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FAM47E Gene

protein-coding   GIFtS: 34
GCID: GC04P077172

Family With Sequence Similarity 47, Member E

  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
Family With Sequence Similarity 47, Member E1 2
Similar To Genethonin 11
Protein FAM47E2

External Ids:    HGNC: 343431   Entrez Gene: 1001295832   Ensembl: ENSG000002724147   UniProtKB: Q6ZV653   
ORGUL members:         

Export aliases for FAM47E gene to outside databases

Previous GC identifers: GC04P077354 GC04P077391 GC04P077135 GC04P072924


(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 FAM47E Gene:
FAM47E (family with sequence similarity 47, member E) is a protein-coding gene. Diseases associated with FAM47E include parkinson's disease. GO annotations related to this gene include transcription cofactor activity. An important paralog of this gene is FAM47A.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the FAM47E gene promoter:
         AhR   HOXA3   ATF-2   c-Jun   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for FAM47E

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM47E


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

Entrez Gene cytogenetic band: 4q21.1   Ensembl cytogenetic band:  4q21.1   HGNC cytogenetic band: 4q21.1

FAM47E Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM47E gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P077172:  view genomic region     (about GC identifiers)

Start:
77,172,853 bp from pter      End:
77,232,282 bp from pter
Size:
59,430 bases      Orientation:
plus strand

1 alternative location:
Chr4+ 77,135,193-77,204,933     

(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: FA47E_HUMAN, Q6ZV65 (See protein sequence)
Recommended Name: Protein FAM47E  
Size: 393 amino acids; 45662 Da
Secondary accessions: D6R8Y4
Alternative splicing: 3 isoforms:  Q6ZV65-3   Q6ZV65-2   Q6ZV65-1   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FAM47E: NX_Q6ZV65

Explore proteomics data for FAM47E at MOPED


See FAM47E Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001130042.1  NP_001229865.1  

ENSEMBL proteins: 
 ENSP00000422067   ENSP00000424458   ENSP00000425528   ENSP00000423044  

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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: Q6ZV65

UniProtKB/Swiss-Prot: FA47E_HUMAN, Q6ZV65
Similarity: Belongs to the FAM47 family


(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
nucleus3
cytoskeleton1
cytosol1
mitochondrion1
plasma membrane1

(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 FAM47E
Interactions:

    Search GeneGlobe Interaction Network for FAM47E

(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 FAM47E (FA47E)



(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 FAM47E gene (2 alternative transcripts): 
NM_001136570.2  NM_001242936.1  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000515604(uc003hjy.3 uc011cbv.2 uc011cbw.2) ENST00000514365
ENST00000509377 ENST00000514140
miRNA
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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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FAM47E expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAATCTTCTC
FAM47E Expression
About this image

FAM47E Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FAM47E Protein Expression
    Custom PCR Arrays for FAM47E
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM47E

(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 chordates.

Orthologs for FAM47E gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Fam47e1 , 5 family with sequence similarity 47, member E1, 5 67.34(n)1
57.87(a)1
  5 (47.09 cM)5
3841981  NM_001033478.21  NP_001028650.21 
 925550695 
lizard
(Anolis carolinensis)
Reptilia --
--
Uncharacterized protein
30(a)
24(a)
many ↔ many
many ↔ many
5(146835883-146858948)
5(147048073-147073721)
tropical clawed frog
(Xenopus tropicalis)
Amphibia LOC1001278121 uncharacterized LOC100127812 49.85(n)
39(a)
  100127812  NM_001113123.1  NP_001106594.1 
zebrafish
(Danio rerio)
Actinopterygii LOC1005367531 protein FAM47E-like 45.38(n)
33.11(a)
  100536753  XM_003198680.2  XP_003198728.1 


ENSEMBL Gene Tree for FAM47E (if available)
TreeFam Gene Tree for FAM47E (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FAM47E gene
FAM47A2  FAM47C2  FAM47B2  
1 SIMAP similar gene for FAM47E using alignment to 5 protein entries:     FA47E_HUMAN (see all proteins):
FAM47DP

FAM47E 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), 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 FAM47E (see all 681)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 4 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1505635451,2
--77137095(+) TACTCA/GGTAGA 1 -- int10--------
rs1395903511,2
--77137111(+) GGAGCA/GGATGG 1 -- int10--------
rs1492669451,2
--77137199(+) GTTCAA/GATAGA 1 -- int10--------
rs1872281541,2
--77137357(+) GCTCTC/GTGCCC 1 -- int10--------
rs623030001,2
C,F--77137580(+) CTGTTT/AGCGGG 1 -- int16Minor allele frequency- A:0.47NA CSA WA 246
rs1917243351,2
--77137582(+) GTTTGC/TGGGCT 1 -- int10--------
rs1473857321,2
C--77137648(+) ATCCCA/GGGGTA 1 -- int10--------
rs1140182771,2
C,F--77137820(+) TTTACC/TTGCTC 1 -- int11Minor allele frequency- T:0.02WA 118
rs1838925891,2
--77137831(+) TCTGAA/GGATCT 1 -- int10--------
rs1119906181,2
F--77137859(+) GTCAGG/TCGGTT 1 -- int11Minor allele frequency- T:0.50CSA 2

HapMap Linkage Disequilibrium report for FAM47E (77172853 - 77232282 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for FAM47E:    About this table    
Variant IDTypeSubtypePubMed ID
esv2661271CNV Deletion23128226
esv2421530CNV Deletion20811451
nsv516357CNV Loss19592680
nsv461559CNV Loss19166990
nsv7363OTHER Inversion18451855

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 FAM47E:    
About MalaCards
parkinson's disease


FAM47E for disorders           About GeneDecksing

Genetic Association Database (GAD): FAM47E
Human Genome Epidemiology (HuGE) Navigator: FAM47E (1 document)

Export disorders for FAM47E 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 FAM47E gene integrated from 10 sources:
(articles sorted by number of sources associating them with FAM47E)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. (PubMed id 21738487)1, 4 Do C.B....Eriksson N. (PLoS Genet. 2011)
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
  3. Genome-wide association study reveals genetic risk underlying Parkinson's disease. (PubMed id 19915575)1, 4 SimA^n-SA!nchez J....Gasser T. (Nat. Genet. 2009)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  7. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
  8. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)
  9. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
  10. Generation and analysis of 280,000 human expressed sequence tags. (PubMed id 8889549)1 Hillier L.D....Marra M. (Genome Res. 1996)

(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: 100129583 HGNC: 34343 Ensembl:ENSG00000272414 euGenes: HUgn100129583 ECgene: FAM47E
H-InvDB: FAM47E

(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 FAM47E 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 FAM47E gene:
Search GeneIP for patents involving FAM47E

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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