vdra vitamin D receptor a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vdraprovided by ZNC
Official Full Name: vitamin D receptor aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-000210-31
See related: AllianceGenome:ZFIN:ZDB-GENE-000210-31
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: vdr; VDR-A; nr1i1a; NR1I1-A; VDRalpha
Summary: Enables calcitriol binding activity; lithocholic acid binding activity; and nuclear receptor activity. Contributes to DNA-binding transcription factor activity and vitamin D response element binding activity. Acts upstream of or within several processes, including calcium ion homeostasis; determination of heart left/right asymmetry; and hematopoietic stem cell proliferation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Is expressed in several structures, including brain; head; heart; integument; and pleuroperitoneal region. Used to study hematopoietic system disease and vitamin D-dependent rickets. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); carcinoma (multiple); liver disease (multiple); lung disease (multiple); and melanoma (multiple). Orthologous to human VDR (vitamin D receptor). [provided by Alliance of Genome Resources, Dec 2024]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: 23

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (45770161..45825632)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (44951960..45980632)

Chromosome 23 - NC_007134.7 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: 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?

Enhanced insulin activity achieved in VDRa/b ablation zebrafish.
Title: Enhanced insulin activity achieved in VDRa/b ablation zebrafish.
Loss of Cyp27b1-mediated biosynthesis or vitamin D receptor (VDR) function by gene knockdown resulted in significantly reduced runx1 expression and Flk1(+)cMyb(+) HSPC numbers.
Title: Developmental Vitamin D Availability Impacts Hematopoietic Stem Cell Production.
Taken together, these results suggest that VDR signaling plays an essential role in heart development.
Title: Vitamin D receptor signaling is required for heart development in zebrafish embryo.
The data suggest that VDR is widely distributed in tissues of the zebrafish, D. rerio, and is likely to play important roles in epithelial transport, bone, and endocrine function.
Title: Expression and regulation of the vitamin D receptor in the zebrafish, Danio rerio.
investigation of binding of ligands that induce significant conformational changes at the protein level
Title: Structural investigation of the ligand binding domain of the zebrafish VDR in complexes with 1alpha,25(OH)2D3 and Gemini: purification, crystallization and preliminary X-ray diffraction analysis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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
contributes_to 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcitriol binding	IDA Inferred from Direct Assay more info	PubMed
enables lithocholic acid binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	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 receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables vitamin D binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to vitamin D response element binding	IBA Inferred from Biological aspect of Ancestor more info
contributes_to vitamin D response element binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart jogging	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hematopoietic stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ossification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: vitamin D3 receptor A

Names: 1,25-dihydroxyvitamin D3 receptor A; nuclear receptor subfamily 1 group I member 1-A; vitamin D (1,25- dihydroxyvitamin D3) receptor a; vitamin D receptor alpha

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_130919.1 → NP_570994.1 vitamin D3 receptor A

See identical proteins and their annotated locations for NP_570994.1

Status: PROVISIONAL

Source sequence(s)

AF164512

UniProtKB/Swiss-Prot

B3DFZ0, Q9PTN2

Conserved Domains (2) summary

cd06933
Location:156 → 452

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:48 → 154

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers