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C5orf46 Gene

protein-coding   GIFtS: 38
GCID: GC05M147253

Chromosome 5 Open Reading Frame 46

  Search for C5orf46
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): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 5 Open Reading Frame 461 2
Skin And Saliva Secreted Protein 11 2
SSSP12
Uncharacterized Protein C5orf462

External Ids:    HGNC: 337681   Entrez Gene: 3893362   Ensembl: ENSG000001787767   UniProtKB: Q6UWT43   
ORGUL members:         

Export aliases for C5orf46 gene to outside databases

Previous GC identifer: GC05M142419


(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 C5orf46 Gene:
C5orf46 (chromosome 5 open reading frame 46) 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_000005.10  NT_029289.12  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C5orf46 gene promoter:
         TBP   GATA-1   PPAR-alpha   POU2F1   POU2F1b   POU2F1a   Zic1   POU2F1c   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C5orf46

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C5orf46


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

Entrez Gene cytogenetic band: 5q32   Ensembl cytogenetic band:  5q32   HGNC cytogenetic band: 5q33.1

C5orf46 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C5orf46 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M147253:  view genomic region     (about GC identifiers)

Start:
147,260,289 bp from pter      End:
147,286,101 bp from pter
Size:
25,813 bases      Orientation:
minus 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: CE046_HUMAN, Q6UWT4 (See protein sequence)
Recommended Name: Uncharacterized protein C5orf46 precursor  
Size: 87 amino acids; 9693 Da
Secondary accessions: A8K038 Q8WU04
Alternative splicing: 2 isoforms:  Q6UWT4-1   Q6UWT4-2   

Explore the universe of human proteins at neXtProt for C5orf46: NX_Q6UWT4

Explore proteomics data for C5orf46 at MOPED


See C5orf46 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_996849.2  
ENSEMBL proteins: 
 ENSP00000315370   ENSP00000425984  

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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:
 IPR027950 DUF4576

Graphical View of Domain Structure for InterPro Entry Q6UWT4

ProtoNet protein and cluster: Q6UWT4


C5orf46 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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
C5orf46 for ontologies           About GeneDecksing


Phenotypes:
     1 MGI phenotypic allele for Gm94 (no phenotypes)

C5orf46 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-out Gm94tm1Lex for C5orf46

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C5orf46
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hsa-miR-3650 hsa-miR-4254 hsa-miR-875-3p hsa-miR-146a hsa-miR-3148 hsa-miR-146b-5p
SwitchGear 3'UTR luciferase reporter plasmidC5orf46 3' UTR sequence
Inhib. RNA
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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 UniProtKB/Swiss-Prot
CE046_HUMAN, Q6UWT4: Secreted (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular3

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--
GO:0005576extracellular region ----
GO:0070062extracellular vesicular exosome IDA19199708

C5orf46 for ontologies           About GeneDecksing


(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 C5orf46
Interactions:

    Search GeneGlobe Interaction Network for C5orf46

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

C5orf46 for ontologies           About GeneDecksing



(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 C5orf46 (CE046)



(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 C5orf46 gene: 
NM_206966.2  

Unigene Cluster for C5orf46:

Chromosome 5 open reading frame 46
Hs.660038  [show with all ESTs]
Unigene Representative Sequence: CD556191
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000510432 ENST00000318315(uc010jgp.3 uc003lou.3) ENST00000515291(uc003lov.4)

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hsa-miR-3650 hsa-miR-4254 hsa-miR-875-3p hsa-miR-146a hsa-miR-3148 hsa-miR-146b-5p
SwitchGear 3'UTR luciferase reporter plasmidC5orf46 3' UTR sequence
Inhib. RNA
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Primer
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  QuantiFast Probe-based Assays in human, mouse, rat C5orf46

Additional mRNA sequence: 

AK289403.1 AY358656.1 BC021680.1 

2 DOTS entries:

DT.75154212  DT.451991 

Selected AceView cDNA sequences (see all 91):

AA436233 BU581519 BM843311 AI362470 NM_003122 BG141336 CK905024 BU581710 
BC025790 AI362622 AA845156 BM843236 CB159576 BM855672 AI459618 AY358656 
BX115935 BX497081 AI591033 AW005713 AA740207 AA436232 BM830452 BM855648 

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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C5orf46 expression in normal human tissues (normalized intensities)      C5orf46 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGAAACAAAA
C5orf46 Expression
About this image


C5orf46 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Paraxial Mesoderm (Gastrulation Derivatives)
         PureStem E15, Meso-prx/latp Progenitor
 
 Neural Crest (Gastrulation Derivatives)
         PureStem 4D20.8, NCr-fac Progenitor
 
 Lung (Respiratory System)
         Basal Cells Trachea
 
 Lateral Plate Mesoderm (Gastrulation Derivatives)
         PureStem E15, Meso-prx/latp Progenitor
C5orf46 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C5orf46 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.660038
    Custom PCR Arrays for C5orf46
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C5orf46

(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 mouse.

Orthologs for C5orf46 gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Gm941 , 5 predicted gene 941, 5 76.47(n)1
64.71(a)1
  18 (23.49 cM)5
2254431  NM_001033280.21  NP_001028452.11 
 437771965 


ENSEMBL Gene Tree for C5orf46 (if available)
TreeFam Gene Tree for C5orf46 (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 C5orf46 (see all 360)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs797793811,2
C,F--147271872(+) CCTGAC/TACTGC 1 -- int11Minor allele frequency- T:0.02NA 120
rs1145778811,2
F--147271882(+) CTATTT/CTATGA 1 -- int11Minor allele frequency- C:0.03WA 118
rs1417288611,2
--147271928(+) ATTAAC/TTTTAA 1 -- int10--------
rs1462215891,2
--147271942(+) GGTCAC/GTTTTT 1 -- int10--------
rs1479996891,2
--147271978(+) CTCAGA/TTAGTT 1 -- int10--------
rs1416361861,2
--147272031(+) GAAATG/TGCATA 1 -- int10--------
rs1884091391,2
--147272069(+) GAGGTC/GAGGTT 1 -- int10--------
rs594041831,2
C--147272112(+) GAATTC/AGAACT 1 -- int12Minor allele frequency- A:0.11CSA WA 120
rs1922274841,2
--147272225(+) ATCATC/TAAAAC 1 -- int10--------
rs1504982291,2
--147272238(+) TAAACA/GTGGCC 1 -- int10--------

HapMap Linkage Disequilibrium report for C5orf46 (147260289 - 147286101 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for C5orf46:    About this table    
Variant IDTypeSubtypePubMed ID
nsv329560CNV Loss16902084
nsv520730CNV Gain19592680

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing C5orf46
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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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(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 C5orf46 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C5orf46)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
  2. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PubMed id 19199708)1 Gonzalez-Begne M....Yates J.R. (J. Proteome Res. 2009)
  3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
  4. 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)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. 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)

(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: 389336 HGNC: 33768 AceView: SPINK1andMGC23985 Ensembl:ENSG00000178776 euGenes: HUgn389336
ECgene: C5orf46 H-InvDB: C5orf46

(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 C5orf46 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 C5orf46 gene:
Search GeneIP for patents involving C5orf46

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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 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C5orf46
 SwitchGear 3'UTR luciferase reporter plasmids for C5orf46
 Browse SwitchGear Promoter luciferase reporter plasmids for C5orf46
 Search ThermoFisher Antibodies for C5orf46
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C5orf46
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C5orf46
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for C5orf46
 Search LSBio for Antibodies for C5orf46
Customized transgenic rodents for:
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 Tissue-specific gene expresssion
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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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