tp53 tumor protein p53 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: tp53provided by ZNC
Official Full Name: tumor protein p53provided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-270
See related: Ensembl:ENSDARG00000035559 AllianceGenome:ZFIN:ZDB-GENE-990415-270
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: p53; brp53; drp53; fb40d06; wu:fb40d06; zgc:111919; etID22686.5
Summary: Enables DNA-binding transcription factor activity; identical protein binding activity; and sequence-specific DNA binding activity. Involved in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator and regulation of transcription by RNA polymerase II. Acts upstream of or within with a positive effect on transforming growth factor beta receptor signaling pathway involved in endodermal cell fate specification and transforming growth factor beta receptor signaling pathway involved in mesodermal cell fate specification. Acts upstream of or within several processes, including hemopoiesis; intracellular signal transduction; and regulation of nucleobase-containing compound metabolic process. Located in chromatin. Is expressed in several structures, including digestive system; head; musculature system; nervous system; and reproductive system. Used to study Li-Fraumeni syndrome; aggressive NK-cell leukemia; angiosarcoma; cancer; and malignant peripheral nerve sheath tumor. Human ortholog(s) of this gene implicated in several diseases, including Li-Fraumeni syndrome (multiple); carcinoma (multiple); hematologic cancer (multiple); open-angle glaucoma (multiple); and pancreatic cancer (multiple). Orthologous to human TP53 (tumor protein p53). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (24086227..24097805)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (23582427..23594005)

Chromosome 5 - NC_007116.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

Lack of telomerase reduces cancer incidence and increases lifespan of zebrafish tp53[M214K] mutants.
Title: Lack of telomerase reduces cancer incidence and increases lifespan of zebrafish tp53(M214K) mutants.
Defining function of wild-type and three patient-specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma.
Title: Defining function of wild-type and three patient-specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma.
Rbbp4 loss disrupts neural progenitor cell cycle regulation independent of Rb and leads to Tp53 acetylation and apoptosis.
Title: Rbbp4 loss disrupts neural progenitor cell cycle regulation independent of Rb and leads to Tp53 acetylation and apoptosis.
Zebrafish imaging reveals TP53 mutation switching oncogene-induced senescence from suppressor to driver in primary tumorigenesis.
Title: Zebrafish imaging reveals TP53 mutation switching oncogene-induced senescence from suppressor to driver in primary tumorigenesis.
The Proapoptotic Gene Bad Regulates Brain Development via p53-Mediated Stress Signals in Zebrafish.
Title: The Proapoptotic Gene Bad Regulates Brain Development via p53-Mediated Stress Signals in Zebrafish.
Puma, noxa, p53, and p63 differentially mediate stress pathway induced apoptosis.
Title: Puma, noxa, p53, and p63 differentially mediate stress pathway induced apoptosis.
Loss-of-function of p53 isoform Delta113p53 accelerates brain aging in zebrafish.
Title: Loss-of-function of p53 isoform Δ113p53 accelerates brain aging in zebrafish.
Tp53 Suppression Promotes Cardiomyocyte Proliferation during Zebrafish Heart Regeneration.
Title: Tp53 Suppression Promotes Cardiomyocyte Proliferation during Zebrafish Heart Regeneration.
p53 isoform Delta113p53 promotes zebrafish heart regeneration by maintaining redox homeostasis.
Title: p53 isoform Δ113p53 promotes zebrafish heart regeneration by maintaining redox homeostasis.
Opposing p53 and mTOR/AKT promote an in vivo switch from apoptosis to senescence upon telomere shortening in zebrafish.
Title: Opposing p53 and mTOR/AKT promote an in vivo switch from apoptosis to senescence upon telomere shortening in zebrafish.

Submit: New GeneRIF Correction See all GeneRIFs (86)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fe13d08.y1 (e-PCR)
- UniSTS:196146

U60804 (e-PCR)
- UniSTS:187015

fb40d06.x1 (e-PCR)
- UniSTS:203202

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables molecular condensate scaffold activity	ISS Inferred from Sequence or Structural Similarity more info
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in anatomical structure morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within apoptotic process involved in blood vessel morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of apoptotic process involved in development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of apoptotic process involved in development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within autophagy	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cellular response to hypoxia	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular senescence	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within definitive hemopoiesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryo development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epidermis morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelium development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within erythrocyte development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within erythrocyte maturation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hematopoietic stem cell homeostasis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of hematopoietic stem cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of hematopoietic stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intestinal epithelial structure maintenance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within intrinsic apoptotic signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of angiogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell division	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neuron apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of programmed cell death involved in cell development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of programmed cell death involved in cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein tetramerization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cell population proliferation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of intrinsic apoptotic signaling pathway by p53 class mediator	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of oogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of protein stability	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to UV	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to X-ray	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to methylmercury	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within retrotransposon silencing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spermatogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within_positive_effect transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: cellular tumor antigen p53

Names: delta113 p53; tumor suppressor p53

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_001271820.1 → NP_001258749.1 cellular tumor antigen p53 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).

Source sequence(s)

AL928875, CT619016, CT704385, EH435782, EH479527

UniProtKB/TrEMBL

A0A8M1NZV2, G1K2L5

Related

ENSDARP00000051548.3, ENSDART00000051549.5

Conserved Domains (2) summary

pfam00870
Location:64 → 258

P53; P53 DNA-binding domain

pfam07710
Location:294 → 335

P53_tetramer; P53 tetramerization motif
NM_001328587.1 → NP_001315516.1 cellular tumor antigen p53 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AL928875

UniProtKB/TrEMBL

A0A8M1P568, B0R0M3

Related

ENSDARP00000116736.1, ENSDART00000135934.3

Conserved Domains (2) summary

pfam00870
Location:63 → 257

P53; P53 DNA-binding domain

pfam07710
Location:289 → 330

P53_tetramer; P53 tetramerization motif
NM_001328588.1 → NP_001315517.1 cellular tumor antigen p53 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate 5' most exon whic hresults in the use of a downstream start codon compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AL928875

UniProtKB/TrEMBL

A0A0B4VFS7, A0A8M2BC97

Related

ENSDARP00000151125.1, ENSDART00000183748.1

Conserved Domains (2) summary

pfam07710
Location:181 → 222

P53_tetramer; P53 tetramerization motif

cl14608
Location:1 → 145

P53; P53 DNA-binding domain
NM_131327.2 → NP_571402.1 cellular tumor antigen p53 isoform 2

See identical proteins and their annotated locations for NP_571402.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AL928875, CT619016, CT635558, CT704385, EH479527

UniProtKB/Swiss-Prot

P79734, Q7ZW62, Q90440

Related

ENSDARP00000144168.2, ENSDART00000177458.2

Conserved Domains (2) summary

pfam00870
Location:63 → 257

P53; P53 DNA-binding domain

pfam07710
Location:293 → 334

P53_tetramer; P53 tetramerization motif

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007116.7 Reference GRCz11 Primary Assembly

Range

24086227..24097805

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005165101.5 → XP_005165158.1 cellular tumor antigen p53 isoform X1

UniProtKB/TrEMBL

A0A8M2BCD8

Conserved Domains (2) summary

pfam00870
Location:64 → 258

P53; P53 DNA-binding domain

pfam07710
Location:290 → 331

P53_tetramer; P53 tetramerization motif
XM_005165103.5 → XP_005165160.1 cellular tumor antigen p53 isoform X2

See identical proteins and their annotated locations for XP_005165160.1

UniProtKB/TrEMBL

A0A0B4VFS7, A0A8M2BC97

Conserved Domains (2) summary

pfam07710
Location:181 → 222

P53_tetramer; P53 tetramerization motif

cl14608
Location:1 → 145

P53; P53 DNA-binding domain