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

Gene ID: 55183, updated on 16-Apr-2024

Summary

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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; AllianceGenome:HGNC:23207
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
mouse all
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Genomic context

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Location:
2q23.3
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (151409902..151534435)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (151861663..151986225)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (152266416..152338686)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16636 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 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:152265327-152266025 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:152266026-152266724 Neighboring gene uncharacterized LOC124906081 Neighboring gene nebulin Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:152410007-152411206 Neighboring gene Sharpr-MPRA regulatory region 15124 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:152560612-152561164 Neighboring gene CRISPRi-validated cis-regulatory element chr2.5074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12007 Neighboring gene NEB-ARL5A intergenic CAGE-defined B cell enhancer Neighboring gene Sharpr-MPRA regulatory region 4301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12009 Neighboring gene ADP ribosylation factor like GTPase 5A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair. Blasiak J, et al. Int J Mol Sci, 2021 Oct 23. PMID 34768871, Free PMC Article
  2. Replication timing maintains the global epigenetic state in human cells. Klein KN, et al. Science, 2021 Apr 23. PMID 33888635, Free PMC Article
  3. Investigation of the expression of RIF1 gene on head and neck, pancreatic and brain cancer and cancer stem cells. GursesCila HE, et al. Clin Invest Med, 2016 Dec 1. PMID 27917791
  4. Rif1 Is Required for Resolution of Ultrafine DNA Bridges in Anaphase to Ensure Genomic Stability. Hengeveld RC, et al. Dev Cell, 2015 Aug 24. PMID 26256213
  5. Rif1 regulates the replication timing domains on the human genome. Yamazaki S, et al. EMBO J, 2012 Sep 12. PMID 22850674, Free PMC Article

See all (140) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer.
    Title: Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer.
  2. Shedding Light on the Interaction Between Rif1 and Telomeres in Ovarian Cancer.
    Title: Shedding Light on the Interaction Between Rif1 and Telomeres in Ovarian Cancer.
  3. RIF1 suppresses the formation of single-stranded ultrafine anaphase bridges via protein phosphatase 1.
    Title: RIF1 suppresses the formation of single-stranded ultrafine anaphase bridges via protein phosphatase 1.
  4. MiR-30a-5p Enhances Cisplatin Sensitivity by Downregulating RIF1 in Ovarian Cancer.
    Title: MiR-30a-5p Enhances Cisplatin Sensitivity by Downregulating RIF1 in Ovarian Cancer.
  5. Histone chaperone ASF1 acts with RIF1 to promote DNA end joining in BRCA1-deficient cells.
    Title: Histone chaperone ASF1 acts with RIF1 to promote DNA end joining in BRCA1-deficient cells.
  6. Rif1-Dependent Control of Replication Timing.
    Title: Rif1-Dependent Control of Replication Timing.
  7. RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity.
    Title: RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity.
  8. CXCR4 and RIF1 overexpression induces resistance of epithelial ovarian cancer to cisplatin-based chemotherapy.
    Title: CXCR4 and RIF1 overexpression induces resistance of epithelial ovarian cancer to cisplatin-based chemotherapy.
  9. Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action.
    Title: Protein phosphatase 1 acts as a RIF1 effector to suppress DSB resection prior to Shieldin action.
  10. RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair.
    Title: RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair.
Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12870, DKFZp434D1026, DKFZp781N1478

Gene Ontology Provided by GOA

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

General protein information

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Preferred Names
telomere-associated protein RIF1
Names
RAP1 interacting factor homolog
rap1-interacting factor 1 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.

Genomic

  1. NG_017162.2 RefSeqGene

    Range
    5002..77272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001177663.2 → NP_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:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  2. NM_001177664.2 → NP_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:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  3. NM_001177665.2 → NP_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:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  4. NM_018151.5 → NP_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
    A6NC27, C9JBR1, Q5H9R3, Q5UIP0, Q5UIP2, Q66YK6, Q6PRU2, Q8TE94, Q99772, Q9H830, Q9H9B9, Q9NVP5, Q9Y4R4
    Related
    ENSP00000390181.2, ENST00000444746.7
    Conserved Domains (1) summary
    pfam12231
    Location:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    151409902..151534435
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444875.1 → XP_047300831.1  telomere-associated protein RIF1 isoform X8

  2. XM_047444884.1 → XP_047300840.1  telomere-associated protein RIF1 isoform X15

  3. XM_047444879.1 → XP_047300835.1  telomere-associated protein RIF1 isoform X12

  4. XM_047444882.1 → XP_047300838.1  telomere-associated protein RIF1 isoform X14

  5. XM_017004422.2 → XP_016859911.1  telomere-associated protein RIF1 isoform X2

    Conserved Domains (1) summary
    pfam12231
    Location:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  6. XM_047444870.1 → XP_047300826.1  telomere-associated protein RIF1 isoform X4

  7. XM_047444885.1 → XP_047300841.1  telomere-associated protein RIF1 isoform X16

  8. XM_047444868.1 → XP_047300824.1  telomere-associated protein RIF1 isoform X3

  9. XM_047444872.1 → XP_047300828.1  telomere-associated protein RIF1 isoform X6

  10. XM_017004424.2 → XP_016859913.1  telomere-associated protein RIF1 isoform X5

  11. XM_005246665.4 → XP_005246722.1  telomere-associated protein RIF1 isoform X1

    See identical proteins and their annotated locations for XP_005246722.1

    UniProtKB/Swiss-Prot
    A6NC27, C9JBR1, Q5H9R3, Q5UIP0, Q5UIP2, Q66YK6, Q6PRU2, Q8TE94, Q99772, Q9H830, Q9H9B9, Q9NVP5, Q9Y4R4
    Conserved Domains (1) summary
    pfam12231
    Location:20 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  12. XM_047444880.1 → XP_047300836.1  telomere-associated protein RIF1 isoform X12

  13. XM_047444883.1 → XP_047300839.1  telomere-associated protein RIF1 isoform X14

  14. XM_047444867.1 → XP_047300823.1  telomere-associated protein RIF1 isoform X2

  15. XM_047444869.1 → XP_047300825.1  telomere-associated protein RIF1 isoform X4

  16. XM_047444881.1 → XP_047300837.1  telomere-associated protein RIF1 isoform X13

  17. XM_017004423.2 → XP_016859912.1  telomere-associated protein RIF1 isoform X3

    Conserved Domains (1) summary
    pfam12231
    Location:20 → 330
    Rif1_N; Rap1-interacting factor 1 N terminal

  18. XM_047444887.1 → XP_047300843.1  telomere-associated protein RIF1 isoform X18

  19. XM_047444873.1 → XP_047300829.1  telomere-associated protein RIF1 isoform X6

  20. XM_047444871.1 → XP_047300827.1  telomere-associated protein RIF1 isoform X5

  21. XM_047444876.1 → XP_047300832.1  telomere-associated protein RIF1 isoform X9

  22. XM_047444886.1 → XP_047300842.1  telomere-associated protein RIF1 isoform X17

  23. XM_047444874.1 → XP_047300830.1  telomere-associated protein RIF1 isoform X7

  24. XM_047444877.1 → XP_047300833.1  telomere-associated protein RIF1 isoform X10

  25. XM_047444878.1 → XP_047300834.1  telomere-associated protein RIF1 isoform X11

RNA

  1. XR_007077544.1 RNA Sequence

  2. XR_007077534.1 RNA Sequence

  3. XR_007077537.1 RNA Sequence

  4. XR_007077543.1 RNA Sequence

  5. XR_007077535.1 RNA Sequence

  6. XR_007077532.1 RNA Sequence

  7. XR_007077533.1 RNA Sequence

  8. XR_007077536.1 RNA Sequence

  9. XR_007077530.1 RNA Sequence

  10. XR_007077529.1 RNA Sequence

  11. XR_007077531.1 RNA Sequence

  12. XR_007077541.1 RNA Sequence

  13. XR_007077539.1 RNA Sequence

  14. XR_007077542.1 RNA Sequence

  15. XR_007077540.1 RNA Sequence

  16. XR_007077538.1 RNA Sequence

  17. XR_007077545.1 RNA Sequence

  18. XR_007077546.1 RNA Sequence

  19. XR_007077547.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    151861663..151986225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342755.1 → XP_054198730.1  telomere-associated protein RIF1 isoform X8

  2. XM_054342764.1 → XP_054198739.1  telomere-associated protein RIF1 isoform X15

  3. XM_054342759.1 → XP_054198734.1  telomere-associated protein RIF1 isoform X12

  4. XM_054342762.1 → XP_054198737.1  telomere-associated protein RIF1 isoform X14

  5. XM_054342744.1 → XP_054198719.1  telomere-associated protein RIF1 isoform X2

  6. XM_054342749.1 → XP_054198724.1  telomere-associated protein RIF1 isoform X4

  7. XM_054342765.1 → XP_054198740.1  telomere-associated protein RIF1 isoform X16

  8. XM_054342747.1 → XP_054198722.1  telomere-associated protein RIF1 isoform X3

  9. XM_054342752.1 → XP_054198727.1  telomere-associated protein RIF1 isoform X6

  10. XM_054342751.1 → XP_054198726.1  telomere-associated protein RIF1 isoform X5

  11. XM_054342743.1 → XP_054198718.1  telomere-associated protein RIF1 isoform X1

  12. XM_054342760.1 → XP_054198735.1  telomere-associated protein RIF1 isoform X12

  13. XM_054342763.1 → XP_054198738.1  telomere-associated protein RIF1 isoform X14

  14. XM_054342745.1 → XP_054198720.1  telomere-associated protein RIF1 isoform X2

  15. XM_054342748.1 → XP_054198723.1  telomere-associated protein RIF1 isoform X4

  16. XM_054342761.1 → XP_054198736.1  telomere-associated protein RIF1 isoform X13

  17. XM_054342746.1 → XP_054198721.1  telomere-associated protein RIF1 isoform X3

  18. XM_054342767.1 → XP_054198742.1  telomere-associated protein RIF1 isoform X18

  19. XM_054342753.1 → XP_054198728.1  telomere-associated protein RIF1 isoform X6

  20. XM_054342750.1 → XP_054198725.1  telomere-associated protein RIF1 isoform X5

  21. XM_054342756.1 → XP_054198731.1  telomere-associated protein RIF1 isoform X9

  22. XM_054342766.1 → XP_054198741.1  telomere-associated protein RIF1 isoform X17

  23. XM_054342754.1 → XP_054198729.1  telomere-associated protein RIF1 isoform X7

  24. XM_054342757.1 → XP_054198732.1  telomere-associated protein RIF1 isoform X10

  25. XM_054342758.1 → XP_054198733.1  telomere-associated protein RIF1 isoform X11

RNA

  1. XR_008486439.1 RNA Sequence

  2. XR_008486430.1 RNA Sequence

  3. XR_008486432.1 RNA Sequence

  4. XR_008486438.1 RNA Sequence

  5. XR_008486428.1 RNA Sequence

  6. XR_008486424.1 RNA Sequence

  7. XR_008486429.1 RNA Sequence

  8. XR_008486431.1 RNA Sequence

  9. XR_008486426.1 RNA Sequence

  10. XR_008486425.1 RNA Sequence

  11. XR_008486427.1 RNA Sequence

  12. XR_008486436.1 RNA Sequence

  13. XR_008486434.1 RNA Sequence

  14. XR_008486437.1 RNA Sequence

  15. XR_008486435.1 RNA Sequence

  16. XR_008486433.1 RNA Sequence

  17. XR_008486440.1 RNA Sequence

  18. XR_008486441.1 RNA Sequence

  19. XR_008486442.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5UIP0.2 GenPept UniProtKB/Swiss-Prot:Q5UIP0

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