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

    Gene ID: 55183, updated on 3-Nov-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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    See RIF1 in Genome Data Viewer
    Location:
    2q23.3
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (151409902..151534435)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (151861663..151986225)
    RS_2024_09 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 ARF 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 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. 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
    2. Rif1 regulates the replication timing domains on the human genome. Yamazaki S, et al. EMBO J, 2012 Sep 12. PMID 22850674, Free PMC Article
    3. Replication timing maintains the global epigenetic state in human cells. Klein KN, et al. Science, 2021 Apr 23. PMID 33888635, Free PMC Article
    4. 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
    5. Human RIF1 encodes an anti-apoptotic factor required for DNA repair. Wang H, et al. Carcinogenesis, 2009 Aug. PMID 19483192, Free PMC Article

    See all (164) 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 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
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    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 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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    NEW Try the new Transcript table

    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_2024_08

    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

    Gene LinkOut

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