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

Gene ID: 295602, updated on 27-Apr-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
Ensembl: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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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
  • 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
part_of 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 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

  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
    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

    UniProtKB/TrEMBL
    A0A8I5ZP39
    Related
    ENSRNOP00000079724.1
    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
    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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