disease for C12orf42:    About MalaCards
    lymphoblastic lymphoma

    Human Genome Epidemiology (HuGE) Navigator: C12orf42 (1 document)

    Export disorders for C12orf42 gene to outside databases

    Publications
    for C12orf42 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 C12orf42 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C12orf42)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutan eous coronary intervention. (PubMed id 21878436)1 Sampietro M.L....Jukema J.W. (2011)
    4. Molecular characterization of a novel chromosomal tra nslocation t(12;14)(q23;q11.2) in T-lymphoblastic lymphoma between the T-cell r eceptor delta-deleting elements (TRDREC and TRAJ61) and the hypothetical gene C 12orf42. (PubMed id 20659153)1 Przybylski G.K....Schmidt C.A. (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. (2010)
    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. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (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. (2002)

    External Searches for C12orf42 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 C12orf42 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 374470 HGNC: 24729 AceView: FLJ25323 Ensembl:ENSG00000179088 euGenes: HUgn374470
    ECgene: C12orf42 H-InvDB: C12orf42

    Other Databases showing C12orf42 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C12orf42 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 C12orf42 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C12orf42 gene

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



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    for C12orf42 gene

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    About This Section

     
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