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C6orf223 Gene

protein-coding   GIFtS: 40
GCID: GC06P043968

Chromosome 6 Open Reading Frame 223

  See related disease
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 6 Open Reading Frame 2231 2
Uncharacterized Protein C6orf2232

External Ids:    HGNC: 286921   Entrez Gene: 2214162   Ensembl: ENSG000001815777   UniProtKB: Q8N3193   
ORGUL members:         

Export aliases for C6orf223 gene to outside databases

Previous GC identifers: GC06P044077 GC06P043690


(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 C6orf223 Gene:
C6orf223 (chromosome 6 open reading frame 223) is a protein-coding gene. Diseases associated with C6orf223 include endotheliitis.


(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_000006.12  NT_007592.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C6orf223 gene promoter:
         STAT5B   STAT1   RFX1   Pax-5   STAT4   STAT1beta   STAT5A   STAT1alpha   STAT2   STAT3   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C6orf223

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C6orf223


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

Entrez Gene cytogenetic band: 6p21.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21.1

C6orf223 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf223 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P043968:  view genomic region     (about GC identifiers)

Start:
43,968,317 bp from pter      End:
43,973,695 bp from pter
Size:
5,379 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: CF223_HUMAN, Q8N319 (See protein sequence)
Recommended Name: Uncharacterized protein C6orf223  
Size: 242 amino acids; 26113 Da
Sequence caution: Sequence=AAH32706.1; Type=Miscellaneous discrepancy; Note=Intron retention;
Secondary accessions: E9PB59 Q8N575
Alternative splicing: 2 isoforms:  Q8N319-3   Q8N319-4   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for C6orf223: NX_Q8N319

Explore proteomics data for C6orf223 at MOPED


See C6orf223 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001165463.1  NP_694978.2  

ENSEMBL proteins: 
 ENSP00000477091   ENSP00000426159   ENSP00000423262  

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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: Q8N319


(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 C6orf223:
 Increased G1 DNA content 

Animal Models:
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miRNA
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miRTarBase miRNAs that target C6orf223:
hsa-mir-335-5p (MIRT017127)

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Selected qRT-PCR Assays for microRNAs that regulate C6orf223 (see all 14):
hsa-miR-1298 hsa-miR-1226 hsa-miR-922 hsa-miR-622 hsa-miR-128 hsa-miR-3681* hsa-miR-3175 hsa-miR-339-5p
SwitchGear 3'UTR luciferase reporter plasmidC6orf223 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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(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 C6orf223
Interactions:

    Search GeneGlobe Interaction Network for C6orf223

(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 C6orf223 (CF223)



(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 C6orf223 gene (2 alternative transcripts): 
NM_001171992.1  NM_153246.4  

Unigene Cluster for C6orf223:

Chromosome 6 open reading frame 223
Hs.531926  [show with all ESTs]
Unigene Representative Sequence: NM_001171992
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000442114(uc003owo.3 uc003own.3) ENST00000336600 ENST00000439969
ENST00000448947
miRNA
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SwitchGear 3'UTR luciferase reporter plasmidC6orf223 3' UTR sequence
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Additional mRNA sequence: BC029071.2 

5 DOTS entries:

DT.97783955  DT.40196064  DT.75123914  DT.92416763  DT.95147876 

Selected AceView cDNA sequences (see all 52):

BM714177 CR590223 AW136542 AW849503 BC029071 AI655624 BX090075 CR590009 
BF591275 AW651749 BX099829 AW297349 AI917732 BX342526 AI739595 BX391989 
AA552719 BF591021 AI962299 BC032706 AA857189 AI391645 AW024064 BX328225 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for C6orf223    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4
SP1:                    -     -                     
SP2:                    -                           
SP3:                    -     -     -               
SP4:                                                


ECgene alternative splicing isoforms for C6orf223

(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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C6orf223 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCGCCCAGGC
C6orf223 Expression
About this image

C6orf223 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C6orf223 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.531926
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C6orf223

(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 mammals.

Orthologs for C6orf223 gene from Selected species (see all 2)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
cow
(Bos taurus)
Mammalia C23H6orf2231 chromosome 23 open reading frame, human C6orf223 72.27(n)
61.06(a)
  101907252  XM_005228620.1  XP_005228677.1 


ENSEMBL Gene Tree for C6orf223 (if available)
TreeFam Gene Tree for C6orf223 (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 C6orf223 (see all 241)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1159013961,2
C,F--43966466(+) CATGGT/AGAACC 2 -- us2k13Minor allele frequency- A:0.18WA NA EA 358
rs1152651491,2
F--43966496(+) GTAAAC/AGCACC 2 -- us2k12Minor allele frequency- A:0.10NA EA 240
rs1169388881,2
F--43966609(+) CAACCC/TGCTGG 2 -- us2k11Minor allele frequency- T:0.17EA 120
rs1180095481,2
C,F--43966616(+) CTGGGA/GTCCCT 2 -- us2k11Minor allele frequency- G:0.11EA 120
rs1480181231,2
C--43966628(+) TCCACA/GCTGTG 2 -- us2k10--------
rs1808471601,2
--43966692(+) GGTCCA/GCGCTG 2 -- us2k10--------
rs1153085801,2
C,F--43966694(+) TCCACG/ACTGCC 2 -- us2k11Minor allele frequency- A:0.07NA 120
rs1416847701,2
C--43966721(+) CTCACC/TGCGAA 2 -- us2k10--------
rs1854479201,2
--43966722(+) TCACCA/GCGAAG 2 -- us2k10--------
rs1885907691,2
--43966780(+) AGGAAC/GAGACA 2 -- us2k10--------

HapMap Linkage Disequilibrium report for C6orf223 (43968317 - 43973695 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for C6orf223:    About this table    
Variant IDTypeSubtypePubMed ID
esv2732001CNV Deletion23290073
esv2732002CNV Deletion23290073
nsv509131CNV Insertion20534489
nsv462934CNV Loss19166990

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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for C6orf223:    
About MalaCards
endotheliitis


C6orf223 for disorders           About GeneDecksing


Export disorders for C6orf223 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 C6orf223 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C6orf223)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels. (PubMed id 21757650)1 Debette S....Seshadri S. (Circ. Res. 2011)
  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. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (Nature 2003)

(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: 221416 HGNC: 28692 AceView: MGC45491 Ensembl:ENSG00000181577 euGenes: HUgn221416
ECgene: C6orf223 H-InvDB: C6orf223

(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 C6orf223 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 C6orf223 gene:
Search GeneIP for patents involving C6orf223

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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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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