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Aliases for FEN1 Gene

Aliases for FEN1 Gene

  • Flap Structure-Specific Endonuclease 1 2 3 4
  • DNase IV 2 3 4
  • Maturation Factor-1 2 3
  • Maturation Factor 1 3 4
  • FEN-1 3 4
  • RAD2 3 4
  • MF1 3 4
  • Flap Endonuclease 1 3
  • 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 werner syndrome. Among its related pathways are Disease and Cell Cycle, Mitotic. 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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FEN1 Gene

Genomics for FEN1 Gene

Regulatory Elements for FEN1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for FEN1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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
    Secondary Accessions:

    Protein attributes for FEN1 Gene

    Size:
    380 amino acids
    Molecular mass:
    42593 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Note=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.;
    Quaternary structure:
    • 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.

    Three dimensional structures from OCA and Proteopedia for FEN1 Gene

    Alternative splice isoforms for FEN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FEN1 Gene

Proteomics data for FEN1 Gene at MOPED

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, Lys171, Lys254, and Lys345
  • Modification sites at PhosphoSitePlus

Other Protein References for FEN1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for FEN1 (FEN1)

No data available for DME Specific Peptides for FEN1 Gene

Domains for FEN1 Gene

Suggested Antigen Peptide Sequences for FEN1 Gene

Graphical View of Domain Structure for InterPro Entry

P39748

UniProtKB/Swiss-Prot:

FEN1_HUMAN :
  • P39748
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:0000287 magnesium ion binding IEA --
GO:0003677 DNA binding IMP 11986308
GO:0003684 damaged DNA binding TAS 8007985
GO:0003690 double-stranded DNA binding TAS 8131753
GO:0003824 catalytic activity --
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

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for FEN1

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting 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
Jensen Localization Image for FEN1 Gene COMPARTMENTS Subcellular localization image for FEN1 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2
chloroplast 1

Gene Ontology (GO) - Cellular Components for FEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005739 mitochondrion IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with FEN1: view

Pathways 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
2 Cell Signaling Technology pathways for FEN1 Gene
24 Reactome pathways for FEN1 Gene

PCR Array Products

Gene Ontology (GO) - Biological Process for FEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle TAS --
GO:0000722 telomere maintenance via recombination TAS --
GO:0000723 telomere maintenance TAS --
GO:0000737 DNA catabolic process, endonucleolytic --
GO:0000738 DNA catabolic process, exonucleolytic --
genes like me logo Genes that share ontologies with FEN1: view

Compounds for FEN1 Gene

(13) Novoseek inferred chemical compound relationships for FEN1 Gene

Compound -log(P) Hits PubMed IDs
methylmethanesulfonate 60.5 3
oligonucleotide 28 1
alanine 4.38 3
calcium 3.01 2
lipid 2.42 1
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:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for FEN1

Primer Products

Flow Cytometry Products

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 for FEN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for FEN1 Gene

SOURCE GeneReport for Unigene cluster for FEN1 Gene Hs.409065

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

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 99.91 (n)
  • 100 (a)
FEN1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia FEN1 35
  • 91.84 (n)
  • 97.89 (a)
FEN1 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FEN1 35
  • 93.77 (n)
  • 98.16 (a)
FEN1 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Fen1 35
  • 90.26 (n)
  • 96.58 (a)
Fen1 16
Fen1 36
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FEN1 36
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia FEN1 36
  • 67 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Fen1 35
  • 89.56 (n)
  • 95.79 (a)
chicken
(Gallus gallus)
Aves FEN1 35
  • 79.91 (n)
  • 84.47 (a)
FEN1 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FEN1 36
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia fen1-B 35
tropical clawed frog
(Silurana tropicalis)
Amphibia fen1 35
  • 74.39 (n)
  • 80.53 (a)
Str.3319 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.569 35
zebrafish
(Danio rerio)
Actinopterygii fen1 35
  • 72.08 (n)
  • 79.82 (a)
fen1 36
  • 76 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011448 35
  • 64.39 (n)
  • 63.68 (a)
fruit fly
(Drosophila melanogaster)
Insecta Fen1 35
  • 62.89 (n)
  • 63.68 (a)
Fen1 36
  • 62 (a)
ManyToMany
Fen1 37
  • 65 (a)
worm
(Caenorhabditis elegans)
Secernentea crn-1 35
  • 61.9 (n)
  • 62.96 (a)
crn-1 36
  • 60 (a)
OneToMany
Y47G6A.8 37
  • 64 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABL052C 35
  • 60.42 (n)
  • 58.68 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD27 35
  • 57.77 (n)
  • 59.67 (a)
RAD27 36
  • 58 (a)
OneToMany
RAD27 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F02992g 35
  • 55.38 (n)
  • 56.45 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G26680 35
  • 57.47 (n)
  • 55.7 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.6646 35
corn
(Zea mays)
Liliopsida Zm.3072 35
rice
(Oryza sativa)
Liliopsida Os.4469 35
Os05g0540100 35
  • 56.09 (n)
  • 53.6 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU10776 35
  • 59.83 (n)
  • 56.36 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rad2 35
  • 55.79 (n)
  • 55.7 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2215 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7233 36
  • 63 (a)
OneToOne
Species with no ortholog for FEN1:
  • 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

Selected 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 MAF
rs393487 -- 61,795,333(+) CTTTC(C/T)TTTTT intron-variant
rs445606 -- 61,797,557(+) ACTAC(A/C)TCATA downstream-variant-500B
rs695868 -- 61,796,534(+) TCACC(C/G)CAGAA utr-variant-3-prime
rs695869 -- 61,796,587(+) CTTCA(C/G/T)GGGGT utr-variant-3-prime
rs1803573 -- 61,796,432(+) AAGGA(G/T)CCAGA reference, missense

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

Variant ID Type Subtype PubMed ID
dgv1152n71 CNV Loss 21882294
nsv528697 CNV Loss 19592680
dgv1153n71 CNV Loss 21882294
nsv343 CNV Insertion 18451855

Relevant External Links for FEN1 Gene

HapMap Linkage Disequilibrium report
FEN1
Human Gene Mutation Database (HGMD)
FEN1

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

Disorders for FEN1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (2) Diseases for FEN1 Gene including...

Search for FEN1 Gene in MalaCards »

(2) University of Copenhagen DISEASES for FEN1 Gene

(15) Novoseek inferred disease relationships for FEN1 Gene

Disease -log(P) Hits PubMed IDs
werner syndrome 68.2 3
bloom syndrome 59.5 2
macular dystrophy, vitelliform 52.3 1
sezary syndrome 33.3 2
xeroderma pigmentosum 29.2 2

Relevant External Links for FEN1

Genetic Association Database (GAD)
FEN1
Human Genome Epidemiology (HuGE) Navigator
FEN1
genes like me logo Genes that share disorders with FEN1: view

No data available for UniProtKB/Swiss-Prot 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 23
  2. 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. (PMID: 8007985) Murray J.M. … Watts F.Z. (Mol. Cell. Biol. 1994) 3 4 23
  3. Essential amino acids for substrate binding and catalysis of human flap endonuclease 1. (PMID: 8621570) Shen B. … Park M.S. (J. Biol. Chem. 1996) 3 4 23
  4. 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. (PMID: 9305916) Gary R. … Park M.S. (J. Biol. Chem. 1997) 3 4 23
  5. The "flap" endonuclease gene FEN1 is excluded as a candidate gene implicated in the CAG repeat expansion underlying Huntington disease. (PMID: 11260214) Otto C.J. … Andrew S.E. (Clin. Genet. 2001) 3 23 48

Products for FEN1 Gene

  • Addgene plasmids for FEN1

Sources for FEN1 Gene

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