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C12orf56 Gene

protein-coding   GIFtS: 37
GCID: GC12M064661

Chromosome 12 Open Reading Frame 56

  Search for C12orf56
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 561 2
Uncharacterized Protein C12orf562

External Ids:    HGNC: 269671   Entrez Gene: 1157492   Ensembl: ENSG000001853067   UniProtKB: Q8IXR93   

Export aliases for C12orf56 gene to outside databases

Previous GC identifers: GC12M062948 GC12M061713


(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 C12orf56 Gene:
C12orf56 (chromosome 12 open reading frame 56) 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  NC_018923.2  NT_029419.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the C12orf56 gene promoter:
         C/EBPbeta   Pbx1a   MyoD   Pax-2   CUTL1   Pax-2a   E47   N-Myc   ATF6   Hlf   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C12orf56

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C12orf56


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

Entrez Gene cytogenetic band: 12q14.2   Ensembl cytogenetic band:  12q14.2   HGNC cytogenetic band: 12q14.2

C12orf56 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C12orf56 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M064661:  view genomic region     (about GC identifiers)

Start:
64,660,217 bp from pter      End:
64,784,972 bp from pter
Size:
124,756 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, 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: CL056_HUMAN, Q8IXR9 (See protein sequence)
Recommended Name: Uncharacterized protein C12orf56  
Size: 622 amino acids; 71046 Da
Alternative splicing: 2 isoforms:  Q8IXR9-1   Q8IXR9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C12orf56: NX_Q8IXR9

Explore proteomics data for C12orf56 at MOPED


See C12orf56 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001093146.1  NP_001164104.1  

ENSEMBL proteins: 
 ENSP00000446101   ENSP00000329698   ENSP00000443341  

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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:
 IPR027878 DUF4551

Graphical View of Domain Structure for InterPro Entry Q8IXR9

ProtoNet protein and cluster: Q8IXR9


C12orf56 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 C12orf56:
 Synthetic lethal with Ras 

Animal Models:
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miRNA
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miRTarBase miRNAs that target C12orf56:
hsa-mir-335-5p (MIRT016956)

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hsa-miR-3143 hsa-miR-543
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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
cytosol2
mitochondrion2
peroxisome1

(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 C12orf56
Interactions:

    Search GeneGlobe Interaction Network for C12orf56

(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 C12orf56 (CL056)



(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 C12orf56 gene (2 alternative transcripts): 
NM_001099676.2  NM_001170633.1  

Unigene Cluster for C12orf56:

Chromosome 12 open reading frame 56
Hs.535190  [show with all ESTs]
Unigene Representative Sequence: NM_001170633
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000543942(uc021qzu.1) ENST00000535515 ENST00000542397(uc001srz.3)
ENST00000536975(uc001sry.3) ENST00000333722(uc001ssa.4) ENST00000541802
ENST00000543259
miRNA
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hsa-miR-3143 hsa-miR-543
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Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat C12orf56

Additional mRNA sequence: 

BC014352.1 BC015121.1 BC039369.1 

5 DOTS entries:

DT.121176749  DT.75100718  DT.95366682  DT.121176762  DT.100747090 

21 AceView cDNA sequences:

BI462190 AI635775 BM694463 BC014352 BC015121 BX089271 AI468255 AI522132 
AI632021 BC039369 AW450302 BI830702 AI473408 AI242842 R66203 BF029659 
BE566584 R67081 BF028589 BE565136 BE565030 

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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C12orf56 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCAGCCTTGC
C12orf56 Expression
About this image

C12orf56 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C12orf56 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.535190
    Custom PCR Arrays for C12orf56
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C12orf56

(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 C12orf56 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia D930020B18Rik1 , 5 RIKEN cDNA D930020B18 gene1, 5 79.67(n)1
75.73(a)1
  10 (69.89 cM)5
2163931  NM_177335.41  NP_796309.31 
 1216415885 
zebrafish
(Danio rerio)
Actinopterygii si:ch211-258f14.21 si:ch211-258f14.2 49.43(n)
37.21(a)
  100330213  XM_002661359.2  XP_002661405.2 


ENSEMBL Gene Tree for C12orf56 (if available)
TreeFam Gene Tree for C12orf56 (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 C12orf56 (see all 2386)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 12 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1916658261,2
--64660888(+) AAAAAA/TGTTTC 2 -- ut310--------
rs1841237671,2
C--64660896(+) TTCTCG/ATGAAT 2 -- ut311Minor allele frequency- A:0.00EU 569
rs1885711901,2
--64660955(+) ACATTG/TTTTGT 2 -- ut310--------
rs1500722381,2
C--64660970(+) ATTCAA/GCCAAT 4 A V mis10--------
rs1443824921,2
--64661123(+) TTCACA/GTTGGT 2 -- int10--------
rs1149810371,2
C,F--64661199(+) GGTCAG/ACATTT 2 -- int11Minor allele frequency- A:0.09WA 118
rs16570571,2
C,H--64661209(+) TTCAGC/ATCTCC 2 -- int15Minor allele frequency- A:0.02WA NA 130
rs16570581,2
C,H--64661210(+) TCAGAC/TCTCCA 2 -- int17Minor allele frequency- T:0.01WA NA EA 368
rs1486194581,2
--64661304(+) GACATA/GTGGAC 2 -- int10--------
rs79567261,2
C,F,A,H--64661374(+) TGAGGT/AGTTGA 2 -- int126Minor allele frequency- A:0.30NS EA NA WA 2886

HapMap Linkage Disequilibrium report for C12orf56 (64660217 - 64784972 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for C12orf56:    About this table    
Variant IDTypeSubtypePubMed ID
esv1457683CNV Deletion17803354
esv2745987CNV Deletion23290073
nsv517246CNV Loss19592680
nsv469456CNV Loss19166990

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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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C12orf56 for disorders           About GeneDecksing

Human Genome Epidemiology (HuGE) Navigator: C12orf56 (2 documents)

Export disorders for C12orf56 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 C12orf56 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C12orf56)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)
  3. 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)
  4. 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: 115749 HGNC: 26967 AceView: LOC115749 Ensembl:ENSG00000185306 euGenes: HUgn115749
ECgene: C12orf56 H-InvDB: C12orf56

(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 C12orf56 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 C12orf56 gene:
Search GeneIP for patents involving C12orf56

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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