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FAM47A Gene

protein-coding   GIFtS: 40
GCID: GC0XM034057

Family With Sequence Similarity 47, Member A

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(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
Family With Sequence Similarity 47, Member A1 2
Similar To Hypothetical Protein FLJ357821
Protein FAM47A2

External Ids:    HGNC: 299621   Entrez Gene: 1587242   Ensembl: ENSG000001854487   UniProtKB: Q5JRC93   

Export aliases for FAM47A gene to outside databases

Previous GC identifers: GC0XM033907 GC0XM031885


(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 FAM47A Gene:
FAM47A (family with sequence similarity 47, member A) is a protein-coding gene. An important paralog of this gene is FAM47C.


(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 at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_167197.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM47A gene promoter:
         POU2F2 (Oct-2.1)   HFH-3   NF-AT   FOXI1   POU2F2C   NF-AT4   NF-AT2   NF-AT3   POU2F2B   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM47A promoter sequence
   Search Chromatin IP Primers for FAM47A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM47A


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

Entrez Gene cytogenetic band: Xp21.1   Ensembl cytogenetic band:  Xp21.1   HGNC cytogenetic band: Xp21.1

FAM47A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM47A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM034057:  view genomic region     (about GC identifiers)

Start:
34,147,869 bp from pter      End:
34,150,447 bp from pter
Size:
2,579 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FA47A_HUMAN, Q5JRC9 (See protein sequence)
Recommended Name: Protein FAM47A  
Size: 791 amino acids; 90592 Da
Secondary accessions: A8K8I9 Q8TAA0

Explore the universe of human proteins at neXtProt for FAM47A: NX_Q5JRC9

Explore proteomics data for FAM47A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FAM47A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_981953.2  
    ENSEMBL proteins: 
     ENSP00000345029  

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    antibodies-online proteins for FAM47A (2 products) 

     
    antibodies-online peptides for FAM47A

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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:
     IPR026083 FAM47

    Graphical View of Domain Structure for InterPro Entry Q5JRC9

    ProtoNet protein and cluster: Q5JRC9

    UniProtKB/Swiss-Prot: FA47A_HUMAN, Q5JRC9
    Similarity: Belongs to the FAM47 family


    Find genes that share domains with FAM47A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for FAM47A

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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
    cytosol2
    golgi apparatus1

    (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 FAM47A
    Interactions:

        Search GeneGlobe Interaction Network for FAM47A

    (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 FAM47A (FA47A)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for FAM47A gene: 
    NM_203408.3  

    Unigene Cluster for FAM47A:

    Family with sequence similarity 47, member A
    Hs.143268  [show with all ESTs]
    Unigene Representative Sequence: NM_203408
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000346193(uc004ddg.3)
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat FAM47A

    Additional mRNA sequence: 

    AK292354.1 BC026171.2 

    2 DOTS entries:

    DT.92067633  DT.121285225 

    6 AceView cDNA sequences:

    BE041525 BG721764 BC026171 AI141715 AA927584 NM_203408 

    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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    FAM47A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTACCTCAAG
    FAM47A Expression
    About this image

    FAM47A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FAM47A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.143268
        Custom PCR Arrays for FAM47A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM47A

    (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 FAM47A gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fam47c1 , 5 family with sequence similarity 47, member A, pseudogene5
    family with sequence similarity 47, member C1
    61.96(n)1
    44.8(a)1
      X (38.35 cM)5
    708641  NM_001164739.11  NP_001158211.11 
     787377635 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    28(a)
    23(a)
    many ↔ many
    many ↔ many
    5(146835883-146858948)
    5(147048073-147073721)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1582606
    zgc:1582606
    zgc:158260
    22(a)
    21(a)
    many ↔ many
    many ↔ many
    5(56670876-56683246) ENSDARG00000067694
    5(56751666-56763258) ENSDARG00000089020


    ENSEMBL Gene Tree for FAM47A (if available)
    TreeFam Gene Tree for FAM47A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FAM47A gene
    FAM47C2  FAM47E2  FAM47B2  
    2 SIMAP similar genes for FAM47A using alignment to 1 protein entry:     FA47A_HUMAN:
    FAM47B    FAM47C

    Find genes that share paralogs with FAM47A           About GenesLikeMe



    (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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    Polymorphic Variants from UniProtKB/Swiss-Prot
    FA47A_HUMAN, Q5JRC9: The repeat encompassing Pro-495 to Glu-507 may be polymorphic


    Selected SNPs for FAM47A (see all 166)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs348446211,2
    C--31885393(+) GCACA-/TTTTTT 1 -- int11Minor allele frequency- T:0.00CSA 2
    rs29399981,2
    C,A--34061373(-) CTACCC/TGGGGG 1 -- int15Minor allele frequency- T:0.00WA NA CSA 7
    rs1824036471,2
    --34061436(+) ATAGAC/GACCAG 1 -- int10--------
    rs30061261,2
    C,F,A--34061449(+) TTCACC/TATGTT 1 -- int16Minor allele frequency- T:0.20NA WA CSA 10
    rs1889942241,2
    --34061614(+) ACAAAC/TAATTG 1 -- int10--------
    rs1931149081,2
    --34061753(+) TAGGTA/GTTGAA 1 -- ut310--------
    rs1997699551,2
    --34061829(+) AAATGA/CGAGCA 1 -- ut310--------
    rs2006317601,2
    C--34062054(+) GATCGC/TCAAGA 2 D G mis10--------
    rs2014400401,2
    C--34062198(+) AATTCA/GATGGC 2 S L mis10--------
    rs1851827641,2
    C--34062375(+) TGATGG/TATTCT 2 Y S mis10--------

    HapMap Linkage Disequilibrium report for FAM47A (34147869 - 34150447 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for FAM47A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2752322CNV Gain17911159
    nsv820274CNV Gain19587683

    Locus Specific Mutation Databases (LSDB): FAM47A

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for FAM47A

    (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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      --

    (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 FAM47A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with FAM47A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. 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)
    4. Genome-wide association study of chronic periodontitis in a general German population. (PubMed id 24024966)1 Teumer A....Kocher T. (J. Clin. Periodontol. 2013)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    6. Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross- validation of MS/MS and MS/MS/MS spectra. (PubMed id 17924679)1 Yu L.R.... Veenstra T.D. (J. Proteome Res. 2007)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (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: 158724 HGNC: 29962 AceView: FAM47A Ensembl:ENSG00000185448 euGenes: HUgn158724
    ECgene: FAM47A H-InvDB: FAM47A

    (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 FAM47A 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 FAM47A gene:
    Search GeneIP for patents involving FAM47A

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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     ELISAs for FAM47A
     CLIAs for FAM47A



     Browse ESI BIO Cell Lines and PureStem Progenitors for FAM47A
     Gene Synthesis
     Protein Engineering
     Variant Library Synthesis
     Codon Optimization
     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM47A
     Browse SwitchGear 3'UTR luciferase reporter plasmids for FAM47A
     SwitchGear Promoter luciferase reporter plasmids for FAM47A
     Search ThermoFisher Antibodies for FAM47A
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FAM47A
     Browse compounds at ApexBio
     Search Addgene for plasmids for FAM47A
      Search eBioscience for proteins for FAM47A
      Search eBioscience for elisas for FAM47A
      eBioscience FlowRNA Probe Sets
     genOway: Develop your customized and physiologically relevant rodent model for FAM47A
     antibodies-online antibodies for FAM47A (4 products)
     antibodies-online kits for FAM47A (2 products)
     antibodies-online peptides for FAM47A
     antibodies-online proteins for FAM47A (2 products)
           
    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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