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    Rif1 replication timing regulatory factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 295602, updated on 10-Oct-2024

    Summary

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    Official Symbol
    Rif1provided by RGD
    Official Full Name
    replication timing regulatory factor 1provided by RGD
    Primary source
    RGD:1562474
    See related
    EnsemblRapid:ENSRNOG00000054901 AllianceGenome:RGD:1562474
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1562474
    Summary
    Predicted to be involved in positive regulation of histone H3-K9 methylation; regulation of nucleobase-containing compound metabolic process; and telomere organization. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and stem cell population maintenance. Predicted to be located in several cellular components, including chromosome; nucleus; and spindle midzone. Predicted to be active in nucleus. Orthologous to human RIF1 (replication timing regulatory factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 168.9), Thymus (RPKM 148.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rif1 in Genome Data Viewer
    Location:
    3q12
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (56963840..57017106)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (36554689..36607961)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (37599540..37648818)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene lactate dehydrogenase A, pseudogene 11 Neighboring gene TNF alpha induced protein 6 Neighboring gene transfer RNA alanine (anticodon AGC) 59 Neighboring gene nebulin Neighboring gene uncharacterized LOC120101548

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Human Rif1 protein binds aberrant telomeres and aligns along anaphase midzone microtubules. Xu L, et al. J Cell Biol, 2004 Dec 6. PMID 15583028, Free PMC Article
    2. 53BP1 regulates DSB repair using Rif1 to control 5' end resection. Zimmermann M, et al. Science, 2013 Feb 8. PMID 23306437, Free PMC Article
    3. RIF1 is essential for 53BP1-dependent nonhomologous end joining and suppression of DNA double-strand break resection. Chapman JR, et al. Mol Cell, 2013 Mar 7. PMID 23333305, Free PMC Article
    4. Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching. Di Virgilio M, et al. Science, 2013 Feb 8. PMID 23306439, Free PMC Article
    5. Identification and characterisation of mRif1: a mouse telomere-associated protein highly expressed in germ cells and embryo-derived pluripotent stem cells. Adams IR, et al. Dev Dyn, 2004 Apr. PMID 15042697

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of isotype switching ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within somatic stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in subtelomeric heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in telomere maintenance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in telomere maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in telomere maintenance in response to DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in chromosome, telomeric repeat region IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in chromosome, telomeric repeat region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in condensed chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in female pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in male pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in spindle midzone ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    telomere-associated protein RIF1
    Names
    RAP1 interacting factor homolog

    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_001427744.1 → NP_001414673.1  telomere-associated protein RIF1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      Related
      ENSRNOP00000092899.1, ENSRNOT00000109963.2

    2. NM_001429786.1 → NP_001416715.1  telomere-associated protein RIF1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      56963840..57017106
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039106256.2 → XP_038962184.1  telomere-associated protein RIF1 isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZP39
      Related
      ENSRNOP00000075681.3, ENSRNOT00000090575.3
      Conserved Domains (2) summary
      cd14267
      Location:2216 → 2263
      Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
      pfam12231
      Location:29 → 361
      Rif1_N; Rap1-interacting factor 1 N terminal

    2. XM_039106257.2 → XP_038962185.1  telomere-associated protein RIF1 isoform X5

      Related
      ENSRNOP00000079724.2, ENSRNOT00000094327.2
      Conserved Domains (2) summary
      cd14267
      Location:2190 → 2237
      Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
      pfam12231
      Location:29 → 361
      Rif1_N; Rap1-interacting factor 1 N terminal

    3. XM_039106254.2 → XP_038962182.1  telomere-associated protein RIF1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AHX2
      Conserved Domains (2) summary
      cd14267
      Location:2257 → 2304
      Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
      pfam12231
      Location:29 → 361
      Rif1_N; Rap1-interacting factor 1 N terminal

    4. XM_039106255.2 → XP_038962183.1  telomere-associated protein RIF1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AHX2, A0A8I6AQP3
      Related
      ENSRNOP00000096382.1, ENSRNOT00000097817.2
      Conserved Domains (2) summary
      cd14267
      Location:2239 → 2286
      Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
      pfam12231
      Location:29 → 361
      Rif1_N; Rap1-interacting factor 1 N terminal

    5. XM_039106253.2 → XP_038962181.1  telomere-associated protein RIF1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AHX2
      Conserved Domains (2) summary
      cd14267
      Location:2265 → 2312
      Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
      pfam12231
      Location:29 → 361
      Rif1_N; Rap1-interacting factor 1 N terminal

    6. XM_063283247.1 → XP_063139317.1  telomere-associated protein RIF1 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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