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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C6orf52 Gene

protein-coding   GIFtS: 36
GCID: GC06M010671          (predicted)

Chromosome 6 Open Reading Frame 52

  Search for C6orf52
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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 521 2
Putative Uncharacterized Protein C6orf522

External Ids:    HGNC: 208811   Entrez Gene: 3477442   Ensembl: ENSG000001374347   UniProtKB: Q5T4I83   
ORGUL members:         
NONCODE14:n407267 n407268      

Export aliases for C6orf52 gene to outside databases

Previous GC identifers: GC06M010734 GC06M010779 GC06M010547


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for C6orf52 Gene: 
C6orf52 (chromosome 6 open reading frame 52) is a protein-coding gene, and is affiliated with the lncRNA class. An important paralog of this gene is TRNAU1AP.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C6orf52 gene promoter:
         PPAR-gamma1   STAT1   PPAR-gamma2   CUTL1   GATA-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C6orf52

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C6orf52


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

Entrez Gene cytogenetic band: 6p24.1   Ensembl cytogenetic band:  6p24.2   HGNC cytogenetic band: 6p24.2

C6orf52 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C6orf52 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M010671:  view genomic region     (about GC identifiers)

Start:
10,671,651 bp from pter      End:
10,695,030 bp from pter
Size:
23,380 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for C6orf52

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CF052_HUMAN, Q5T4I8 (See protein sequence)
Recommended Name: Putative uncharacterized protein C6orf52  
Size: 152 amino acids; 17383 Da
Sequence caution: Sequence=AAH16820.1; Type=Erroneous initiation; Sequence=CAI14001.1; Type=Erroneous initiation;
Secondary accessions: Q5T4I7 Q96AS6
Alternative splicing: 2 isoforms:  Q5T4I8-1   Q5T4I8-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C6orf52: NX_Q5T4I8

Explore proteomics data for C6orf52 at MOPED 

C6orf52 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

C6orf52 Protein Expression

REFSEQ proteins: NP_001138492.1  
ENSEMBL proteins: 
 ENSP00000421264   ENSP00000410749   ENSP00000368905   ENSP00000421837   ENSP00000259983  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q5T4I8


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C6orf52

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for C6orf52 (CF052)

Search CenterWatch for drugs/clinical trials and news about C6orf52 / CF052

(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,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for C6orf52 gene: 
NM_001145020.1  

Unigene Cluster for C6orf52:

Chromosome 6 open reading frame 52
Hs.61389  [show with all ESTs]
Unigene Representative Sequence: NR_026736
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000460742 ENST00000426700 ENST00000467832 ENST00000379586 ENST00000503680(uc011dil.2)
ENST00000259983(uc011dij.2 uc011dik.2 uc003mzf.4)
miRNA
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Inhib. RNA
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                     Customized lentivirus expression plasmids for stable overexpression of C6orf52 
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat C6orf52

Additional mRNA sequence: 

BC016820.1 NR_026736.1 NR_026737.1 

7 DOTS entries:

DT.95158307  DT.75102633  DT.121391275  DT.75102632  DT.92419064  DT.92419065  DT.100755196 

24/29 AceView cDNA sequences (see all 29):

BX280692 AW072546 AI492917 AI621292 AW082283 AI809192 AI743034 BE670432 
AI201400 AI376550 AW182440 AW293245 AW025669 BC016820 AI299086 BG186993 
AW183488 T50351 AW183566 AW001000 AW771859 BG216657 AA026303 AA026648 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for C6orf52    About this scheme

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6
SP1:        -                                 
SP2:              -           -               


ECgene alternative splicing isoforms for C6orf52

(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

C6orf52 expression in normal human tissues (normalized intensities)      C6orf52 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AATTGCCACT
C6orf52 Expression
About this image


C6orf52 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/4 selected tissues (see all 4) fully expand
 
 Epithelium (Respiratory System)    fully expand to see all 2 entries
         bronchial epithelial cells   
 
 Pancreas (Endocrine System)
         Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
 
 Ovary (Reproductive System)
         Secondary Oocyte Antral Follicle
 
 Gonad
         Secondary Oocyte Antral Follicle

See C6orf52 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for C6orf52

SOURCE GeneReport for Unigene cluster: Hs.61389
    SABiosciences Custom PCR Arrays for C6orf52
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C6orf52

(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)
About This Section

This gene was present in the common ancestor of animals and fungi.

Orthologs for C6orf52 gene from 7/11 species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
rat
(Rattus norvegicus)
Mammalia RGD15629631 similar to chromosome 6 open reading frame 52 69.27(n)
52.34(a)
  498729  NM_001145021.1  NP_001138493.1 
chicken
(Gallus gallus)
Aves TRNAU1AP6
tRNA selenocysteine 1-associated protein 1
20(a)
1 ↔ 1
2(62174550-62183690)
lizard
(Anolis carolinensis)
Reptilia C6orf526
chromosome 6 open reading frame 52
17(a)
1 ↔ 1
4(59170535-59182112)
zebrafish
(Danio rerio)
Actinopterygii C2H6orf526
chromosome 6 open reading frame 52
10(a)
1 ↔ 1
2(23546710-23553511)
fruit fly
(Drosophila melanogaster)
Insecta CG154406
--
2(a)
1 → many
2L(4453167-4454457)
worm
(Caenorhabditis elegans)
Secernentea T07F10.36
Protein T07F10.3
1(a)
1 → many
V(12868026-12870035)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NGR16
NAM86
RNA binding protein that negatively regulates grow...
RNA binding protein, component of the U1 snRNP pro...
3(a)
3(a)
many ↔ many
many ↔ many
II(647886-649904)
VIII(278153-279724)


ENSEMBL Gene Tree for C6orf52 (if available)
TreeFam Gene Tree for C6orf52 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for C6orf52 gene
TRNAU1AP2  

C6orf52 for paralogs           About GeneDecksing



(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/389 SNPs in C6orf52 are shown (see all 389)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs737213531,2
C,F--10671232(+) CTTATG/CGGGCC 3 -- int11Minor allele frequency- C:0.50WA 2
rs1135849601,2
F--10671329(+) TTTCTC/TTCCAT 3 -- int11Minor allele frequency- T:0.50CSA 2
rs1129871391,2
F--10671333(+) TCTCCG/ATGAGA 3 -- int11Minor allele frequency- A:0.50CSA 2
rs1860287081,2
--10671337(+) CATGAC/GAGTTT 3 -- int10--------
rs728215651,2
C--10671658(+) AGTATA/GATAAT 3 -- ut31 nc-transcript-variant0--------
rs412717851,2
C,F--10671667(+) ATTGCG/AGAGTT 3 -- ut31 nc-transcript-variant2Minor allele frequency- A:0.03NA EU 697
rs1410548141,2
--10671670(+) GCGGAG/TTTTAA 3 -- ut31 nc-transcript-variant0--------
rs37372781,2
C,F,H--10671764(+) GAGTCG/ATAGAG 4 /Y syn1 ese320Minor allele frequency- A:0.09EA NS NA WA EU 4181
rs2022089241,2
F--10671862(+) AAAAAA/GTAGAG 3 -- int11Minor allele frequency- G:0.01EU 569
rs94671651,2
C,F--10671966(+) TAAATT/GGCATA 3 -- int11Minor allele frequency- G:0.06WA 118

HapMap Linkage Disequilibrium report for C6orf52 (10671651 - 10695030 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for C6orf52:    About this table     
Variant IDTypeSubtypePubMed ID
nsv520853CNV Loss19592680
nsv462631CNV Gain19166990
nsv470800CNV Gain18288195

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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.)
About This Section
  --

(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)
About This Section

PubMed articles for C6orf52 gene integrated from 9 sources:
(articles sorted by number of sources associating them with C6orf52)
    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. (2002)
  2. 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. (2004)
  3. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (2003)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 347744 HGNC: 20881 AceView: C6orf52 Ensembl:ENSG00000137434 euGenes: HUgn347744
ECgene: C6orf52 H-InvDB: C6orf52

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for C6orf52 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for C6orf52 gene:
Search GeneIP for patents involving C6orf52

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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