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

Gene ID: 51507, updated on 11-Apr-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, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 40.3), bone marrow (RPKM 39.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q13.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (56468627..56519449)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (58246116..58296943)
105.20220307 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
  • 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 (41) 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 DNA replication termination IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

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