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Rif1 replication timing regulatory factor 1 [ Mus musculus (house mouse) ]

Gene ID: 51869, updated on 22-Nov-2020

Summary

Official Symbol
Rif1provided by MGI
Official Full Name
replication timing regulatory factor 1provided by MGI
Primary source
MGI:MGI:1098622
See related
Ensembl:ENSMUSG00000036202
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
AU016181; AW549474; D2Ertd145; D2Ertd145e; 5730435J01Rik; 6530403D07Rik
Expression
Broad expression in CNS E11.5 (RPKM 5.0), cerebellum adult (RPKM 4.1) and 23 other tissues See more
Orthologs

Genomic context

See Rif1 in Genome Data Viewer
Location:
2 C1.1; 2 29.98 cM
Exon count:
35
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (51962725..52016781)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (52072815..52126769)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (51928357..51977901)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene N-myc (and STAT) interactor Neighboring gene tumor necrosis factor alpha induced protein 6 Neighboring gene nebulin Neighboring gene RIKEN cDNA 4930573O16 gene Neighboring gene predicted gene 13521

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA repair IEA
Inferred from Electronic Annotation
more info
 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cellular response to DNA damage stimulus ISO
Inferred from Sequence Orthology
more info
 
cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
PubMed 
chromatin silencing at telomere IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
 
positive regulation of histone H3-K9 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of isotype switching IMP
Inferred from Mutant Phenotype
more info
PubMed 
stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomere maintenance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomere maintenance in response to DNA damage ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromosome IEA
Inferred from Electronic Annotation
more info
 
chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
condensed chromosome ISO
Inferred from Sequence Orthology
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
female pronucleus IDA
Inferred from Direct Assay
more info
PubMed 
male pronucleus IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body ISO
Inferred from Sequence Orthology
more info
 
nuclear membrane ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane ISO
Inferred from Sequence Orthology
more info
 
site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
site of double-strand break IMP
Inferred from Mutant Phenotype
more info
PubMed 
site of double-strand break ISO
Inferred from Sequence Orthology
more info
 
spindle midzone ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
telomere-associated protein RIF1
Names
Rap1 interacting factor 1 homolog
mRif1
rap1-interacting factor 1 homolog

NCBI Reference Sequences (RefSeq)

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_001355414.1NP_001342343.1  telomere-associated protein RIF1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL844571, AL929138
    Consensus CDS
    CCDS50583.1
    Conserved Domains (1) summary
    pfam12231
    Location:25368
    Rif1_N; Rap1-interacting factor 1 N terminal
  2. NM_001355415.1NP_001342344.1  telomere-associated protein RIF1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL844571, AL929138
    Conserved Domains (1) summary
    pfam12231
    Location:25361
    Rif1_N; Rap1-interacting factor 1 N terminal
  3. NM_175238.6NP_780447.4  telomere-associated protein RIF1 isoform a

    See identical proteins and their annotated locations for NP_780447.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL844571, AL929138
    Consensus CDS
    CCDS50583.1
    UniProtKB/Swiss-Prot
    Q6PR54
    Related
    ENSMUSP00000108313.2, ENSMUST00000112693.9
    Conserved Domains (1) summary
    pfam12231
    Location:25368
    Rif1_N; Rap1-interacting factor 1 N terminal

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    51962725..52016781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162373.1XP_036018266.1  telomere-associated protein RIF1 isoform X4

  2. XM_011239136.3XP_011237438.1  telomere-associated protein RIF1 isoform X2

    UniProtKB/Swiss-Prot
    Q6PR54
    Conserved Domains (2) summary
    cd14267
    Location:22342281
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:25361
    Rif1_N; Rap1-interacting factor 1 N terminal
  3. XM_011239135.3XP_011237437.1  telomere-associated protein RIF1 isoform X1

    Conserved Domains (2) summary
    cd14267
    Location:22522299
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:25361
    Rif1_N; Rap1-interacting factor 1 N terminal
  4. XM_030251862.1XP_030107722.1  telomere-associated protein RIF1 isoform X3

  5. XM_011239137.4XP_011237439.1  telomere-associated protein RIF1 isoform X5

    Conserved Domains (1) summary
    cd14267
    Location:12411288
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
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