tdp2b tyrosyl-DNA phosphodiesterase 2b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: tdp2bprovided by ZNC
Official Full Name: tyrosyl-DNA phosphodiesterase 2bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050816-1
See related: Ensembl:ENSDARG00000035954 AllianceGenome:ZFIN:ZDB-GENE-050816-1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: tdp2; ttrap; ttrapl
Summary: Enables DNA binding activity and tyrosyl-DNA phosphodiesterase activity. Involved in determination of left/right symmetry and gastrulation. Acts upstream of or within convergent extension involved in gastrulation and negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be located in nucleus. Predicted to be active in PML body and cytoplasm. Is expressed in Kupffer's vesicle; forerunner cell group; and tail bud. 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, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 19

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (31568993..31576017, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	19	NC_007130.6 (31981680..31988704, complement)

Chromosome 19 - NC_007130.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

although the role of Smad proteins in mediating Nodal signaling is well-documented, the functional characterization of Ttrap provides insight into a novel Smad partner that plays an essential role in the fine-tuning of this signal transduction cascade
Title: Ttrap is an essential modulator of Smad3-dependent Nodal signaling during zebrafish gastrulation and left-right axis determination.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

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	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables catalytic activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables manganese ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	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	ISS Inferred from Sequence or Structural Similarity more info
enables tyrosyl-DNA phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within convergent extension involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in PML body	IBA Inferred from Biological aspect of Ancestor more info
located_in PML body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation 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 homolog; immune transcriptional repressor; traf and tnf receptor associated protein, like; tyr-DNA phosphodiesterase 2

NP_001073171.1

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_001079703.1 → NP_001073171.1 tyrosyl-DNA phosphodiesterase 2

See identical proteins and their annotated locations for NP_001073171.1

Status: PROVISIONAL

Source sequence(s)

DQ524846

UniProtKB/Swiss-Prot

A0SKZ8, A4FUK7, Q1LU95, Q1LWU3, Q4V912, Q5XJA0

Related

ENSDARP00000094388.4, ENSDART00000103612.5

Conserved Domains (2) summary

cd09080
Location:123 → 367

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

cd14344
Location:10 → 46

UBA_TYDP2; UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins