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Aliases for RIF1 Gene

Aliases for RIF1 Gene

  • Replication Timing Regulatory Factor 1 2 3 5
  • RAP1 Interacting Factor Homolog (Yeast) 2
  • Rap1-Interacting Factor 1 Homolog 4

External Ids for RIF1 Gene

Previous GeneCards Identifiers for RIF1 Gene

  • GC01M110591
  • GC01M110788
  • GC01M111201
  • GC02P152093
  • GC02P151974
  • GC02P152266
  • GC02P144162

Summaries for RIF1 Gene

Entrez Gene Summary for RIF1 Gene

  • This gene encodes a protein that shares homology with the yeast teleomere binding protein, Rap1 interacting factor 1. This protein localizes to aberrant telomeres may be involved in DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

GeneCards Summary for RIF1 Gene

RIF1 (Replication Timing Regulatory Factor 1) is a Protein Coding gene. Diseases associated with RIF1 include Candida Glabrata. Among its related pathways are DNA Damage and Signaling pathways regulating pluripotency of stem cells. GO annotations related to this gene include binding.

UniProtKB/Swiss-Prot for RIF1 Gene

  • Key regulator of TP53BP1 that plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage: acts by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs (PubMed:15342490, PubMed:28241136). In response to DNA damage, interacts with ATM-phosphorylated TP53BP1 (PubMed:23333306, PubMed:28241136). Interaction with TP53BP1 leads to dissociate the interaction between NUDT16L1/TIRR and TP53BP1, thereby unmasking the tandem Tudor-like domain of TP53BP1 and allowing recruitment to DNA DSBs (PubMed:28241136). Once recruited to DSBs, RIF1 and TP53BP1 act by promoting NHEJ-mediated repair of DSBs (PubMed:23333306). In the same time, RIF1 and TP53BP1 specifically counteract the function of BRCA1 by blocking DSBs resection via homologous recombination (HR) during G1 phase (PubMed:23333306). Also required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (By similarity). Promotes NHEJ of dysfunctional telomeres (By similarity).

Gene Wiki entry for RIF1 Gene

Additional gene information for RIF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RIF1 Gene

Genomics for RIF1 Gene

Regulatory Elements for RIF1 Gene

Enhancers for RIF1 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
GH02H151408 1.2 ENCODE 46.5 +0.1 66 3.2 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 RIF1 STAM2 RPL30P2 RBM43 PIR42149
GH02H151287 1.4 FANTOM5 ENCODE 37.7 -120.2 -120161 3.5 PKNOX1 ARNT SIN3A ARID4B DMAP1 YY1 CBX5 ZNF207 FOS MXD4 TNFAIP6 RIF1 NMI STAM2 RPL30P2 RBM43
GH02H151788 1 dbSUPER 31.8 +380.1 380050 2.3 PKNOX1 ATF1 ARNT ZFP64 TCF12 ZNF766 GATA2 ATF7 ZNF202 ZC3H11A STAM2 PRPF40A RIF1 RPL30P2 NEB LOC101929356
GH02H152042 0.8 ENCODE 35.7 +633.1 633099 0.2 ZNF766 ELK1 EGR1 CAVIN1 ZBTB11 MEF2D ZNF589 NR2C1 FOXJ2 KLF1 RIF1 STAM2 PRPF40A RPL30P2 ENSG00000225214 ENSG00000283228
GH02H151780 1 dbSUPER 20.4 +372.6 372551 3 HDGF PKNOX1 ATF1 ARNT YBX1 TCF12 ZNF766 GATA2 ELK1 ATF7 RIF1 NEB STAM2 PRPF40A RPL30P2 LOC101929356
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RIF1 on UCSC Golden Path with GeneCards custom track

Promoters for RIF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000124626 517 2001 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF143

Genomic Locations for RIF1 Gene

Genomic Locations for RIF1 Gene
chr2:151,409,883-151,534,202
(GRCh38/hg38)
Size:
124,320 bases
Orientation:
Plus strand
chr2:152,266,397-152,364,527
(GRCh37/hg19)

Genomic View for RIF1 Gene

Genes around RIF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RIF1 Gene

Proteins for RIF1 Gene

  • Protein details for RIF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5UIP0-RIF1_HUMAN
    Recommended name:
    Telomere-associated protein RIF1
    Protein Accession:
    Q5UIP0
    Secondary Accessions:
    • A6NC27
    • C9JBR1
    • Q5H9R3
    • Q5UIP2
    • Q66YK6
    • Q6PRU2
    • Q8TE94
    • Q99772
    • Q9H830
    • Q9H9B9
    • Q9NVP5
    • Q9Y4R4

    Protein attributes for RIF1 Gene

    Size:
    2472 amino acids
    Molecular mass:
    274466 Da
    Quaternary structure:
    • Interacts with TP53BP1 (when phosphorylated by ATM) (PubMed:23333306, PubMed:28241136). May interact with TRF2 (By similarity).
    SequenceCaution:
    • Sequence=BAA91705.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14313.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14792.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB85058.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI45961.1; Type=Frameshift; Positions=470; Evidence={ECO:0000305};

    Alternative splice isoforms for RIF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RIF1 Gene

Post-translational modifications for RIF1 Gene

  • Ubiquitination at isoforms=2125, Lys198, Lys251, Lys702, and Lys2328
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RIF1 Gene

Domains & Families for RIF1 Gene

Gene Families for RIF1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RIF1 Gene

Suggested Antigen Peptide Sequences for RIF1 Gene

Graphical View of Domain Structure for InterPro Entry

Q5UIP0

UniProtKB/Swiss-Prot:

RIF1_HUMAN :
  • Belongs to the RIF1 family.
Family:
  • Belongs to the RIF1 family.
genes like me logo Genes that share domains with RIF1: view

Function for RIF1 Gene

Molecular function for RIF1 Gene

UniProtKB/Swiss-Prot Function:
Key regulator of TP53BP1 that plays a key role in the repair of double-strand DNA breaks (DSBs) in response to DNA damage: acts by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs (PubMed:15342490, PubMed:28241136). In response to DNA damage, interacts with ATM-phosphorylated TP53BP1 (PubMed:23333306, PubMed:28241136). Interaction with TP53BP1 leads to dissociate the interaction between NUDT16L1/TIRR and TP53BP1, thereby unmasking the tandem Tudor-like domain of TP53BP1 and allowing recruitment to DNA DSBs (PubMed:28241136). Once recruited to DSBs, RIF1 and TP53BP1 act by promoting NHEJ-mediated repair of DSBs (PubMed:23333306). In the same time, RIF1 and TP53BP1 specifically counteract the function of BRCA1 by blocking DSBs resection via homologous recombination (HR) during G1 phase (PubMed:23333306). Also required for immunoglobulin class-switch recombination (CSR) during antibody genesis, a process that involves the generation of DNA DSBs (By similarity). Promotes NHEJ of dysfunctional telomeres (By similarity).

Phenotypes From GWAS Catalog for RIF1 Gene

Gene Ontology (GO) - Molecular Function for RIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22321011
genes like me logo Genes that share ontologies with RIF1: view
genes like me logo Genes that share phenotypes with RIF1: view

Animal Models for RIF1 Gene

MGI Knock Outs for RIF1:

Clone Products

  • Addgene plasmids for RIF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RIF1 Gene

Localization for RIF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIF1 Gene

Nucleus. Chromosome. Chromosome, telomere. Cytoplasm, cytoskeleton, spindle. Note=Following interaction with TP53BP1, recruited to sites of DNA damage, such as DSBs (By similarity). Exhibits ATM- and TP53BP1-dependent localization to uncapped or aberrant telomeres and to DNA double strand breaks (DSBs) (PubMed:15342490). Does not associate with normal telomere structures (PubMed:15342490, PubMed:15583028). Localizes to microtubules of the midzone of the mitotic spindle during anaphase, and to condensed chromosomes in telophase (PubMed:15583028). {ECO:0000250 UniProtKB:Q6PR54, ECO:0000269 PubMed:15342490, ECO:0000269 PubMed:15583028}.

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 RIF1 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytoskeleton 4
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleus (3)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region IEA --
GO:0000790 nuclear chromatin ISS --
GO:0000793 condensed chromosome IDA 15583028
GO:0001939 female pronucleus IEA --
GO:0001940 male pronucleus IEA --
genes like me logo Genes that share ontologies with RIF1: view

Pathways & Interactions for RIF1 Gene

genes like me logo Genes that share pathways with RIF1: view

Pathways by source for RIF1 Gene

1 Cell Signaling Technology pathway for RIF1 Gene
1 BioSystems pathway for RIF1 Gene

Gene Ontology (GO) - Biological Process for RIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0000723 telomere maintenance ISS --
GO:0006281 DNA repair IEA --
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
GO:0006348 chromatin silencing at telomere ISS --
genes like me logo Genes that share ontologies with RIF1: view

No data available for SIGNOR curated interactions for RIF1 Gene

Drugs & Compounds for RIF1 Gene

No Compound Related Data Available

Transcripts for RIF1 Gene

Unigene Clusters for RIF1 Gene

RAP1 interacting factor homolog (yeast):
Representative Sequences:

Clone Products

  • Addgene plasmids for RIF1

Alternative Splicing Database (ASD) splice patterns (SP) for RIF1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^
SP1: - -
SP2:
SP3:
SP4:
SP5:

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28a · 28b
SP1:
SP2:
SP3: -
SP4:
SP5:

Relevant External Links for RIF1 Gene

GeneLoc Exon Structure for
RIF1
ECgene alternative splicing isoforms for
RIF1

Expression for RIF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RIF1 Gene

Protein differential expression in normal tissues from HIPED for RIF1 Gene

This gene is overexpressed in Nasal epithelium (41.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RIF1 Gene



NURSA nuclear receptor signaling pathways regulating expression of RIF1 Gene:

RIF1

SOURCE GeneReport for Unigene cluster for RIF1 Gene:

Hs.655671

mRNA Expression by UniProt/SwissProt for RIF1 Gene:

Q5UIP0-RIF1_HUMAN
Tissue specificity: Highly expressed in testis.

Evidence on tissue expression from TISSUES for RIF1 Gene

  • Nervous system(4.6)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with RIF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIF1 Gene

Orthologs for RIF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RIF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RIF1 33 34
  • 99.45 (n)
dog
(Canis familiaris)
Mammalia RIF1 33 34
  • 86.16 (n)
cow
(Bos Taurus)
Mammalia RIF1 33 34
  • 86.12 (n)
mouse
(Mus musculus)
Mammalia Rif1 33 16 34
  • 79.99 (n)
rat
(Rattus norvegicus)
Mammalia Rif1 33
  • 79.61 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 73 (a)
OneToMany
-- 34
  • 54 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia RIF1 34
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves RIF1 33 34
  • 64.07 (n)
lizard
(Anolis carolinensis)
Reptilia RIF1 34
  • 47 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii rif1 34
  • 38 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG30085 34
  • 21 (a)
OneToOne
Species where no ortholog for RIF1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RIF1 Gene

ENSEMBL:
Gene Tree for RIF1 (if available)
TreeFam:
Gene Tree for RIF1 (if available)

Paralogs for RIF1 Gene

No data available for Paralogs for RIF1 Gene

Variants for RIF1 Gene

Sequence variations from dbSNP and Humsavar for RIF1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_035983 A breast cancer sample
VAR_035984 A breast cancer sample
rs1057515573 Pathogenic 151,519,019(-) GACAT(-/G)AAGGA intron-variant, reference, frameshift-variant
rs1057515574 Pathogenic 151,508,057(-) TGTTT(-/GTTT)TGGAC intron-variant, reference, frameshift-variant
rs1057515575 Pathogenic 151,524,310(-) GCCAG(C/G)TAATG intron-variant, splice-donor-variant

Structural Variations from Database of Genomic Variants (DGV) for RIF1 Gene

Variant ID Type Subtype PubMed ID
nsv834418 CNV gain 17160897
nsv438374 CNV loss 16468122
nsv437298 CNV loss 16327808
nsv1012891 CNV gain 25217958
esv34659 CNV loss 17911159
esv2467988 CNV deletion 19546169
dgv4094n100 CNV gain 25217958

Variation tolerance for RIF1 Gene

Residual Variation Intolerance Score: 19.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.43; 63.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RIF1 Gene

Human Gene Mutation Database (HGMD)
RIF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIF1 Gene

Disorders for RIF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RIF1 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
candida glabrata
- elite association - COSMIC cancer census association via MalaCards
Search RIF1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RIF1

Genetic Association Database (GAD)
RIF1
Human Genome Epidemiology (HuGE) Navigator
RIF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RIF1
genes like me logo Genes that share disorders with RIF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RIF1 Gene

Publications for RIF1 Gene

  1. Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. (PMID: 15342490) Silverman J … de Lange T (Genes & development 2004) 2 3 4 22 60
  2. Human Rif1 protein binds aberrant telomeres and aligns along anaphase midzone microtubules. (PMID: 15583028) Xu L … Blackburn EH (The Journal of cell biology 2004) 3 4 22 60
  3. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. (PMID: 28241136) Drané P … Chowdhury D (Nature 2017) 3 4 60
  4. A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice. (PMID: 23333306) Escribano-Díaz C … Durocher D (Molecular cell 2013) 3 4 60
  5. Rif1 regulates the replication timing domains on the human genome. (PMID: 22850674) Yamazaki S … Masai H (The EMBO journal 2012) 2 3 60

Products for RIF1 Gene

Sources for RIF1 Gene

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