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RIF1 replication timing regulatory factor 1 [ Homo sapiens (human) ]

Gene ID: 55183, updated on 9-Feb-2020

Summary

Official Symbol
RIF1provided by HGNC
Official Full Name
replication timing regulatory factor 1provided by HGNC
Primary source
HGNC:HGNC:23207
See related
Ensembl:ENSG00000080345 MIM:608952
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 5.5), testis (RPKM 5.3) and 25 other tissues See more
Orthologs

Genomic context

See RIF1 in Genome Data Viewer
Location:
2q23.3
Exon count:
41
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (151409902..151534200)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (152266397..152333860)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929319 Neighboring gene microRNA 4773-1 Neighboring gene microRNA 4773-2 Neighboring gene TNF alpha induced protein 6 Neighboring gene RNA, 7SL, cytoplasmic 124, pseudogene Neighboring gene nebulin Neighboring gene CRISPRi-validated cis-regulatory element chr2.5074 Neighboring gene NEB-ARL5A intergenic CAGE-defined B cell enhancer

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12870, DKFZp434D1026, DKFZp781N1478

Gene Ontology Provided by GOA

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

General protein information

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

Genomic

  1. NG_017162.1 RefSeqGene

    Range
    5001..72464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001177663.2NP_001171134.1  telomere-associated protein RIF1 isoform 2

    See identical proteins and their annotated locations for NP_001171134.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Transcript variant 2, 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC009497, AY727910
    Consensus CDS
    CCDS54406.1
    UniProtKB/Swiss-Prot
    Q5UIP0
    Related
    ENSP00000414615.2, ENST00000453091.6
    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  2. NM_001177664.2NP_001171135.1  telomere-associated protein RIF1 isoform 2

    See identical proteins and their annotated locations for NP_001171135.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Transcript variant 2, 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC009497, AY584066, AY727911
    Consensus CDS
    CCDS54406.1
    UniProtKB/Swiss-Prot
    Q5UIP0
    Related
    ENSP00000415691.2, ENST00000428287.6
    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  3. NM_001177665.2NP_001171136.1  telomere-associated protein RIF1 isoform 2

    See identical proteins and their annotated locations for NP_001171136.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Transcript variant 2, 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AC009311, AC009497, AY584066, AY727912
    Consensus CDS
    CCDS54406.1
    UniProtKB/Swiss-Prot
    Q5UIP0
    Related
    ENSP00000416123.2, ENST00000430328.6
    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  4. NM_018151.5NP_060621.3  telomere-associated protein RIF1 isoform 1

    See identical proteins and their annotated locations for NP_060621.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC009497, AY584066, AY727913
    Consensus CDS
    CCDS2194.1
    UniProtKB/Swiss-Prot
    Q5UIP0
    Related
    ENSP00000390181.2, ENST00000444746.7
    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    151409902..151534200
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246665.3XP_005246722.1  telomere-associated protein RIF1 isoform X1

    See identical proteins and their annotated locations for XP_005246722.1

    UniProtKB/Swiss-Prot
    Q5UIP0
    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  2. XM_017004423.1XP_016859912.1  telomere-associated protein RIF1 isoform X3

    Conserved Domains (1) summary
    pfam12231
    Location:20330
    Rif1_N; Rap1-interacting factor 1 N terminal
  3. XM_017004422.1XP_016859911.1  telomere-associated protein RIF1 isoform X2

    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  4. XM_011511395.3XP_011509697.1  telomere-associated protein RIF1 isoform X6

    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  5. XM_024452972.1XP_024308740.1  telomere-associated protein RIF1 isoform X2

    Conserved Domains (1) summary
    pfam12231
    Location:20361
    Rif1_N; Rap1-interacting factor 1 N terminal
  6. XM_017004425.2XP_016859914.1  telomere-associated protein RIF1 isoform X5

  7. XM_017004424.1XP_016859913.1  telomere-associated protein RIF1 isoform X4

RNA

  1. XR_001738817.2 RNA Sequence

  2. XR_001738811.2 RNA Sequence

  3. XR_001738812.2 RNA Sequence

  4. XR_001738813.2 RNA Sequence

  5. XR_001738814.2 RNA Sequence

  6. XR_001738815.2 RNA Sequence

  7. XR_001738816.2 RNA Sequence

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