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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 Vitelliform Macular Dystrophy and Xeroderma Pigmentosum, Group G. Among its related pathways are DNA Double-Strand Break Repair and Telomere C-strand (Lagging Strand) Synthesis. 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

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

Genomics for FEN1 Gene

Regulatory Elements for FEN1 Gene

Enhancers for FEN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G061731 1.2 Ensembl ENCODE 11.6 -59.7 -59669 2.1 PKNOX1 ATF1 ARNT ARID4B SIN3A BRCA1 ZNF48 ZNF143 DEK MXD4 DAGLA MYRF DKFZP434K028 FEN1 TMEM258 MIR611 SYT7 PIR41833
GH11G062024 2.2 FANTOM5 Ensembl ENCODE dbSUPER 5.7 +232.9 232928 2.9 MLX CREB3L1 AGO1 DMAP1 YY1 ZNF143 SP3 TBX21 MEF2D NBN FTH1 TTC9C HNRNPUL2 EEF1G BEST1 DAGLA FEN1 RPS2P37 GC11P062053
GH11G061819 1.1 Ensembl ENCODE 10.7 +27.9 27930 1.7 PKNOX1 EGR1 SCRT2 FOS EGR2 SP3 ZNF592 SP1 HNF4A PRDM1 FADS2 FEN1 MIR611 TMEM258 MIR1908 PIR43939
GH11G061869 1.8 FANTOM5 Ensembl ENCODE dbSUPER 5.1 +78.1 78071 2.4 HDGF PKNOX1 ARNT AGO1 ARID4B SIN3A ZNF2 ZBTB7B ZNF766 CBX5 FADS2 EEF1G FEN1 MIR6746 FADS1
GH11G062424 1.6 Ensembl ENCODE dbSUPER 5.2 +636.9 636922 10.5 HDGF FOXA2 PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A ZNF2 YY1 ASRGL1 LOC102723765 SCGB1A1 ENSG00000255126 ENSG00000250659 ENSG00000257058 AHNAK EEF1G ENSG00000255508 TUT1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FEN1 on UCSC Golden Path with GeneCards custom track

Promoters for FEN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040338 163 2001 HDGF PKNOX1 CREB3L1 ARNT AGO1 WRNIP1 ARID4B SIN3A DMAP1 ZBTB7B

Genomic Location for FEN1 Gene

Chromosome:
11
Start:
61,792,637 bp from pter
End:
61,797,244 bp from pter
Size:
4,608 bases
Orientation:
Plus strand

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 isoforms=8, Lys171, and Lys345
  • 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

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

No data available for Gene Families for FEN1 Gene

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

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:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for FEN1
  • Applied Biological Materials Clones 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

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 --
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

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:0000722 telomere maintenance via recombination TAS --
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 --
genes like me logo Genes that share ontologies with FEN1: view

Drugs & Compounds for FEN1 Gene

(6) Drugs for FEN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(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:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for FEN1
  • Applied Biological Materials Clones 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(2.1)
  • Heart(2.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with FEN1: view

Primer Products

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 35
  • 99.91 (n)
dog
(Canis familiaris)
Mammalia FEN1 34 35
  • 93.77 (n)
cow
(Bos Taurus)
Mammalia FEN1 34 35
  • 91.84 (n)
mouse
(Mus musculus)
Mammalia Fen1 34 16 35
  • 90.26 (n)
rat
(Rattus norvegicus)
Mammalia Fen1 34
  • 89.56 (n)
oppossum
(Monodelphis domestica)
Mammalia FEN1 35
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia FEN1 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves FEN1 34 35
  • 79.91 (n)
lizard
(Anolis carolinensis)
Reptilia FEN1 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fen1 34
  • 74.39 (n)
Str.3319 34
African clawed frog
(Xenopus laevis)
Amphibia fen1-B 34
zebrafish
(Danio rerio)
Actinopterygii fen1 34 35
  • 72.08 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.569 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011448 34
  • 64.39 (n)
fruit fly
(Drosophila melanogaster)
Insecta Fen1 36 34 35
  • 62.89 (n)
worm
(Caenorhabditis elegans)
Secernentea Y47G6A.8 36
  • 64 (a)
crn-1 34 35
  • 61.9 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABL052C 34
  • 60.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD27 34 35 37
  • 57.77 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F02992g 34
  • 55.38 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G26680 34
  • 57.47 (n)
rice
(Oryza sativa)
Liliopsida Os05g0540100 34
  • 56.09 (n)
Os.4469 34
barley
(Hordeum vulgare)
Liliopsida Hv.6646 34
corn
(Zea mays)
Liliopsida Zm.3072 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7233 35
  • 63 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU10776 34
  • 59.83 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rad2 34
  • 55.79 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2215 34
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 Sequence Context AA Info Type
rs1000006148 -- 61,796,864(+) GGCCA(A/C)CTGGT utr-variant-3-prime
rs1001813317 -- 61,794,721(+) GACTG(A/C)GTGGT intron-variant
rs1002391793 -- 61,794,793(+) TCTTA(C/T)GTGCT intron-variant
rs1002676540 -- 61,792,969(+) ACCGC(A/C)TGCCC upstream-variant-2KB, utr-variant-5-prime
rs1002728911 -- 61,793,307(+) TCCTG(-/CCTA)CCTGT intron-variant, upstream-variant-2KB

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)

Relevant External Links for FEN1 Gene

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

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

Disorders for FEN1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
vitelliform macular dystrophy
  • best disease
xeroderma pigmentosum, group g
  • xeroderma pigmentosum, group g/cockayne syndrome
werner syndrome
  • adult premature ageing syndrome
bloom syndrome
  • bloom-torre-machacek syndrome
best vitelliform macular dystrophy
  • vitelliform macular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search FEN1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for FEN1

Genetic Association Database (GAD)
FEN1
Human Genome Epidemiology (HuGE) Navigator
FEN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FEN1
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 L.R. … Hsieh C.-L. (Genomics 1995) 2 3 4 22 64
  2. Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk. (PMID: 19618370) Yang M. … Lin D. (Hum. Mutat. 2009) 3 22 46 64
  3. Studies with the human cohesin establishment factor, ChlR1. Association of ChlR1 with Ctf18-RFC and Fen1. (PMID: 18499658) Farina A. … Hurwitz J. (J. Biol. Chem. 2008) 3 4 22 64
  4. Associations of DNase IV polymorphisms with autoantibodies in patients with systemic lupus erythematosus. (PMID: 18417526) Kim I. … Bae S.C. (Rheumatology (Oxford) 2008) 3 22 46 64
  5. Structural basis for recruitment of human flap endonuclease 1 to PCNA. (PMID: 15616578) Sakurai S. … Hakoshima T. (EMBO J. 2005) 3 4 22 64

Products for FEN1 Gene

  • Addgene plasmids for FEN1

Sources for FEN1 Gene

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