Tdp1 tyrosyl-DNA phosphodiesterase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tdp1provided by RGD
Official Full Name: tyrosyl-DNA phosphodiesterase 1provided by RGD
Primary source: RGD:1309618
See related: Ensembl:ENSRNOG00000003831 AllianceGenome:RGD:1309618
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable 3'-tyrosyl-DNA phosphodiesterase activity; double-stranded DNA binding activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair and single strand break repair. Predicted to act upstream of or within DNA repair. Predicted to be located in cytoplasm; nucleoplasm; and plasma membrane. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1 with axonal neuropathy. Orthologous to human TDP1 (tyrosyl-DNA phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 34.1), Testes (RPKM 26.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q32

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (124892821..124960646)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (119163192..119231029)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (123895860..123963688)

Chromosome 6 - NC_086024.1 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?

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General gene information

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Markers

RH129987 (e-PCR)
- UniSTS:213275

RH142247 (e-PCR)
- UniSTS:231495

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3'-tyrosyl-DNA phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3'-tyrosyl-DNA phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables 3'-tyrosyl-DNA phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables 3'-tyrosyl-DNA phosphodiesterase activity	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in double-strand break repair	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in single strand break repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within single strand break repair	ISO Inferred from Sequence Orthology more info
involved_in single strand break repair	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
NOT located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tyrosyl-DNA phosphodiesterase 1

Names: tyr-DNA phosphodiesterase 1

NP_001026827.1

EC 3.1.4.-

XP_006240494.1

EC 3.1.4.-

XP_038968275.1

EC 3.1.4.-

XP_038968277.1

EC 3.1.4.-

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_001031657.1 → NP_001026827.1 tyrosyl-DNA phosphodiesterase 1

See identical proteins and their annotated locations for NP_001026827.1

Status: PROVISIONAL

Source sequence(s)

BC098739

UniProtKB/Swiss-Prot

Q4G056

UniProtKB/TrEMBL

A0A8I6AVZ5, A6JEG4

Related

ENSRNOP00000092684.1, ENSRNOT00000111469.1

Conserved Domains (1) summary

pfam06087
Location:167 → 580

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

124892821..124960646

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039112347.2 → XP_038968275.1 tyrosyl-DNA phosphodiesterase 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AVZ5

Conserved Domains (1) summary

pfam06087
Location:172 → 585

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_006240432.5 → XP_006240494.1 tyrosyl-DNA phosphodiesterase 1 isoform X1

UniProtKB/TrEMBL

A0A0H2UHC3, A0A8I6AFL5

Related

ENSRNOP00000005167.6

Conserved Domains (3) summary

cd09193
Location:179 → 347

PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase

cd09195
Location:369 → 562

PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase

pfam06087
Location:183 → 599

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_039112349.2 → XP_038968277.1 tyrosyl-DNA phosphodiesterase 1 isoform X3

Conserved Domains (1) summary

pfam06087
Location:1 → 314

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase