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FDCSP Gene

protein-coding   GIFtS: 35
GCID: GC04P071091

Follicular Dendritic Cell Secreted Protein

(Previous name: chromosome 4 open reading frame 7)
(Previous symbol: C4orf7)
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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
Follicular Dendritic Cell Secreted Protein1 2
C4orf71 2 3
FDC-SP2 3
FDC Secreted Protein2 3
Chromosome 4 Open Reading Frame 71
Follicular Dendritic Cell Secreted Peptide2

External Ids:    HGNC: 192151   Entrez Gene: 2604362   Ensembl: ENSG000001816177   OMIM: 6072415   UniProtKB: Q8NFU43   

Export aliases for FDCSP gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FDCSP Gene:
This gene encodes a small secreted protein that is expressed in follicular dendritic cells. This protein
specifically binds to activated B cells, and functions as a regulator of antibody responses. It is also thought
to contribute to tumor metastases by promoting cancer cell migration and invasion. (provided by RefSeq, Dec 2011)

GeneCards Summary for FDCSP Gene:
FDCSP (follicular dendritic cell secreted protein) is a protein-coding gene.

UniProtKB/Swiss-Prot: FDSCP_HUMAN, Q8NFU4
Function: Can bind to the surface of B-lymphoma cells, but not T-lymphoma cells, consistent with a function as a
secreted mediator acting upon B-cells




(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:
   Search for regulatory transcription factor binding sites for FDCSP
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 4q13|4q13   Ensembl cytogenetic band:  4q13.3   HGNC cytogenetic band: 4q13

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

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P071091:  view genomic region     (about GC identifiers)

Start:
71,091,788 bp from pter      End:
71,100,969 bp from pter
Size:
9,182 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, 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: FDSCP_HUMAN, Q8NFU4 (See protein sequence)
Recommended Name: Follicular dendritic cell secreted peptide precursor  
Size: 85 amino acids; 9700 Da

Explore the universe of human proteins at neXtProt for FDCSP: NX_Q8NFU4

Post-translational modifications: 

  • O-glycosylated with core 1 or possibly core 8 glycans1
  • Modification sites at neXtProt
  • REFSEQ proteins: NP_694542.1  
    ENSEMBL proteins: 
     ENSP00000318437  

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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: Q8NFU4


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FDSCP_HUMAN, Q8NFU4
    Function: Can bind to the surface of B-lymphoma cells, but not T-lymphoma cells, consistent with a function as a
    secreted mediator acting upon B-cells

    Phenotypes:
         1 GenomeRNAi human phenotype for FDCSP:

     Decreased number of cells in m 

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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
    FDSCP_HUMAN, Q8NFU4: Secreted

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with FDCSP           About GenesLikeMe


    (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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    Interactions:

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    (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
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    Browse Tocris compounds for FDCSP (FDSCP)



    (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,
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    REFSEQ mRNAs for FDCSP gene: 
    NM_152997.3  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000317987(uc003hfd.3)
    miRNA
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    Selected AceView cDNA sequences (see all 59):

    NM_152997 AI708198 AW268642 BG059093 CB123365 BG271408 AA614722 AA507382 
    CB130829 AI391465 BE041192 AI862746 AY190326 AW276439 AY358958 AA719940 
    AI637680 CB140082 AI719838 AI734920 AI253742 AI510752 AF435080 AW518210 

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

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

    UniProtKB/Swiss-Prot: FDSCP_HUMAN, Q8NFU4
    Tissue specificity: Abundantly expressed in tonsil, lymph node, and trachea; strong expression in prostate; lower
    expression in thyroid, stomach, and colon

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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 FDCSP gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia FDCSP1 follicular dendritic cell secreted protein 99.22(n)
    98.82(a)
      742341  XM_001160925.2  XP_001160925.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FDCSP gene
    1 SIMAP similar gene for FDCSP using alignment to 1 protein entry:     FDSCP_HUMAN:
    NAP1

    Find genes that share paralogs with FDCSP           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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    Selected SNPs for FDCSP (see all 277)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs176538291,2
    C,F--71089790(+) TACTGC/GGGACA 1 -- us2k110Minor allele frequency- G:0.23NA CSA WA EA 507
    rs1473642691,2
    C--71089794(+) GCGGAC/TAGGGA 1 -- us2k10--------
    rs623074331,2
    C--71089964(+) GAGTCT/CTAGAT 1 -- us2k15Minor allele frequency- C:0.20NA CSA EA 245
    rs1394437791,2
    C--71089989(+) ACTGAC/GTGATT 1 -- us2k10--------
    rs728565811,2
    C,F--71090143(+) AGGCAT/CAGCTT 1 -- us2k12Minor allele frequency- C:0.04WA 120
    rs1842658701,2
    --71090258(+) GTTTCC/TATTAA 1 -- us2k10--------
    rs790443921,2
    C--71090284(+) AAAAAT/ATGGCT 1 -- us2k15Minor allele frequency- A:0.14NA CSA WA EA 361
    rs1896750861,2
    --71090287(+) AATTGG/TCTTAC 1 -- us2k10--------
    rs1811491811,2
    --71090348(+) AAATGC/TCAAAA 1 -- us2k10--------
    rs106366721,2
    C--71090498(+) ATAAT-/AC    
       
    /ACAC
    acaca
    1 -- us2k10--------

    HapMap Linkage Disequilibrium report for FDCSP (71091788 - 71100969 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for FDCSP: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FDCSP
    DNA2.0 Custom Variant and Variant Library Synthesis for FDCSP

    (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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    OMIM gene information: 607241    OMIM disorders: --


    Find genes that share disorders with FDCSP           About GenesLikeMe


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

    1. FDC-SP, a novel secreted protein expressed by follicular dendritic cells. (PubMed id 12193705)1, 2, 3, 9 Marshall A.J....Clark E.A. (J. Immunol. 2002)
    2. C4orf7 contributes to ovarian cancer metastasis by promoting cancer cell migration and invasion. (PubMed id 20811673)1, 3 Wang C....Ma D. (Oncol. Rep. 2010)
    3. Follicular dendritic cell secreted protein (FDC-SP) regulates germinal center and antibody responses. (PubMed id 17548624)1, 3 Al-Alwan M....Marshall A.J. (J. Immunol. 2007)
    4. 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)
    5. 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)
    6. Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD. (PubMed id 22171320)2 Halim A.... Larson G. (Mol. Cell. Proteomics 2011)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    8. Identification of genes preferentially expressed in periodontal ligament: specific expression of a novel secreted protein, FDC-SP. (PubMed id 16259954)1 Nakamura S....Shinomura T. (Biochem. Biophys. Res. Commun. 2005)
    9. 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: 260436 HGNC: 19215 AceView: C4orf7 Ensembl:ENSG00000181617 euGenes: HUgn260436
    ECgene: FDCSP H-InvDB: FDCSP

    (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 FDCSP 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 FDCSP gene:
    Search GeneIP for patents involving FDCSP

    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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     Browse ESI BIO Cell Lines and PureStem Progenitors for FDCSP
     Gene Synthesis
     Protein Engineering
     Variant Library Synthesis
     Codon Optimization
     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FDCSP
     SwitchGear 3'UTR luciferase reporter plasmids for FDCSP
     Browse SwitchGear Promoter luciferase reporter plasmids for FDCSP
     Search ThermoFisher Antibodies for FDCSP
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FDCSP
     Browse compounds at ApexBio
     Search Addgene for plasmids for FDCSP
      Search eBioscience for proteins for FDCSP
      Search eBioscience for elisas for FDCSP
      eBioscience FlowRNA Probe Sets
     genOway: Develop your customized and physiologically relevant rodent model for FDCSP
     antibodies-online antibodies for FDCSP (14 products)
     antibodies-online kits for FDCSP (2 products)
      Search antibodies-online for peptides for FDCSP
     antibodies-online proteins for FDCSP (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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