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C21orf54 Gene

protein-coding   GIFtS: 26
GCID: GC21M034537

Chromosome 21 Open Reading Frame 54

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, 15RNAdb, and/or 11Nature:405,311-319 and CroW21)
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Aliases
Chromosome 21 Open Reading Frame 541 2
Spliced EST AA93497311

External Ids:    HGNC: 12961   Entrez Gene: 7284092   Ensembl: ENSG000002290867   UniProtKB: A6NM663   

Export aliases for C21orf54 gene to outside databases

Previous GC identifers: GC21U990057 GC21M033458 GC21M033459 GC21M019949


(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 C21orf54 Gene:
C21orf54 (chromosome 21 open reading frame 54) 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, Whole Chromsome Sequence According to Nature (Cited Here with Permission):405,311-319 and CroW21)
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RefSeq DNA sequence at NCBI GenBank:
NC_000021.8  NC_018932.2  NT_011512.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the C21orf54 gene promoter:
         AML1a   CUTL1   NF-kappaB   AREB6   MEF-2A   PPAR-gamma1   PPAR-gamma2   aMEF-2   NF-kappaB1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

   Search Chromatin IP Primers for C21orf54

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C21orf54


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

Entrez Gene cytogenetic band: 21q22.11   Ensembl cytogenetic band:  21q22.11   HGNC cytogenetic band: 21q22.11
Nature(405: 311-319) cytogenetic band:   21q22.11
C21orf54 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C21orf54 gene location
GeneLoc information about chromosome 21         GeneLoc Exon Structure

(about GC identifiers)
GC21M034537:   GeneLoc Nature:405,311-319
Start:
34,537,776 bp from pter       20,114,481 bp from centromere
End:
34,542,541 bp from pter 20,118,775 bp from centromere
Size:
4,766 bases 4,295 bases
Orientation:
minus strand minus strand

genomic clones: pQ14E2


(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CU054_HUMAN, A6NM66 (See protein sequence)
Recommended Name: Uncharacterized protein C21orf54  
Size: 108 amino acids; 11668 Da

Explore the universe of human proteins at neXtProt for C21orf54: NX_A6NM66

Explore proteomics data for C21orf54 at MOPED


See C21orf54 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000407868  

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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: A6NM66


(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, 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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Phenotypes:
     1 GenomeRNAi human phenotype for C21orf54:
 Decreased POU5F1-GFP protein e 

Animal Models:
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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
extracellular2
nucleus2
cytoskeleton1

(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 C21orf54
Interactions:

    Search GeneGlobe Interaction Network for C21orf54

(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
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Browse Tocris compounds for C21orf54 (CU054)



(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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Unigene Cluster for C21orf54:

Chromosome 21 open reading frame 54
Hs.125234  [show with all ESTs]
Unigene Representative Sequence: NR_024102
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000451980
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Additional mRNA sequence: 

BC105115.1 BC105117.1 NR_024102.1 

1 DOTS entry:

DT.107378 

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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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

C21orf54 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C21orf54 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.125234
    Custom PCR Arrays for C21orf54
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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 human and chimp.

Orthologs for C21orf54 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C21orf546
chromosome 21 open reading frame 54
97(a)
1 ↔ 1
21(19267271-19271869)


ENSEMBL Gene Tree for C21orf54 (if available)
TreeFam Gene Tree for C21orf54 (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 C21orf54 (see all 164)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 21 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1488146781,2
--34537345(+) TCACTG/TCTCTG 1 -- int10--------
rs1167964671,2
F--34537398(+) ATCCAA/GTGGCT 1 -- int11Minor allele frequency- G:0.03WA 118
rs771466221,2
C,F--34537404(+) TGGCTC/GTCCCA 1 -- int13Minor allele frequency- G:0.10WA NA EA 358
rs1427140711,2
--34537414(+) ATGACA/GTCTGG 1 -- int10--------
rs124830001,2
C,F,A,H--34537449(+) AAATGG/TGGTCA 1 -- int13Minor allele frequency- T:0.01EA NS NA 180
rs1417599321,2
C--34537453(+) GGGTC-/AACCAA 1 -- int10--------
rs1465015461,2
--34537511(+) ACAGCA/GTCCGG 1 -- int10--------
rs1925018441,2
--34537555(+) TGTCCA/GTCCTT 1 -- int10--------
rs1850603031,2
--34537605(+) TGGTCC/TGGCCA 1 -- int10--------
rs2001783561,2
--34537606(+) GGTCC-/GGCCA 
CCACGTGT
GGCTC
1 -- int10--------

HapMap Linkage Disequilibrium report for C21orf54 (34537776 - 34542541 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for C21orf54:    About this table    
Variant IDTypeSubtypePubMed ID
nsv913698CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing C21orf54
DNA2.0 Custom Variant and Variant Library Synthesis for C21orf54

(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 C21orf54           About GenesLikeMe

Genetic Association Database (GAD): C21orf54

Export disorders for C21orf54 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 C21orf54 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C21orf54)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network. (PubMed id 22228203)1, 4 Aslibekyan S....Arnett D.K. (Pharmacogenet. Genomics 2012)
  2. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M.... Yaspo M.-L. (Nature 2000)
  3. 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)
  4. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

(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: 728409 HGNC: 1296 Ensembl:ENSG00000229086 euGenes: HUgn728409 ECgene: C21orf54
H-InvDB: C21orf54

(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 C21orf54 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 C21orf54 gene:
Search GeneIP for patents involving C21orf54

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, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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