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FEN1 flap structure-specific endonuclease 1 [ Homo sapiens (human) ]

Gene ID: 2237, updated on 4-Jan-2025

Summary

Official Symbol
FEN1provided by HGNC
Official Full Name
flap structure-specific endonuclease 1provided by HGNC
Primary source
HGNC:HGNC:3650
See related
Ensembl:ENSG00000168496 MIM:600393; AllianceGenome:HGNC:3650
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MF1; RAD2; FEN-1
Summary
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]
Expression
Broad expression in lymph node (RPKM 16.0), bone marrow (RPKM 13.0) and 24 other tissues See more
Orthologs
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Genomic context

See FEN1 in Genome Data Viewer
Location:
11q12.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61792911..61797238)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61781828..61786155)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61560383..61564710)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:61523524-61524723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61524877-61525520 Neighboring gene MYRF antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61528511-61529267 Neighboring gene myelin regulatory factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61535574-61536150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61536151-61536726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61546818-61547486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61548157-61548825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61552558-61553302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61553303-61554047 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:61559319-61560296 and GRCh37_chr11:61560297-61561272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61562818-61563318 Neighboring gene transmembrane protein 258 Neighboring gene microRNA 611 Neighboring gene fatty acid desaturase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3399 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61582779-61583676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3401 Neighboring gene uncharacterized LOC124902680 Neighboring gene microRNA 1908 Neighboring gene fatty acid desaturase 2

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
EBI GWAS Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
EBI GWAS Catalog
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
EBI GWAS Catalog
Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population.
EBI GWAS Catalog
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
integrase gag-pol FEN-1 is stimulated by HIV-1 Integrase and is hypothesized to play a role in the processing of HIV-1 integration intermediates PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-3' exonuclease activity  
enables 5'-3' exonuclease activity PubMed 
enables 5'-flap endonuclease activity  
enables 5'-flap endonuclease activity PubMed 
enables 5'-flap endonuclease activity PubMed 
enables 5'-flap endonuclease activity  
enables DNA binding PubMed 
enables RNA-DNA hybrid ribonuclease activity  
enables RNA-DNA hybrid ribonuclease activity PubMed 
enables damaged DNA binding PubMed 
enables double-stranded DNA binding PubMed 
enables double-stranded DNA exodeoxyribonuclease activity PubMed 
enables endonuclease activity PubMed 
enables exonuclease activity PubMed 
enables flap endonuclease activity PubMed 
enables magnesium ion binding  
enables manganese ion binding  
enables protein binding PubMed 
Component Evidence Code Pubs
located_in chromosome, telomeric region PubMed 
colocalizes_with chromosome, telomeric region PubMed 
located_in membrane PubMed 
located_in mitochondrion PubMed 
located_in nucleolus  
located_in nucleoplasm  
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 
part_of protein-containing complex PubMed 

General protein information

Preferred Names
flap endonuclease 1
Names
DNase IV
maturation factor-1
NP_004102.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_004111.6NP_004102.1  flap endonuclease 1

    See identical proteins and their annotated locations for NP_004102.1

    Status: REVIEWED

    Source sequence(s)
    BC000323, BP244711
    Consensus CDS
    CCDS8010.1
    UniProtKB/Swiss-Prot
    P39748
    UniProtKB/TrEMBL
    B4DWZ4, Q6FHX6
    Related
    ENSP00000305480.2, ENST00000305885.3
    Conserved Domains (1) summary
    PTZ00217
    Location:1373
    PTZ00217; flap endonuclease-1; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    61792911..61797238
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    61781828..61786155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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