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C11orf42 Gene

protein-coding   GIFtS: 33
GCID: GC11P006226

Chromosome 11 Open Reading Frame 42

  Search for C11orf42
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 11 Open Reading Frame 421 2
Uncharacterized Protein C11orf422

External Ids:    HGNC: 285411   Entrez Gene: 1602982   Ensembl: ENSG000001808787   UniProtKB: Q8N5U03   

Export aliases for C11orf42 gene to outside databases

Previous GC identifers: GC11P006187 GC11P005888


(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 C11orf42 Gene:
C11orf42 (chromosome 11 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:
NC_000011.10  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the C11orf42 gene promoter:
         Spz1   NF-1   RREB-1   MyoD   Lmo2   Gfi-1   HEN1   PPAR-gamma1   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C11orf42

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C11orf42


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

Entrez Gene cytogenetic band: 11p15.4   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.4

C11orf42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C11orf42 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P006226:  view genomic region     (about GC identifiers)

Start:
6,226,796 bp from pter      End:
6,232,365 bp from pter
Size:
5,570 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: CK042_HUMAN, Q8N5U0 (See protein sequence)
Recommended Name: Uncharacterized protein C11orf42  
Size: 333 amino acids; 36368 Da

Explore the universe of human proteins at neXtProt for C11orf42: NX_Q8N5U0

Explore proteomics data for C11orf42 at MOPED


See C11orf42 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_775796.2  
ENSEMBL proteins: 
 ENSP00000321021  

C11orf42 Human Recombinant Protein Products:

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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: Q8N5U0


(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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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C11orf42
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hsa-miR-4260 hsa-miR-646
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In Situ Assay
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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
cytosol1
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 C11orf42
Interactions:

    Search GeneGlobe Interaction Network for C11orf42

(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 C11orf42 (CK042)



(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 C11orf42 gene: 
NM_173525.2  

Unigene Cluster for C11orf42:

Chromosome 11 open reading frame 42
Hs.278221  [show with all ESTs]
Unigene Representative Sequence: BC031612
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000316375(uc001mcj.3)
miRNA
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Inhib. RNA
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Additional mRNA sequence: BC031612.1 

2 DOTS entries:

DT.95360285  DT.100741130 

6 AceView cDNA sequences:

NM_173525 BC031612 BI829639 BM559760 AA909911 AA781757 

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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C11orf42 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCCCTGCCCC
C11orf42 Expression
About this image

C11orf42 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C11orf42 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.278221
    Custom PCR Arrays for C11orf42
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C11orf42

(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 C11orf42 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Gm59011 , 5 predicted gene 59011, 5 87.99(n)1
86.49(a)1
  7 (55.84 cM)5
1005038791  NM_001195727.11  NP_001182656.11 
 1053750985 


ENSEMBL Gene Tree for C11orf42 (if available)
TreeFam Gene Tree for C11orf42 (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 C11orf42 (see all 168)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs47583981,2
C,F,H--6224816(+) GATTCG/AGCCCA 1 -- us2k17Minor allele frequency- A:0.04NS EA WA NA 774
rs1932451781,2
--6224865(+) TAAACC/TACTTG 1 -- us2k10--------
rs1149479021,2
C,F--6224941(+) TAAAGG/TTTCAG 1 -- us2k11Minor allele frequency- T:0.06WA 118
rs1491779191,2
--6225064(+) GTAGTA/GACTAC 1 -- us2k10--------
rs1853115211,2
C--6225161(+) GGCATA/TATTCC 1 -- us2k10--------
rs782782661,2
C,F--6225364(+) GCCCCC/TACTCA 1 -- us2k11Minor allele frequency- T:0.02NA 120
rs1445749981,2
C--6225444(+) CTAGGA/GGAGGA 1 -- us2k10--------
rs588201971,2
C,F--6225489(+) AAGGAG/AACTCT 1 -- us2k11Minor allele frequency- A:0.06WA 118
rs1874470991,2
--6225517(+) AAGGAA/CTCCTT 1 -- us2k10--------
rs1918546121,2
--6225646(+) CTAATA/GTTCCA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for C11orf42 (6226796 - 6232365 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for C11orf42: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C11orf42
DNA2.0 Custom Variant and Variant Library Synthesis for C11orf42

(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 C11orf42 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C11orf42)
    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. (Genome Res. 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)

(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: 160298 HGNC: 28541 AceView: MGC34805 Ensembl:ENSG00000180878 euGenes: HUgn160298
ECgene: C11orf42 H-InvDB: C11orf42

(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 C11orf42 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 C11orf42 gene:
Search GeneIP for patents involving C11orf42

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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