Tdp2 tyrosyl-DNA phosphodiesterase 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tdp2provided by RGD
Official Full Name: tyrosyl-DNA phosphodiesterase 2provided by RGD
Primary source: RGD:1560342
See related: Ensembl:ENSRNOG00000018246 AllianceGenome:RGD:1560342
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
Also known as: Ttrap
Summary: Predicted to enable metal ion binding activity; phosphoric diester hydrolase activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair and neuron development. Predicted to be located in aggresome and nuclear body. Predicted to be active in PML body and cytoplasm. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 23. Orthologous to human TDP2 (tyrosyl-DNA phosphodiesterase 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 166.9), Adrenal (RPKM 160.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17p11

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (40656969..40668362, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (40228943..40240337, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (42229667..42241025, complement)

Chromosome 17 - NC_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5'-tyrosyl-DNA phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-tyrosyl-DNA phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables 5'-tyrosyl-DNA phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables 5'-tyrosyl-DNA phosphodiesterase activity	ISS Inferred from Sequence or Structural Similarity more info
enables magnesium ion binding	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	ISO Inferred from Sequence Orthology more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables manganese ion binding	IEA Inferred from Electronic Annotation more info
enables manganese ion binding	ISO Inferred from Sequence Orthology more info
enables manganese ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables nuclease 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
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables tyrosyl-RNA phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables tyrosyl-RNA phosphodiesterase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor 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 double-strand break repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron development	IEA Inferred from Electronic Annotation more info
involved_in neuron development	ISO Inferred from Sequence Orthology more info
involved_in neuron development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in PML body	IBA Inferred from Biological aspect of Ancestor more info
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in PML body	ISS Inferred from Sequence or Structural Similarity more info
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tyrosyl-DNA phosphodiesterase 2

Names: 5'-Tyr-DNA phosphodiesterase; 5'-tyrosyl-DNA phosphodiesterase; TRAF and TNF receptor-associated protein; Traf and Tnf receptor associated protein; tyr-DNA phosphodiesterase 2

NP_001030119.1

EC 3.1.4.-

XP_063132761.1

EC 3.1.4.-

XP_063132762.1

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_001034947.1 → NP_001030119.1 tyrosyl-DNA phosphodiesterase 2

See identical proteins and their annotated locations for NP_001030119.1

Status: PROVISIONAL

Source sequence(s)

BC101920

UniProtKB/Swiss-Prot

Q3T1H5

UniProtKB/TrEMBL

A6KLF1, G3V9Q6

Related

ENSRNOP00000056326.2, ENSRNOT00000059570.4

Conserved Domains (2) summary

cd09080
Location:120 → 362

TDP2; Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains

cl21463
Location:39 → 70

UBA_like_SF; UBA domain-like superfamily