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C10orf53 Gene

protein-coding   GIFtS: 36
GCID: GC10P050887

Chromosome 10 Open Reading Frame 53

  Search for C10orf53
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 10 Open Reading Frame 531 2
UPF0728 Protein C10orf532

External Ids:    HGNC: 274211   Entrez Gene: 2829662   Ensembl: ENSG000001786457   UniProtKB: Q8N6V43   

Export aliases for C10orf53 gene to outside databases

Previous GC identifers: GC10P050233 GC10P050557 GC10P045152


(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 C10orf53 Gene:
C10orf53 (chromosome 10 open reading frame 53) 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_000010.11  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the C10orf53 gene promoter:
         Spz1   Sp1   Pax-6   POU3F2   Gfi-1   FOXL1   RORalpha1   MZF-1   Msx-1   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C10orf53

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C10orf53


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

Entrez Gene cytogenetic band: 10q11.23   Ensembl cytogenetic band:  10q11.23   HGNC cytogenetic band: 10q11.23

C10orf53 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C10orf53 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P050887:  view genomic region     (about GC identifiers)

Start:
50,887,684 bp from pter      End:
50,918,307 bp from pter
Size:
30,624 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CJ053_HUMAN, Q8N6V4 (See protein sequence)
Recommended Name: UPF0728 protein C10orf53  
Size: 93 amino acids; 10399 Da
Secondary accessions: A6NI81 A6NLE0 B9ZVK6
Alternative splicing: 4 isoforms:  Q8N6V4-1   Q8N6V4-2   Q8N6V4-3   Q8N6V4-4   (No experimental confirmation available. Ref.4 (BI825648) sequence is in conflict in position: 99:R->G)

Explore the universe of human proteins at neXtProt for C10orf53: NX_Q8N6V4

REFSEQ proteins (2 alternative transcripts): 
NP_001035892.1  NP_872360.2  

ENSEMBL proteins: 
 ENSP00000363227   ENSP00000363225   ENSP00000363226   ENSP00000437726  

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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:
 IPR027885 UPF0728

Graphical View of Domain Structure for InterPro Entry Q8N6V4

ProtoNet protein and cluster: Q8N6V4

UniProtKB/Swiss-Prot: CJ053_HUMAN, Q8N6V4
Similarity: Belongs to the UPF0728 family


C10orf53 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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Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidC10orf53 3' UTR sequence
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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
nucleus2
peroxisome2
extracellular1
mitochondrion1

(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 C10orf53
Interactions:

    Search GeneGlobe Interaction Network for C10orf53

(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 C10orf53 (CJ053)



(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,
Conferences by KenesGroup, 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 C10orf53 gene (2 alternative transcripts): 
NM_001042427.1  NM_182554.2  

Unigene Cluster for C10orf53:

Chromosome 10 open reading frame 53
Hs.131287  [show with all ESTs]
Unigene Representative Sequence: AK091773
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000374113(uc001jib.3 uc001jic.1) ENST00000374111 ENST00000374112
ENST00000535836(uc001jid.1)
miRNA
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hsa-miR-205 hsa-miR-33b hsa-miR-454* hsa-miR-3145-3p hsa-miR-33a hsa-miR-4287
SwitchGear 3'UTR luciferase reporter plasmidC10orf53 3' UTR sequence
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Additional mRNA sequence: AK091773.1 

3 DOTS entries:

DT.456121  DT.99931099  DT.95203350 

Selected AceView cDNA sequences (see all 32):

D82342 AF305909 BX102324 S56138 AI990484 NM_020549 BI825648 AK091773 
D82340 BV183664 NM_020984 D82339 BX280506 NM_020985 D82341 NM_020986 
AI917746 AF305908 AI216456 AX747176 AF305907 BI826396 AW665925 NM_182554 

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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C10orf53 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCTCAATCTC
C10orf53 Expression
About this image

C10orf53 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.131287
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In Situ
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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 C10orf53 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 1700024G13Rik1 , 5 RIKEN cDNA 1700024G13 gene1, 5 80.29(n)1
77.42(a)1
  14 (19.40 cM)5
670851  NM_001034037.11  NP_001029209.11 
 323765025 
tropical clawed frog
(Xenopus tropicalis)
Amphibia LOC1004853771 chromosome unknown open reading frame, human C10orf53 64.52(n)
64.52(a)
  100485377  XM_002933914.2  XP_002933960.2 
zebrafish
(Danio rerio)
Actinopterygii zgc:1531421 zgc:153142 60.51(n)
61.96(a)
  768197  NM_001077339.1  NP_001070807.1 


ENSEMBL Gene Tree for C10orf53 (if available)
TreeFam Gene Tree for C10orf53 (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 C10orf53 (see all 697)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 10 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1885672121,2
--50885735(+) AAATAA/CCTATC 2 -- us2k10--------
rs1439911871,2
--50885744(+) TCTTTA/CCTACA 2 -- us2k10--------
rs1388326221,2
C--50885827(+) CAAAC-/TGTAAAA 2 -- us2k10--------
rs761310351,2
F--50885885(+) GCTTTT/CCTTCT 2 -- us2k11Minor allele frequency- C:0.02EA 120
rs70718191,2
C,F,H--50885898(+) GTTAAG/AAGCCA 2 -- us2k17Minor allele frequency- A:0.05NS EA WA CSA 541
rs1807456301,2
--50885946(+) AATGAA/CTGCAT 2 -- us2k10--------
rs1145946021,2
F--50885992(+) GTATGG/AAAGAA 2 -- us2k11Minor allele frequency- A:0.01WA 118
rs1851515681,2
--50886020(+) CAGAGA/GAGACA 2 -- us2k10--------
rs761186661,2
--50886029(+) CACATA/GCAGAT 2 -- us2k10--------
rs1908416611,2
--50886188(+) AAGAGA/GGGTAA 2 -- us2k10--------

HapMap Linkage Disequilibrium report for C10orf53 (50887684 - 50918307 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for C10orf53:    About this table    
Variant IDTypeSubtypePubMed ID
nsv895365CNV Loss21882294
nsv895375CNV Gain21882294
nsv895378CNV Gain21882294
nsv7203OTHER Inversion18451855

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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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C10orf53 for disorders           About GeneDecksing

Human Genome Epidemiology (HuGE) Navigator: C10orf53 (1 document)

Export disorders for C10orf53 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 C10orf53 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C10orf53)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. 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)
  4. 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)
  5. 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)
  6. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (Nature 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: 282966 HGNC: 27421 AceView: CHAT Ensembl:ENSG00000178645 euGenes: HUgn282966
ECgene: C10orf53 H-InvDB: C10orf53

(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 C10orf53 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 C10orf53 gene:
Search GeneIP for patents involving C10orf53

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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