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Aliases for FEN1 Gene

Aliases for FEN1 Gene

  • Flap Structure-Specific Endonuclease 1 2 3 4 5
  • DNase IV 2 3 4
  • Maturation Factor-1 2 3
  • FEN-1 3 4
  • RAD2 3 4
  • MF1 3 4
  • Flap Endonuclease 1 3
  • Maturation Factor 1 4
  • EC 3.1.-.- 4
  • HFEN-1 4

External Ids for FEN1 Gene

Previous HGNC Symbols for FEN1 Gene

  • RAD2

Previous GeneCards Identifiers for FEN1 Gene

  • GC11P064074
  • GC11P063135
  • GC11P061335
  • GC11P061316
  • GC11P061560
  • GC11P057888

Summaries for FEN1 Gene

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 Werner Syndrome and Bloom Syndrome. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (GO) annotations related to this gene include magnesium ion binding and damaged DNA binding. An important paralog of this gene is GEN1.

UniProtKB/Swiss-Prot for FEN1 Gene

  • 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 Gene

Additional gene information for FEN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FEN1 Gene

Genomics for FEN1 Gene

GeneHancer (GH) Regulatory Elements for FEN1 Gene

Promoters and enhancers for FEN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I061791 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.1 88 3.1 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZBTB7B FADS2 FEN1 MIR611 TMEM258 CPSF7 CSKMT GANAB TMEM138 EML3 TUT1
GH11I061731 Enhancer 1.1 Ensembl ENCODE 11.6 -59.7 -59668 2.1 PKNOX1 CLOCK ATF1 ARNT ARID4B SIN3A BRCA1 ZNF48 ZNF143 ATF7 DAGLA MYRF DKFZP434K028 TMEM258 FEN1 MIR611 SYT7 PIR41833
GH11I062024 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 5.7 +232.9 232927 2.9 PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 POLR2B FTH1 BEST1 DAGLA FEN1 TTC9C RPS2P37 GC11P062053
GH11I061819 Enhancer 0.9 Ensembl ENCODE 10.7 +27.9 27929 1.7 KLF1 RXRA MAFG ZNF592 FOSL1 ZNF316 ATF3 SCRT2 HNF4G FOSL2 FADS2 FEN1 MIR611 TMEM258 FADS1 PIR43939 MIR1908
GH11I061869 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 5.1 +78.1 78070 2.4 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 ZNF766 CBX5 ZNF143 FADS2 EEF1G FEN1 MIR6746 FADS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FEN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FEN1 gene promoter:

Genomic Locations for FEN1 Gene

Genomic Locations for FEN1 Gene
chr11:61,792,637-61,797,244
(GRCh38/hg38)
Size:
4,608 bases
Orientation:
Plus strand
chr11:61,560,109-61,564,716
(GRCh37/hg19)

Genomic View for FEN1 Gene

Genes around FEN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FEN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FEN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FEN1 Gene

Proteins for FEN1 Gene

  • Protein details for FEN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P39748-FEN1_HUMAN
    Recommended name:
    Flap endonuclease 1
    Protein Accession:
    P39748

    Protein attributes for FEN1 Gene

    Size:
    380 amino acids
    Molecular mass:
    42593 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer (PubMed:15616578). PCNA stimulates the nuclease activity without altering cleavage specificity (PubMed:15616578). The C-terminal domain binds EP300; can bind simultaneously to both PCNA and EP300 (PubMed:11430825). Interacts with PCNA; can bind simultaneously to both PCNA and EP300 (PubMed:9305916, PubMed:11430825). Interacts with DDX11; this interaction is direct and increases flap endonuclease activity of FEN1 (PubMed:18499658).

    Three dimensional structures from OCA and Proteopedia for FEN1 Gene

    Alternative splice isoforms for FEN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FEN1 Gene

Post-translational modifications for FEN1 Gene

  • Acetylated by EP300. Acetylation inhibits both endonuclease and exonuclease activity. Acetylation also reduces DNA-binding activity but does not affect interaction with PCNA or EP300.
  • Methylation at Arg-192 by PRMT5 impedes Ser-187 phosphorylation and increases interaction with PCNA.
  • 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 PCNA.
  • Ubiquitination at Lys8, posLast=171171, and posLast=345345
  • Modification sites at PhosphoSitePlus

Other Protein References for FEN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FEN1 Gene

Domains & Families for FEN1 Gene

Gene Families for FEN1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for FEN1 Gene

Graphical View of Domain Structure for InterPro Entry

P39748

UniProtKB/Swiss-Prot:

FEN1_HUMAN :
  • Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.
Family:
  • Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.
genes like me logo Genes that share domains with FEN1: view

Function for FEN1 Gene

Molecular function for FEN1 Gene

GENATLAS Biochemistry:
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
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for FEN1 Gene

Phenotypes From GWAS Catalog for FEN1 Gene

Gene Ontology (GO) - Molecular Function for FEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA,IMP 11986308
GO:0003684 damaged DNA binding TAS 8007985
GO:0003690 double-stranded DNA binding TAS 8131753
GO:0003824 catalytic activity IEA --
GO:0004518 nuclease activity IEA --
genes like me logo Genes that share ontologies with FEN1: view
genes like me logo Genes that share phenotypes with FEN1: view

Animal Models for FEN1 Gene

MGI Knock Outs for FEN1:

Clone Products

  • Addgene plasmids for FEN1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for FEN1 Gene

Localization for FEN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FEN1 Gene

Isoform 1: Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage.
Isoform FENMIT: Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FEN1 gene
Compartment Confidence
mitochondrion 5
nucleus 5
plasma membrane 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0005634 nucleus IDA 7961795
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA,IDA --
GO:0005739 mitochondrion IDA 18995831
genes like me logo Genes that share ontologies with FEN1: view

Pathways & Interactions for FEN1 Gene

genes like me logo Genes that share pathways with FEN1: view

Pathways by source for FEN1 Gene

2 Qiagen pathways for FEN1 Gene
1 Cell Signaling Technology pathway for FEN1 Gene

SIGNOR curated interactions for FEN1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for FEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination TAS --
GO:0006260 DNA replication TAS 9778254
GO:0006281 DNA repair TAS,IEA 8007985
GO:0006284 base-excision repair IEA --
GO:0006302 double-strand break repair TAS 8131753
genes like me logo Genes that share ontologies with FEN1: view

Drugs & Compounds for FEN1 Gene

(7) Drugs for FEN1 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Iron Approved Pharma Target 1259

(7) Additional Compounds for FEN1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with FEN1: view

Transcripts for FEN1 Gene

mRNA/cDNA for FEN1 Gene

Unigene Clusters for FEN1 Gene

Flap structure-specific endonuclease 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for FEN1

Alternative Splicing Database (ASD) splice patterns (SP) for FEN1 Gene

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

Relevant External Links for FEN1 Gene

GeneLoc Exon Structure for
FEN1
ECgene alternative splicing isoforms for
FEN1

Expression for FEN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FEN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FEN1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (11.7) and Lavage (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FEN1 Gene



Protein tissue co-expression partners for FEN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of FEN1 Gene:

FEN1

SOURCE GeneReport for Unigene cluster for FEN1 Gene:

Hs.409065

Evidence on tissue expression from TISSUES for FEN1 Gene

  • Lung(4.8)
  • Liver(4.3)
  • Nervous system(4.2)
  • Eye(2.8)
  • Bone marrow(2.2)
  • Heart(2.1)
  • Intestine(2.1)
  • Blood(2)
genes like me logo Genes that share expression patterns with FEN1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FEN1 Gene

Orthologs for FEN1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for FEN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FEN1 34 33
  • 99.91 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FEN1 33 34
  • 93.77 (n)
cow
(Bos Taurus)
Mammalia FEN1 34 33
  • 91.84 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Fen1 16 34 33
  • 90.26 (n)
rat
(Rattus norvegicus)
Mammalia Fen1 33
  • 89.56 (n)
oppossum
(Monodelphis domestica)
Mammalia FEN1 34
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia FEN1 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves FEN1 34 33
  • 79.91 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FEN1 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fen1 33
  • 74.39 (n)
Str.3319 33
African clawed frog
(Xenopus laevis)
Amphibia fen1-B 33
zebrafish
(Danio rerio)
Actinopterygii fen1 34 33
  • 72.08 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.569 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011448 33
  • 64.39 (n)
fruit fly
(Drosophila melanogaster)
Insecta Fen1 35 33 34
  • 62.89 (n)
worm
(Caenorhabditis elegans)
Secernentea Y47G6A.8 35
  • 64 (a)
crn-1 34 33
  • 61.9 (n)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABL052C 33
  • 60.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD27 34 36 33
  • 57.77 (n)
OneToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F02992g 33
  • 55.38 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G26680 33
  • 57.47 (n)
rice
(Oryza sativa)
Liliopsida Os05g0540100 33
  • 56.09 (n)
Os.4469 33
barley
(Hordeum vulgare)
Liliopsida Hv.6646 33
corn
(Zea mays)
Liliopsida Zm.3072 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7233 34
  • 63 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU10776 33
  • 59.83 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rad2 33
  • 55.79 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2215 33
Species where no ortholog for FEN1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for FEN1 Gene

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

Paralogs for FEN1 Gene

Paralogs for FEN1 Gene

(1) SIMAP similar genes for FEN1 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for FEN1 Gene

genes like me logo Genes that share paralogs with FEN1: view

Variants for FEN1 Gene

Sequence variations from dbSNP and Humsavar for FEN1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000006148 -- 61,796,864(+) A/C 3_prime_UTR_variant
rs1001813317 -- 61,794,721(+) A/C intron_variant
rs1002391793 -- 61,794,793(+) T/C intron_variant
rs1002676540 -- 61,792,969(+) C/A 5_prime_UTR_variant
rs1002728911 -- 61,793,307(+) CCTACCT/CCT intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FEN1 Gene

Variant ID Type Subtype PubMed ID
nsv343 CNV insertion 18451855
nsv528697 CNV loss 19592680
nsv975935 CNV duplication 23825009

Variation tolerance for FEN1 Gene

Residual Variation Intolerance Score: 10.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.24; 40.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FEN1 Gene

Human Gene Mutation Database (HGMD)
FEN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FEN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FEN1 Gene

Disorders for FEN1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for FEN1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search FEN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for FEN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FEN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FEN1 Gene

Publications for FEN1 Gene

  1. Sequence of human FEN-1, a structure-specific endonuclease, and chromosomal localization of the gene (FEN1) in mouse and human. (PMID: 7774922) Hiraoka LR … Hsieh CL (Genomics 1995) 2 3 4 22 58
  2. Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk. (PMID: 19618370) Yang M … Lin D (Human mutation 2009) 3 22 44 58
  3. Studies with the human cohesin establishment factor, ChlR1. Association of ChlR1 with Ctf18-RFC and Fen1. (PMID: 18499658) Farina A … Hurwitz J (The Journal of biological chemistry 2008) 3 4 22 58
  4. Associations of DNase IV polymorphisms with autoantibodies in patients with systemic lupus erythematosus. (PMID: 18417526) Kim I … Bae SC (Rheumatology (Oxford, England) 2008) 3 22 44 58
  5. Structural basis for recruitment of human flap endonuclease 1 to PCNA. (PMID: 15616578) Sakurai S … Hakoshima T (The EMBO journal 2005) 3 4 22 58

Products for FEN1 Gene

  • Addgene plasmids for FEN1

Sources for FEN1 Gene

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