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FEN1 Gene

protein-coding   GIFtS: 71
GCID: GC11P061560

Flap Structure-Specific Endonuclease 1


(Previous symbol: RAD2)
  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
Flap Structure-Specific Endonuclease 11 2 3     FEN-12 3
RAD21 2 3     MF12 3
DNase IV1 2 3     Flap Endonuclease 12
Maturation Factor-11 2     EC 3.1.-.-3
Maturation Factor 12 3     hFEN-13

External Ids:    HGNC: 36501   Entrez Gene: 22372   Ensembl: ENSG000001684967   OMIM: 6003935   UniProtKB: P397483   

Export aliases for FEN1 gene to outside databases

Previous GC identifers: GC11P064074 GC11P063135 GC11P061811 GC11P061335 GC11P061316 GC11P057888


(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 FEN1 Gene:
The protein encoded by this gene removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki
fragments in lagging strand DNA synthesis. Direct physical interaction between this protein and AP endonuclease 1
during long-patch base excision repair provides coordinated loading of the proteins onto the substrate, thus
passing the substrate from one enzyme to another. The protein is a member of the XPG/RAD2 endonuclease family and
is one of ten proteins essential for cell-free DNA replication. DNA secondary structure can inhibit flap
processing at certain trinucleotide repeats in a length-dependent manner by concealing the 5' end of the flap
that is necessary for both binding and cleavage by the protein encoded by this gene. Therefore, secondary
structure can deter the protective function of this protein, leading to site-specific trinucleotide expansions.
(provided by RefSeq, Jul 2008)

GeneCards Summary for FEN1 Gene:
FEN1 (flap structure-specific endonuclease 1) is a protein-coding gene. Diseases associated with FEN1 include xeroderma pigmentosum, group g, and best vitelliform macular dystrophy. GO annotations related to this gene include damaged DNA binding and magnesium ion binding. An important paralog of this gene is GEN1.

UniProtKB/Swiss-Prot: FEN1_HUMAN, P39748
Function: Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA
replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by
displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the
flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the
long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP)
site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs
that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped
double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in
repairing mitochondrial DNA

Gene Wiki entry for FEN1 (Flap structure-specific endonuclease 1) 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_000011.10  NC_018922.2  NT_167190.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FEN1 gene promoter:
         COUP-TF1   NRSF form 1   COUP   MIF-1   HNF-4alpha2   NRSF form 2   HNF-4alpha1   COUP-TF   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFEN1 promoter sequence
   Search Chromatin IP Primers for FEN1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FEN1


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

Entrez Gene cytogenetic band: 11q12   Ensembl cytogenetic band:  11q12.2   HGNC cytogenetic band: 11q12

FEN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FEN1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P061560:  view genomic region     (about GC identifiers)

Start:
61,560,109 bp from pter      End:
61,564,716 bp from pter
Size:
4,608 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: FEN1_HUMAN, P39748 (See protein sequence)
Recommended Name: Flap endonuclease 1  
Size: 380 amino acids; 42593 Da
Cofactor: Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme.
May bind an additional third magnesium ion after substrate binding
Subunit: Interacts with PCNA. Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one
PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity. The C-terminal domain
binds EP300. Can bind simultaneously to both PCNA and EP300. Interacts with DDX11
6 PDB 3D structures from and Proteopedia for FEN1:
1U7B (3D)        1UL1 (3D)        3Q8K (3D)        3Q8L (3D)        3Q8M (3D)        3UVU (3D)    
Alternative initiation: 2 isoforms:  P39748-1   P39748-2   (No nuclease activity. Binds preferentially to RNA flap structures and R-loops)

Explore the universe of human proteins at neXtProt for FEN1: NX_P39748

Explore proteomics data for FEN1 at MOPED

Post-translational modifications: 

  • Acetylated by EP300. Acetylation inhibits both endonuclease and exonuclease activity. Acetylation also reduces
    DNA-binding activity but does not affect interaction with PCNA or EP3001
  • Phosphorylation upon DNA damage induces relocalization to the nuclear plasma. Phosphorylation at Ser-187 by CDK2
    occurs during late S-phase and results in dissociation from PCNA1
  • Methylation at Arg-192 by PRMT5 impedes Ser-187 phosphorylation and increases interaction with PCNA1
  • Ubiquitination2 at Lys8, Lys171, Lys254, Lys345
  • Modification sites at PhosphoSitePlus

  • See FEN1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004102.1  
    ENSEMBL proteins: 
     ENSP00000305480   ENSP00000445692   ENSP00000460402  
    Reactome Protein details: P39748

    FEN1 Human Recombinant Protein Products:

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    Novus Biologicals FEN1 Proteins
    Novus Biologicals FEN1 Lysates
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    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for FEN1
    Cloud-Clone Corp. Proteins for FEN1

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    FEN1 Assay Products:

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    Cloud-Clone Corp. ELISAs for FEN1
    Cloud-Clone Corp. CLIAs for FEN1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 7):
     IPR006084 XPG/Rad2
     IPR023426 Flap_endonuc
     IPR006086 XPG-I_dom
     IPR006085 XPG_DNA_repair_N
     IPR019974 XPG_CS

    Graphical View of Domain Structure for InterPro Entry P39748

    ProtoNet protein and cluster: P39748

    2 Blocks protein domains:
    IPB006084 Xeroderma pigmentosum group G/yeast RAD superfamily signature
    IPB008918 Helix-hairpin-helix motif


    UniProtKB/Swiss-Prot: FEN1_HUMAN, P39748
    Similarity: Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily


    FEN1 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FEN1_HUMAN, P39748
    Function: Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA
    replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by
    displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the
    flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the
    long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP)
    site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs
    that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped
    double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in
    repairing mitochondrial DNA

         Genatlas biochemistry entry for FEN1:
    flap structure specific endonuclease 1,with an 5'- 3' exonuclease activity,involved in long patch base excision
    repair,DNA replication,where it processes Okazaki fragments,recombination and repair where it interacts with PCNA
    complex and DNA and acts as an exonuclease

         Enzyme Number (IUBMB): EC 3.1.-.-1

         Gene Ontology (GO): Selected molecular function terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000287magnesium ion binding IEA--
    GO:0003677DNA binding IMP11986308
    GO:0003684damaged DNA binding TAS8007985
    GO:0003690double-stranded DNA binding TAS8131753
    GO:0003824catalytic activity ----
         
    FEN1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for FEN1:
     Decreased DCP1a protein expres 

         15 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Fen1):
     adipose tissue  cellular  digestive/alimentary  embryogenesis  endocrine/exocrine gland 
     growth/size/body  hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  nervous system  normal  respiratory system  tumorigenesis 

    FEN1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for FEN1: Fen1tm1Rak Fen1tm1Klng Fen1tm1Bew

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FEN1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for FEN1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for FEN1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for FEN1

    miRNA
    Products:
        
    miRTarBase miRNAs that target FEN1:
    hsa-mir-1229-3p (MIRT036309), hsa-mir-192-5p (MIRT026838), hsa-mir-183-5p (MIRT047080), hsa-mir-215-5p (MIRT024421), hsa-mir-24-3p (MIRT000116), hsa-mir-324-3p (MIRT042974), hsa-mir-193b-3p (MIRT016610), hsa-let-7b-5p (MIRT052079), hsa-mir-34a-5p (MIRT025481)

    Block miRNA regulation of human, mouse, rat FEN1 using miScript Target Protectors
    7 qRT-PCR Assays for microRNAs that regulate FEN1:
    hsa-miR-140-5p hsa-miR-4324 hsa-miR-544b hsa-miR-610 hsa-miR-4251 hsa-miR-378* hsa-miR-4293
    SwitchGear 3'UTR luciferase reporter plasmidFEN1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for FEN1
    Predesigned siRNA for gene silencing in human, mouse, rat FEN1

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for FEN1

    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: FEN1 (NM_004111)
    Sino Biological Human cDNA Clone for FEN1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for FEN1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FEN1

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    Browse ESI BIO Cell Lines and PureStem Progenitors for FEN1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FEN1


    (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
    FEN1_HUMAN, P39748: Isoform 1: Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Resides mostly in the nucleoli and
    relocalizes to the nucleoplasm upon DNA damage
    FEN1_HUMAN, P39748: Isoform FENMIT: Mitochondrion
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    nucleus5
    cytosol2
    chloroplast1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730nucleolus IDA--
    GO:0005739mitochondrion IDA18995831

    FEN1 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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    SuperPaths for FEN1 About   (see all 12)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Telomere C-strand (Lagging Strand) Synthesis
    Telomere C-strand (Lagging Strand) Synthesis0.79
    Removal of the Flap Intermediate from the C-strand0.00
    Extension of Telomeres0.79
    Removal of the Flap Intermediate0.00
    Mismatch Repair in Eukaryotes0.54
    Lagging Strand Synthesis0.00
    Cell cycle Transition and termination of DNA replication0.43
    Processive synthesis on the C-strand of the telomere0.00
    2Resolution of Abasic Sites (AP sites)
    Resolution of Abasic Sites (AP sites)0.89
    Base Excision Repair0.00
    Resolution of AP sites via the multiple-nucleotide patch replacement pathway0.89
    Removal of DNA patch containing abasic residue0.00
    Base excision repair0.53
    3DNA strand elongation
    DNA strand elongation0.63
    DNA replication0.63
    4Non-homologous end-joining
    Non-homologous end-joining0.37
    DNA damage NHEJ mechanisms of DSBs repair0.37
    5HIV Life Cycle
    HIV Life Cycle0.91
    Early Phase of HIV Life Cycle0.00
    HIV Infection0.62

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for FEN1
        Mismatch Repair in Eukaryotes
    DNA Repair Mechanisms

    2 Cell Signaling Technology (CST) Pathways for FEN1
        Cell Cycle / Checkpoint Control
    DNA Damage

    2 GeneGo (Thomson Reuters) Pathways for FEN1
        DNA damage NHEJ mechanisms of DSBs repair
    Cell cycle Transition and termination of DNA replication


    3 Reactome Pathways for FEN1
        Removal of DNA patch containing abasic residue
    Removal of the Flap Intermediate
    Removal of the Flap Intermediate from the C-strand


    3 Kegg Pathways  (Kegg details for FEN1):
        DNA replication
    Base excision repair
    Non-homologous end-joining


    FEN1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including FEN1: 
              DNA Damage Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for FEN1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for FEN1 (P397481, 2, 3 ENSP000003054804) via UniProtKB, MINT, STRING, and/or I2D (see all 1027)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000278mitotic cell cycle TAS--
    GO:0000722telomere maintenance via recombination TAS--
    GO:0000723telomere maintenance TAS--
    GO:0000737DNA catabolic process, endonucleolytic IMP11986308
    GO:0000738DNA catabolic process, exonucleolytic TAS8131753

    FEN1 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 FEN1

    Selected Novoseek inferred chemical compound relationships for FEN1 gene (see all 13)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    methylmethanesulfonate 60.5 7 11687589 (2), 19596913 (1)
    oligonucleotide 28 1 11601988 (1)
    alanine 4.38 5 15131255 (1), 8621570 (1), 11053418 (1)
    calcium 3.01 2 11078214 (1), 17656006 (1)
    lipid 2.42 1 11090277 (1)
    magnesium 0 7 11258937 (4), 9880491 (2), 8247134 (1)
    atp 0 1 15579905 (1)
    phospholipid 0 1 12225777 (1)
    adp 0 1 9679139 (1)
    arginine 0 2 9305916 (1), 16912194 (1)



    FEN1 for compounds           About GeneDecksing



    (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 FEN1 gene: 
    NM_004111.5  

    Unigene Cluster for FEN1:

    Flap structure-specific endonuclease 1
    Hs.409065  [show with all ESTs]
    Unigene Representative Sequence: NM_004111
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000305885(uc001nsg.3) ENST00000535723 ENST00000535307
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate FEN1:
    hsa-miR-140-5p hsa-miR-4324 hsa-miR-544b hsa-miR-610 hsa-miR-4251 hsa-miR-378* hsa-miR-4293
    SwitchGear 3'UTR luciferase reporter plasmidFEN1 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: FEN1 (NM_004111)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FEN1
    Primer
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    OriGene qPCR primer pairs and template standards for FEN1
    OriGene qSTAR qPCR primer pairs in human, mouse for FEN1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat FEN1
      QuantiTect SYBR Green Assays in human, mouse, rat FEN1
      QuantiFast Probe-based Assays in human, mouse, rat FEN1

    Additional mRNA sequence: 

    AK301743.1 AK312761.1 BC000323.2 BT019524.1 CR536562.1 L37374.1 X76771.1 

    23 DOTS entries:

    DT.100815303  DT.95364169  DT.100815307  DT.455329  DT.120739964  DT.86858976  DT.100815314  DT.100771302 
    DT.97853756  DT.120740130  DT.120740129  DT.100815305  DT.100815306  DT.121390749  DT.100815302  DT.100815313 
    DT.120740117  DT.91777025  DT.95364166  DT.100815301  DT.100815311  DT.70104817  DT.95364167 

    Selected AceView cDNA sequences (see all 427):

    AW194154 CR618866 BQ068879 BE794549 BQ061097 BU165752 AW192592 AI832123 
    CB151489 BP363986 BG177207 BQ229826 BU931957 BM450370 AA305950 BG260900 
    BP364327 AI581126 BQ061094 BQ772499 CR591287 CB143393 AA306861 BG825257 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for FEN1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c
    SP1:                    -                           
    SP2:                    -                           
    SP3:                                                


    ECgene alternative splicing isoforms for FEN1

    (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)
    About This Section

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    FEN1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CGCTGTTTTT
    FEN1 Expression
    About this image


    FEN1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Bone (Muscoskeletal System)
             Bone Marrow
    FEN1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FEN1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.409065
        Pathway & Disease-focused RT2 Profiler PCR Arrays including FEN1: 
              DNA Damage Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

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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 eukaryotes.

    Orthologs for FEN1 gene from Selected species (see all 28)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fen11 , 5 flap structure specific endonuclease 11, 5 90.26(n)1
    96.58(a)1
      19 (6.54 cM)5
    141561  NM_007999.41  NP_032025.21 
     101991325 
    chicken
    (Gallus gallus)
    Aves FEN11 flap structure-specific endonuclease 1 79.91(n)
    84.47(a)
      769677  NM_001079491.1  NP_001072959.1 
    lizard
    (Anolis carolinensis)
    Reptilia FEN16
    flap structure-specific endonuclease 1
    81(a)
    1 ↔ 1
    GL343235.1(1794007-1795155)
    African clawed frog
    (Xenopus laevis)
    Amphibia fen1-B2 flap endonuclease 1 76.84(n)    U68141.1 
    zebrafish
    (Danio rerio)
    Actinopterygii fen12 flap structure-specific endonuclease 1 75.87(n)   386707  AY391423.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Fen11 , 3 DNA repair endonuclease3
    Flap endonuclease 11
    65(a)3
    62.89(n)1
    63.68(a)1
      53D143
    368871  NM_079041.11  NP_523765.11 
    worm
    (Caenorhabditis elegans)
    Secernentea Y47G6A.83
    crn-11
    endonuclease3
    crn-11
    64(a)3
    61.9(n)1
    62.96(a)1
      I(3482031-3484366)3
    1719171  NM_058767.61  NP_491168.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RAD27(YKL113C)4
    RAD271
    5' to 3' exonuclease, 5' flap endonuclease, required more4
    RAD271
    57.77(n)1
    59.67(a)1
      11(225875-224727)4
    8537471, 4  NP_012809.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G266801 AT5G26680 57.47(n)
    55.7(a)
      832721  NM_001161268.1  NP_001154740.1 
    rice
    (Oryza sativa)
    Liliopsida Os.44692 Oryza sativa (japonica cultivar-group) OsFEN-1a mRNA more 72.3(n)    AB021666.2 


    ENSEMBL Gene Tree for FEN1 (if available)
    TreeFam Gene Tree for FEN1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FEN1 gene
    GEN12  
    1 SIMAP similar gene for FEN1 using alignment to 4 protein entries:     FEN1_HUMAN (see all proteins):
    GEN1

    FEN1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for FEN1
    PGOHUM00000244791


    (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 FEN1 (see all 88)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1845696851,2
    C--61562197(+) GAGTGA/GTGGCG 1 -- int10--------
    rs1902888361,2
    --61562201(+) GGTGGC/TGAGAA 1 -- int10--------
    rs32188371,2
    C,F,H--61562224(+) AAGACT/GTGAAA 1 -- int15Minor allele frequency- G:0.01NS EA 594
    rs1923249261,2
    --61562589(+) AGCACA/GTGGTT 1 -- int10--------
    rs1844395851,2
    --61562622(+) CTTACG/TATTGA 1 -- int10--------
    rs32188381,2
    C,H--61562776(+) CTTTCT/GCCTTT 1 -- int1 trp35Minor allele frequency- G:0.00NS EA 580
    rs3934871,2
    C,H--61562805(+) CTTTCT/CTTTTT 1 -- int1 trp36Minor allele frequency- C:0.00MN NS EA NA 655
    rs1478818141,2
    C--61562917(+) TTTGGC/TCGTAA 2 G syn11Minor allele frequency- T:0.00NA 4548
    rs1404588641,2
    C,F--61562973(+) TGTTCG/ACCAGG 2 /H /R mis12Minor allele frequency- A:0.00NA EU 5875
    rs1895888181,2
    C--61562980(+) CAGGGG/TGGGGA 2 G syn10--------

    HapMap Linkage Disequilibrium report for FEN1 (61560109 - 61564716 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for FEN1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv343CNV Insertion18451855
    nsv528697CNV Loss19592680
    dgv1153n71CNV Loss21882294
    dgv1152n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): FEN1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FEN1
    DNA2.0 Custom Variant and Variant Library Synthesis for FEN1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600393    OMIM disorders: --

    Selected diseases for FEN1 (see all 39):    
    About MalaCards
    xeroderma pigmentosum, group g    best vitelliform macular dystrophy    vitelliform macular dystrophy    werner syndrome
    macular dystrophy    bloom syndrome    xeroderma pigmentosum    autosomal recessive disease
    traumatic brain injury    huntington's disease    cockayne syndrome    brain injury
    myelofibrosis    vaccinia    graft versus host disease    esophageal cancer
    herpes simplex    colorectal cancer    sepsis    coronary artery disease

    2 diseases from the University of Copenhagen DISEASES database for FEN1:
    Autosomal recessive disease     Vitelliform macular dystrophy

    FEN1 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for FEN1 gene (see all 15)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    werner syndrome 68.2 3 15592449 (1), 11598021 (1), 14688284 (1)
    bloom syndrome 59.5 2 16326861 (1), 14688284 (1)
    macular dystrophy, vitelliform 52.3 4 10769175 (1)
    sezary syndrome 33.3 2 9613981 (1), 8695857 (1)
    xeroderma pigmentosum 29.2 2 7989298 (1), 9305916 (1)
    huntington disease 19.6 1 12917330 (1)
    promyelocytic leukemia 15.6 2 9894157 (1), 10771101 (1)
    microsatellite instability 5.17 3 8782829 (1), 14562054 (1)
    cancer 5.04 26 19010819 (4), 17589521 (3), 19068479 (1), 16879693 (1) (see all 9)
    shock 0 5 15942332 (2), 14673135 (1), 11275689 (1), 15152009 (1)

    Genetic Association Database (GAD): FEN1
    Human Genome Epidemiology (HuGE) Navigator: FEN1 (12 documents)

    Export disorders for FEN1 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 FEN1 gene, integrated from 10 sources (see all 273):
    (articles sorted by number of sources associating them with FEN1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sequence of human FEN-1, a structure-specific endonuclease, and chromosomal localization of the gene (FEN1) in mouse and human. (PubMed id 7774922)1, 2, 3, 9 Hiraoka L.R.... Hsieh C.-L. (Genomics 1995)
    2. Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk. (PubMed id 19618370)1, 4, 9 Yang M....Lin D. (Hum. Mutat. 2009)
    3. Structural basis for recruitment of human flap endonuclease 1 to PCNA. (PubMed id 15616578)1, 2, 9 Sakurai S.... Hakoshima T. (EMBO J. 2005)
    4. Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300. (PubMed id 11430825)1, 2, 9 Hasan S.... Hottiger M.O. (Mol. Cell 2001)
    5. The DNA repair endonuclease XPG binds to proliferating cell nuclear antigen (PCNA) and shares sequence elements with the PCNA-binding regions of FEN-1 and cyclin-dependent kinase inhibitor p21. (PubMed id 9305916)1, 2, 9 Gary R.... Park M.S. (J. Biol. Chem. 1997)
    6. Structural and functional conservation of the human homolog of the Schizosaccharomyces pombe rad2 gene, which is required for chromosome segregation and recovery from DNA damage. (PubMed id 8007985)1, 2, 9 Murray J.M.... Watts F.Z. (Mol. Cell. Biol. 1994)
    7. The &quot;flap&quot; endonuclease gene FEN1 is excluded as a candidate gene implicated in the CAG repeat expansion underlying Huntington disease. (PubMed id 11260214)1, 4, 9 Otto C.J....Andrew S.E. (Clin. Genet. 2001)
    8. Studies with the human cohesin establishment factor, ChlR1. Association of ChlR1 with Ctf18-RFC and Fen1. (PubMed id 18499658)1, 2, 9 Farina A....Hurwitz J. (J. Biol. Chem. 2008)
    9. Associations of DNase IV polymorphisms with autoantibodies in patients with systemic lupus erythematosus. (PubMed id 18417526)1, 4, 9 Kim I....Bae S.C. (Rheumatology (Oxford) 2008)
    10. Essential amino acids for substrate binding and catalysis of human flap endonuclease 1. (PubMed id 8621570)1, 2, 9 Shen B.... Park M.S. (J. Biol. Chem. 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 2237 HGNC: 3650 AceView: FEN1 Ensembl:ENSG00000168496 euGenes: HUgn2237
    ECgene: FEN1 Kegg: 2237 H-InvDB: FEN1

    (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 FEN1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for FEN1 Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/fen1/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for FEN1 gene:
    Search GeneIP for patents involving FEN1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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