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C5orf56 Gene

protein-coding   GIFtS: 33
GCID: GC05P131775

Chromosome 5 Open Reading Frame 56

  See related diseases
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 5 Open Reading Frame 561 2

External Ids:    HGNC: 338381   Entrez Gene: 4411082   Ensembl: ENSG000001975367   UniProtKB: Q8N8D93   

Export aliases for C5orf56 gene to outside databases

Previous GC identifer: GC05P126938


(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 C5orf56 Gene:
C5orf56 (chromosome 5 open reading frame 56) is a protein-coding gene. Diseases associated with C5orf56 include crohn's disease, and psoriasis.


(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_000005.10  NC_018916.2  NT_034772.7  
Regulatory elements:
   Regulatory transcription factor binding sites in the C5orf56 gene promoter:
         c-Fos   C/EBPbeta   AP-1   E47   GATA-2   c-Ets-1   MEF-2A   aMEF-2   c-Jun   Pax-4a   
         Other transcription factors

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   Search Chromatin IP Primers for C5orf56

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C5orf56


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

Entrez Gene cytogenetic band: 5q31.1   Ensembl cytogenetic band:  5q31.1   HGNC cytogenetic band: 5q31.1

C5orf56 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C5orf56 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P131775:  view genomic region     (about GC identifiers)

Start:
131,746,328 bp from pter      End:
131,822,549 bp from pter
Size:
76,222 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: CE056_HUMAN, Q8N8D9 (See protein sequence)
Recommended Name: Uncharacterized protein C5orf56  
Size: 126 amino acids; 14652 Da
Secondary accessions: A1L3V9 A6NKA0
Alternative splicing: 2 isoforms:  Q8N8D9-1   Q8N8D9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for C5orf56: NX_Q8N8D9


ENSEMBL proteins: 
 ENSP00000368236   ENSP00000338228   ENSP00000368230   ENSP00000385513  

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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: Q8N8D9


(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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(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

(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 C5orf56
Interactions:

    Search GeneGlobe Interaction Network for C5orf56

(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 C5orf56 (CE056)



(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 C5orf56 gene (4 alternative transcripts): 
NM_001013717.2  NM_001207001.1  NM_001207002.1  NM_001207003.1  

Unigene Cluster for C5orf56:

Chromosome 5 open reading frame 56
Hs.658288  [show with all ESTs]
Unigene Representative Sequence: AL713721
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000378953(uc003kwz.2 uc010jds.2) ENST00000461203 ENST00000337752(uc003kwy.2 uc021ydl.1)
ENST00000378947 ENST00000407797 ENST00000464024
miRNA
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Inhib. RNA
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Additional mRNA sequence: 

AK096941.1 AK128882.1 AK309191.1 AL713721.1 BC130299.1 BC130656.1 NR_045116.1 

15 DOTS entries:

DT.211638  DT.120846158  DT.97832204  DT.99930770  DT.120846277  DT.211640  DT.95136413  DT.86852360 
DT.91666246  DT.100652196  DT.206801  DT.211639  DT.40245309  DT.92436975  DT.95220220 

Selected AceView cDNA sequences (see all 49):

BX456850 AW014287 BM985103 AA358892 CN480423 AA295106 CR615570 AW002034 
AK128882 AA324298 BE221920 BM998490 AW967562 AK096941 AI377899 AI018587 
AK025221 AA357749 AL713721 AW661720 CK429631 AI033261 BQ187613 BM007885 

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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C5orf56 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTCCTTTTAC
C5orf56 Expression
About this image

C5orf56 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.658288
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In Situ
Assay Products:
 

 
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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 C5orf56 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia C5orf566
chromosome 5 open reading frame 56
99(a)
1 ↔ 1
5(133077417-133142592)


ENSEMBL Gene Tree for C5orf56 (if available)
TreeFam Gene Tree for C5orf56 (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 C5orf56 (see all 1268)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs131900011,2
C,F,A,H--131744482(+) GTTCCC/TGACAG 1 -- us2k112Minor allele frequency- T:0.14NS EA NA WA CSA 788
rs1432006551,2
--131744550(+) CAAACA/CCTGCC 1 -- us2k10--------
rs562900201,2
C,F--131744567(+) ATACAT/CAGTAA 1 -- us2k13Minor allele frequency- C:0.03WA CSA 122
rs10169881,2
C,F,H--131744574(+) gtaacT/Catgtg 1 -- us2k117Minor allele frequency- C:0.21NS EA NA WA 2338
rs1879300021,2
--131744594(+) TTTCCC/TTCATC 1 -- us2k10--------
rs1912404021,2
--131744638(+) TAATAC/TACCAC 1 -- us2k10--------
rs1482701801,2
--131744651(+) GATAGC/TAGGGA 1 -- us2k10--------
rs131528791,2
C,F,H--131744728(+) AATCAG/ATCAGT 1 -- us2k111Minor allele frequency- A:0.06NS EA NA WA CSA 786
rs131528851,2
C--131744751(+) TTTATG/CCAACA 1 -- us2k13Minor allele frequency- C:0.15NA EA 242
rs801203661,2
C,F--131744765(+) CTAATC/TGACTC 1 -- us2k11Minor allele frequency- T:0.10WA 118

HapMap Linkage Disequilibrium report for C5orf56 (131746328 - 131822549 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for C5orf56:    About this table    
Variant IDTypeSubtypePubMed ID
esv2730790CNV Deletion23290073
nsv5002CNV Insertion18451855
nsv882898CNV Loss21882294
nsv462452CNV Gain19166990
nsv471048CNV 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.)
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4 diseases for C5orf56:    About MalaCards
crohn's disease    psoriasis    asthma    inflammatory bowel disease


C5orf56 for disorders           About GeneDecksing

Genetic Association Database (GAD): C5orf56
Human Genome Epidemiology (HuGE) Navigator: C5orf56 (4 documents)

Export disorders for C5orf56 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 C5orf56 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with C5orf56)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. (PubMed id 20570966)1, 4 McGovern D.P....Rotter J.I. (Hum. Mol. Genet. 2010)
  2. Analysis of 39 Crohn's disease risk loci in Swedish inflammatory bowel disease patients. (PubMed id 19760754)1, 4 TAPrkvist L....Pettersson S. (Inflamm. Bowel Dis. 2010)
  3. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. (PubMed id 21102463)1, 4 Franke A....Parkes M. (Nat. Genet. 2010)
  4. Molecular reclassification of Crohn's disease by cluster analysis of genetic variants. (PubMed id 20886065)1, 4 Cleynen I....Vermeire S. (PLoS ONE 2010)
  5. Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study. (PubMed id 20031577)1, 4 Danik J.S....Ridker P.M. (Circ Cardiovasc Genet 2009)
  6. Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. (PubMed id 20031576)1, 4 Dehghan A....Folsom A.R. (Circ Cardiovasc Genet 2009)
  7. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. (PubMed id 18587394)1, 4 Barrett J.C....Daly M.J. (Nat. Genet. 2008)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  9. Multiethnic meta-analysis of genome-wide association studies in &gt;100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease. (PubMed id 23969696)1 Sabater-Lleal M....O'Donnell C.J. (Circulation 2013)
  10. Genome-wide association study to identify genetic determinants of severe asthma. (PubMed id 22561531)1 Wan Y.I....Hall I.P. (Thorax 2012)

(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: 441108 HGNC: 33838 AceView: LOC441108 Ensembl:ENSG00000197536 euGenes: HUgn441108
ECgene: C5orf56 H-InvDB: C5orf56

(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 C5orf56 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 C5orf56 gene:
Search GeneIP for patents involving C5orf56

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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