esr1 estrogen receptor 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: esr1provided by ZNC
Official Full Name: estrogen receptor 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-020806-5
See related: Ensembl:ENSDARG00000004111 AllianceGenome:ZFIN:ZDB-GENE-020806-5
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: ESR; ER[a]; NR3A1; abrrl; eralpha; zfER[a]
Summary: Enables estradiol binding activity; nuclear estrogen receptor activity; and steroid hormone binding activity. Acts upstream of or within several processes, including cellular response to estrogen stimulus; posterior lateral line neuromast primordium migration; and swimming behavior. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleus. Is expressed in several structures, including diencephalon; head; liver; male organism; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); bone disease (multiple); breast cancer (multiple); type 2 diabetes mellitus; and vitiligo. Orthologous to human ESR1 (estrogen receptor 1). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 20

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	20	NC_133195.1 (29074291..29097905, complement)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (26359752..26383368, complement)

Chromosome 20 - NC_133195.1 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?

High temperature induced masculinization of zebrafish by down-regulation of sox9b and esr1 via DNA methylation.
Title: High temperature induced masculinization of zebrafish by down-regulation of sox9b and esr1 via DNA methylation.
A combined FSTRA-shotgun proteomics approach to identify molecular changes in zebrafish upon chemical exposure.
Title: A combined FSTRA-shotgun proteomics approach to identify molecular changes in zebrafish upon chemical exposure.
ER-alpha is the central factor, acting interactively with ERbeta1, ERbeta2 and GPER, and GPER regulates vitellogenesis directly and interactively with nuclear estrogen receptors.
Title: Interaction of nuclear ERs and GPER in vitellogenesis in zebrafish.
Comprehensive genetic analysis for differential functions of esr1, esr2a, and esr2b in fish reproduction.
Title: Functional Analysis of Nuclear Estrogen Receptors in Zebrafish Reproduction by Genome Editing Approach.
This study revealed similar patterns of transcript abundance across reproductive morphs for ERbeta1, ERbeta2, ERalpha, and aromatase in the forebrain and saccule.
Title: Localization and divergent profiles of estrogen receptors and aromatase in the vocal and auditory networks of a fish with alternative mating tactics.
It was concluded that morpholino (MO) oligonucleotid technology in zebrafish embryos is an good approach for investigating the interplay of estrogen receptor subtypes in a true physiological context.
Title: Morpholino-mediated knockdown of ERα, ERβa, and ERβb mRNAs in zebrafish (Danio rerio) embryos reveals differential regulation of estrogen-inducible genes.
Report stable reporter gene assays based on stable expression of subtypes of zebrafish ER (zfERalpha, zfERbeta1, and zfERbeta2) coupled to estrogen response element-driven luciferase in a zebrafish liver cell line.
Title: Selective activation of zebrafish estrogen receptor subtypes by chemicals by using stable reporter gene assay developed in a zebrafish liver cell line.
during embryogenesis two of the three 17beta-estradiol receptor genes, esr1 and esr2b are expressed, and in presence of ligand the mRNA levels of these two genes increase
Title: Levels of 17beta-estradiol receptors expressed in embryonic and adult zebrafish following in vivo treatment of natural or synthetic ligands.
show that inactivation of the estrogen receptor ESR1 results in ectopic expression of cxcr4b throughout the primordium, whereas ESR1 overexpression results in a reciprocal reduction in the domain of cxcr4b expression.
Title: Estrogen receptor ESR1 controls cell migration by repressing chemokine receptor CXCR4 in the zebrafish posterior lateral line system.
Data show that temperature and photoperiod significantly influence the transcription of the estrogen-responsive genes, Vtg1, Vtg2, ER alpha and ER beta after a 21-day exposure to endocrine-disrupting chemicals.
Title: Temperature and photoperiod affect the endocrine disruption effects of ethinylestradiol, nonylphenol and their binary mixture in zebrafish (Danio rerio).

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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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	IEA Inferred from Electronic Annotation more info
enables estradiol binding	IDA Inferred from Direct Assay more info	PubMed
enables estrogen response element binding	IBA Inferred from Biological aspect of Ancestor more info
enables hormone binding	IEA Inferred from Electronic Annotation more info
enables lipid binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear estrogen receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear estrogen receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables nuclear steroid receptor activity	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables steroid binding	IEA Inferred from Electronic Annotation more info
enables steroid hormone binding	IDA Inferred from Direct Assay more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to estrogen stimulus	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cellular response to estrogen stimulus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in estrogen receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within posterior lateral line neuromast primordium migration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within posterior lateral line neuromast primordium migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to estradiol	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to estrogen	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within response to xenobiotic stimulus	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within steroid hormone receptor signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within swimming behavior	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: estrogen receptor

Names: ER; ER-alpha; estradiol receptor; estrogen receptor alpha; nuclear receptor subfamily 3 group A member 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_152959.1 → NP_694491.1 estrogen receptor

See identical proteins and their annotated locations for NP_694491.1

Status: PROVISIONAL

Source sequence(s)

AF349412

UniProtKB/Swiss-Prot

P57717, Q98SM9

Related

ENSDARP00000082277.5, ENSDART00000087844.7

Conserved Domains (3) summary

cd06949
Location:278 → 515

NR_LBD_ER; Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

cd07171
Location:147 → 225

NR_DBD_ER; DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

cl23807
Location:1 → 148

WWbp; WW-domain ligand protein

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

NC_133195.1 Reference GRCz12tu Primary Assembly

Range

29074291..29097905 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009299438.4 → XP_009297713.1 estrogen receptor isoform X1

UniProtKB/TrEMBL

A0A8M3B0Y2

Related

ENSDARP00000152126.1, ENSDART00000192966.1

Conserved Domains (3) summary

cd06949
Location:322 → 559

NR_LBD_ER; Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

cd07171
Location:191 → 269

NR_DBD_ER; DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

cl23807
Location:45 → 192

WWbp; WW-domain ligand protein