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    RTF2 replication termination factor 2 [ Homo sapiens (human) ]

    Gene ID: 51507, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RTF2provided by HGNC
    Official Full Name
    replication termination factor 2provided by HGNC
    Primary source
    HGNC:HGNC:15890
    See related
    Ensembl:ENSG00000022277 AllianceGenome:HGNC:15890
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDAO5; RTFDC1; HSPC164; C20orf43; SHUJUN-3
    Summary
    Enables DNA binding activity. Involved in cellular response to hydroxyurea and regulation of DNA stability. Located in replication fork. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in brain (RPKM 40.3), bone marrow (RPKM 39.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RTF2 in Genome Data Viewer
    Location:
    20q13.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (56468627..56519449)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (58246116..58296943)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (55043683..55094505)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18142 Neighboring gene cleavage stimulation factor subunit 1 Neighboring gene Cas scaffold protein family member 4 Neighboring gene ribosomal protein L39 pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene MPRA-validated peak4281 silencer Neighboring gene glucosaminyl (N-acetyl) transferase family member 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55086509-55087317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:55087318-55088125 Neighboring gene family with sequence similarity 209 member A Neighboring gene family with sequence similarity 209 member B Neighboring gene uncharacterized LOC124904971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18143

    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. Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication. Chia BS, et al. J Virol, 2020 Oct 27. PMID 32878895, Free PMC Article
    2. NRIP3 upregulation confers resistance to chemoradiotherapy in ESCC via RTF2 removal by accelerating ubiquitination and degradation of RTF2. Suo D, et al. Oncogenesis, 2020 Aug 24. PMID 32839439, Free PMC Article
    3. Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity. Kottemann MC, et al. Mol Cell, 2018 Jan 4. PMID 29290612, Free PMC Article
    4. A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus. Cai DC, et al. Genes Brain Behav, 2014 Sep. PMID 25130324
    5. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Pao KC, et al. Nature, 2018 Apr. PMID 29643511

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication.
      Title: Loss of the Nuclear Protein RTF2 Enhances Influenza Virus Replication.
    2. The results establish that RTF2 removal is a key determinant for the ability of cells to manage replication stress and maintain genome integrity.
      Title: Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to hydroxyurea IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitotic DNA replication termination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA stability IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in replication fork IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    replication termination factor 2
    Names
    UPF0549 protein C20orf43
    protein RTF2 homolog
    replication termination factor 2 domain containing 1
    replication termination factor 2 domain-containing protein 1

    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_001283035.2 → NP_001269964.1  replication termination factor 2 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AA814039, AK302029, AL109806, BC003359, BG468509, DC397043
      Consensus CDS
      CCDS63316.1
      UniProtKB/TrEMBL
      A0A0A0MQR2, B4DXL5
      Related
      ENSP00000023939.5, ENST00000023939.8
      Conserved Domains (1) summary
      pfam04641
      Location:1 → 319
      Rtf2; Rtf2 RING-finger

    2. NM_001283036.2 → NP_001269965.1  replication termination factor 2 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AA814039, AK225135, AL109806, BC003359, BG468509, DC397043
      UniProtKB/TrEMBL
      B2RB99
      Conserved Domains (1) summary
      pfam04641
      Location:1 → 288
      Rtf2; Rtf2 RING-finger

    3. NM_001283037.2 → NP_001269966.1  replication termination factor 2 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, and lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA814039, AL109806, BC003359, BG468509, CR983692, DC397043
      Consensus CDS
      CCDS63317.1
      UniProtKB/TrEMBL
      A2A2L6
      Related
      ENSP00000379220.3, ENST00000395881.7
      Conserved Domains (1) summary
      pfam04641
      Location:1 → 198
      Rtf2; Rtf2 RING-finger

    4. NM_016407.5 → NP_057491.2  replication termination factor 2 isoform b

      See identical proteins and their annotated locations for NP_057491.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AA814039, AL109806, BC003359, BG468509, DC397043
      Consensus CDS
      CCDS13453.1
      UniProtKB/Swiss-Prot
      E1P5Z9, Q9BY42, Q9BYL7, Q9HCV9, Q9NX29, Q9NZZ8, Q9P002, Q9UHW3
      UniProtKB/TrEMBL
      B2RB99
      Related
      ENSP00000349906.6, ENST00000357348.10
      Conserved Domains (1) summary
      pfam04641
      Location:1 → 289
      Rtf2; Rtf2 RING-finger

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      56468627..56519449
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027872.2 → XP_016883361.1  replication termination factor 2 isoform X1

      UniProtKB/TrEMBL
      B2RB99
      Conserved Domains (1) summary
      pfam04641
      Location:4 → 270
      Rtf2; Rtf2 RING-finger

    2. XM_047440189.1 → XP_047296145.1  replication termination factor 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      58246116..58296943
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323483.1 → XP_054179458.1  replication termination factor 2 isoform X1

    2. XM_054323482.1 → XP_054179457.1  replication termination factor 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BY42.3 GenPept UniProtKB/Swiss-Prot:Q9BY42

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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