Top1 DNA topoisomerase I [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Top1provided by RGD
Official Full Name: DNA topoisomerase Iprovided by RGD
Primary source: RGD:621246
See related: EnsemblRapid:ENSRNOG00000047611 AllianceGenome:RGD:621246
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ab2-086
Summary: Enables DNA topoisomerase type I (single strand cut, ATP-independent) activity and chromatin DNA binding activity. Involved in several processes, including DNA topological change; cellular response to luteinizing hormone stimulus; and rRNA transcription. Located in dense fibrillar component and fibrillar center. Orthologous to human TOP1 (DNA topoisomerase I). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 242.9), Thymus (RPKM 228.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (169713195..169796330)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (149293469..149376618)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (156635688..156717686)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rac1-regulated mechanisms are required for DNA damage induction and subsequent activation of the DDR following treatment with topo II but not topo I poisons
Title: Rac1 protein signaling is required for DNA damage response stimulated by topoisomerase II poisons.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Got129 (e-PCR)
- UniSTS:111877

UniSTS:234589 (e-PCR)
- UniSTS:234589

BM389249 (e-PCR)
- UniSTS:261730

BE115617 (e-PCR)
- UniSTS:248184

BF405031 (e-PCR)
- UniSTS:247770

D3Rat144 (e-PCR), detects polymorphism
- UniSTS:227553

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding, bending	ISO Inferred from Sequence Orthology more info
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	IEA Inferred from Electronic Annotation more info
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables supercoiled DNA binding	IEA Inferred from Electronic Annotation more info
enables supercoiled DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA replication	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA replication	ISO Inferred from Sequence Orthology more info
involved_in DNA topological change	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA topological change	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA topological change	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA topological change	ISO Inferred from Sequence Orthology more info
involved_in DNA topological change	ISO Inferred from Sequence Orthology more info
involved_in animal organ regeneration	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to luteinizing hormone stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromosome segregation	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in embryonic cleavage	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic cleavage	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-serine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in rRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to cAMP	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to gamma radiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to temperature stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in P-body	ISO Inferred from Sequence Orthology more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in dense fibrillar component	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in male germ cell nucleus	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in perikaryon	ISO Inferred from Sequence Orthology more info
part_of protein-DNA complex	IEA Inferred from Electronic Annotation more info
part_of protein-DNA complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA topoisomerase 1

Names: topoisomerase (DNA) I

NP_072137.1

EC 5.6.2.1

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)

NM_022615.2 → NP_072137.1 DNA topoisomerase 1

See identical proteins and their annotated locations for NP_072137.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

Q9WUL0

UniProtKB/TrEMBL

A0A8I5Y067, A6JWZ1

Related

ENSRNOP00000076575.2, ENSRNOT00000113376.2

Conserved Domains (4) summary

smart00435
Location:362 → 739

TOPEUc; DNA Topoisomerase I (eukaryota)

pfam01028
Location:434 → 637

Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core

pfam02919
Location:217 → 431

Topoisom_I_N; Eukaryotic DNA topoisomerase I, DNA binding fragment

pfam14370
Location:697 → 765

Topo_C_assoc; C-terminal topoisomerase domain