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Aliases for GEN1 Gene

Aliases for GEN1 Gene

  • GEN1, Holliday Junction 5' Flap Endonuclease 2
  • GEN1, Holliday Junction 5 Flap Endonuclease 2 3 5
  • Holliday Junction Resolvase 2 3
  • Gen Endonuclease Homolog 1 (Drosophila) 2
  • Flap Endonuclease GEN Homolog 1 3
  • Gen Endonuclease Homolog 1 3
  • EC 3.1.-.- 4
  • Gen 3

External Ids for GEN1 Gene

Previous GeneCards Identifiers for GEN1 Gene

  • GC02P017798
  • GC02P017935

Summaries for GEN1 Gene

Entrez Gene Summary for GEN1 Gene

  • This gene encodes a member of the Rad2/xeroderma pigmentosum group G nuclease family, whose members are characterized by N-terminal and internal xeroderma pigmentosum group G nuclease domains followed by helix-hairpin-helix domains and disordered C-terminal domains. The protein encoded by this gene is involved in resolution of Holliday junctions, which are intermediate four-way structures that covalently link DNA during homologous recombination and double-strand break repair. The protein resolves Holliday junctions by creating dual incisions across the junction to produce nicked duplex products that can be ligated. In addition, this protein has been found to localize to centrosomes where it has been implicated in regulation of centrosome integrity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

GeneCards Summary for GEN1 Gene

GEN1 (GEN1, Holliday Junction 5' Flap Endonuclease) is a Protein Coding gene. Diseases associated with GEN1 include Xeroderma Pigmentosum, Group G and Tick-Borne Relapsing Fever. Among its related pathways are Homologous DNA Pairing and Strand Exchange and Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA). GO annotations related to this gene include nuclease activity and crossover junction endodeoxyribonuclease activity. An important paralog of this gene is FEN1.

UniProtKB/Swiss-Prot for GEN1 Gene

  • Endonuclease which resolves Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated. Four-way DNA intermediates, also known as Holliday junctions, are formed during homologous recombination and DNA repair, and their resolution is necessary for proper chromosome segregation.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GEN1 Gene

Genomics for GEN1 Gene

Regulatory Elements for GEN1 Gene

Enhancers for GEN1 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
GH02F017747 0.9 Ensembl ENCODE 28.9 -5.1 -5137 1.4 PKNOX1 RFX1 CHD1 POU5F1 MNT MAFK GEN1 PIR36041
GH02F017756 0.4 ENCODE 28.7 +3.9 3865 2.2 ELF3 ARID4B RAD21 FOS MIXL1 THAP11 CEBPB KAT8 ETV4 STAT3 GEN1 GC02M017752
GH02F017798 0.8 Ensembl ENCODE 28.7 +46.3 46329 3.4 SOX13 CTCF TBP MXI1 SAP130 WRNIP1 ARID4B MAX FEZF1 EBF1 GEN1 SMC6 GC02M017752
GH02F017786 0.3 FANTOM5 28.3 +33.0 32952 0.0 GEN1 MSGN1 SMC6 GC02M017752
GH02F017803 0.6 Ensembl ENCODE 27.8 +51.4 51363 2.8 MTA2 ZNF133 TRIM22 BMI1 EBF1 TBX21 EP300 RAD51 EED IKZF1 GEN1 VSNL1 LOC105373449 MSGN1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around GEN1 on UCSC Golden Path with GeneCards custom track

Promoters for GEN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000011603 373 3601 PKNOX1 WRNIP1 ZFP64 ARID4B SIN3A ZNF48 SLC30A9 GLIS2 ELK1 FOS

Genomic Location for GEN1 Gene

Chromosome:
2
Start:
17,753,627 bp from pter
End:
17,788,941 bp from pter
Size:
35,315 bases
Orientation:
Plus strand

Genomic View for GEN1 Gene

Genes around GEN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GEN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GEN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GEN1 Gene

Proteins for GEN1 Gene

  • Protein details for GEN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q17RS7-GEN_HUMAN
    Recommended name:
    Flap endonuclease GEN homolog 1
    Protein Accession:
    Q17RS7
    Secondary Accessions:
    • Q17RS9
    • Q6ZN37

    Protein attributes for GEN1 Gene

    Size:
    908 amino acids
    Molecular mass:
    102884 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for GEN1 Gene

neXtProt entry for GEN1 Gene

Post-translational modifications for GEN1 Gene

  • Ubiquitination at Lys 230
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GEN1 Gene

Domains & Families for GEN1 Gene

Suggested Antigen Peptide Sequences for GEN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q17RS7

UniProtKB/Swiss-Prot:

GEN_HUMAN :
  • Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.
Family:
  • Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.
genes like me logo Genes that share domains with GEN1: view

No data available for Gene Families for GEN1 Gene

Function for GEN1 Gene

Molecular function for GEN1 Gene

UniProtKB/Swiss-Prot Function:
Endonuclease which resolves Holliday junctions by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated. Four-way DNA intermediates, also known as Holliday junctions, are formed during homologous recombination and DNA repair, and their resolution is necessary for proper chromosome segregation.

Enzyme Numbers (IUBMB) for GEN1 Gene

Gene Ontology (GO) - Molecular Function for GEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003824 catalytic activity IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0004520 endodeoxyribonuclease activity TAS --
genes like me logo Genes that share ontologies with GEN1: view
genes like me logo Genes that share phenotypes with GEN1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for GEN1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GEN1 Gene

Localization for GEN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GEN1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GEN1 Gene COMPARTMENTS Subcellular localization image for GEN1 gene
Compartment Confidence
cytoskeleton 5
extracellular 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for GEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005813 centrosome IDA 23166748
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with GEN1: view

Pathways & Interactions for GEN1 Gene

genes like me logo Genes that share pathways with GEN1: view

Gene Ontology (GO) - Biological Process for GEN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IMP 23166748
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0010824 regulation of centrosome duplication IMP 23108668
GO:0071139 resolution of recombination intermediates IMP 24080495
genes like me logo Genes that share ontologies with GEN1: view

No data available for SIGNOR curated interactions for GEN1 Gene

Drugs & Compounds for GEN1 Gene

(1) Drugs for GEN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Nutra 0
genes like me logo Genes that share compounds with GEN1: view

Transcripts for GEN1 Gene

Unigene Clusters for GEN1 Gene

Gen endonuclease homolog 1 (Drosophila):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GEN1 Gene

No ASD Table

Relevant External Links for GEN1 Gene

GeneLoc Exon Structure for
GEN1
ECgene alternative splicing isoforms for
GEN1

Expression for GEN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GEN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for GEN1 Gene

This gene is overexpressed in Esophagus (56.1) and Salivary gland (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GEN1 Gene



Protein tissue co-expression partners for GEN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of GEN1 Gene:

GEN1

SOURCE GeneReport for Unigene cluster for GEN1 Gene:

Hs.467793
genes like me logo Genes that share expression patterns with GEN1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for GEN1 Gene

Orthologs for GEN1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GEN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GEN1 34 35
  • 99.6 (n)
dog
(Canis familiaris)
Mammalia GEN1 34 35
  • 86.59 (n)
cow
(Bos Taurus)
Mammalia GEN1 34 35
  • 85.03 (n)
rat
(Rattus norvegicus)
Mammalia Gen1 34
  • 79.86 (n)
mouse
(Mus musculus)
Mammalia Gen1 34 16 35
  • 79.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GEN1 35
  • 45 (a)
OneToOne
chicken
(Gallus gallus)
Aves GEN1 34 35
  • 58.58 (n)
lizard
(Anolis carolinensis)
Reptilia GEN1 35
  • 41 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii GEN1 35
  • 26 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Gen 35
  • 24 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea crn-1 35
  • 23 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RAD27 35
  • 21 (a)
OneToMany
YEN1 37
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G01880 34
  • 46.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 45 (a)
OneToOne
Species where no ortholog for GEN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for GEN1 Gene

ENSEMBL:
Gene Tree for GEN1 (if available)
TreeFam:
Gene Tree for GEN1 (if available)

Paralogs for GEN1 Gene

Paralogs for GEN1 Gene

(2) SIMAP similar genes for GEN1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with GEN1: view

Variants for GEN1 Gene

Sequence variations from dbSNP and Humsavar for GEN1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_037847 A breast cancer sample
rs144389157 Likely benign 17,757,644(+) ATCTG(A/T)AGGAA intron-variant
rs145421265 Likely benign 17,774,596(+) AACAC(A/G)TAGTA intron-variant
rs186660424 Likely benign 17,771,175(+) TTTTT(A/T)AAAAC intron-variant
rs190514572 Likely benign 17,758,468(+) AATAT(C/T)TGTAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GEN1 Gene

Variant ID Type Subtype PubMed ID
dgv1872n106 CNV deletion 24896259
esv2061440 CNV deletion 18987734
esv2719750 CNV deletion 23290073
esv2759031 CNV gain 17122850
esv3589949 CNV gain 21293372
esv3891603 CNV gain 25118596
nsv1135080 CNV deletion 24896259
nsv522195 CNV loss 19592680
nsv997502 CNV gain 25217958

Variation tolerance for GEN1 Gene

Residual Variation Intolerance Score: 65.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.69; 82.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GEN1 Gene

Human Gene Mutation Database (HGMD)
GEN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GEN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GEN1 Gene

Disorders for GEN1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for GEN1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
xeroderma pigmentosum, group g
  • xeroderma pigmentosum, group g/cockayne syndrome
tick-borne relapsing fever
  • relapsing fever, tick-borne
- elite association - COSMIC cancer census association via MalaCards
Search GEN1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for GEN1

Genetic Association Database (GAD)
GEN1
Human Genome Epidemiology (HuGE) Navigator
GEN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GEN1
genes like me logo Genes that share disorders with GEN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GEN1 Gene

Publications for GEN1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Mutation and association analysis of GEN1 in breast cancer susceptibility. (PMID: 20512659) Turnbull C. … Rahman N. (Breast Cancer Res. Treat. 2010) 3 46 64
  3. Gamma-radiation sensitivity and polymorphisms in RAD51L1 modulate glioma risk. (PMID: 20610542) Liu Y. … Bondy M.L. (Carcinogenesis 2010) 3 46 64
  4. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F. … Nebel A. (Mutat. Res. 2010) 3 46 64
  5. Identification of Holliday junction resolvases from humans and yeast. (PMID: 19020614) Ip S.C. … West S.C. (Nature 2008) 3 4 64

Products for GEN1 Gene

Sources for GEN1 Gene

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