rxrba retinoid x receptor, beta a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rxrbaprovided by ZNC
Official Full Name: retinoid x receptor, beta aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-436
See related: Ensembl:ENSDARG00000078954 AllianceGenome:ZFIN:ZDB-GENE-980526-436
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: RXR; RXRA; rxrb; rxre; NR2B2-A; fb93c09; wu:fb93c09; etID309733.19
Summary: Contributes to DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in regulation of DNA-templated transcription. Acts upstream of or within negative regulation of DNA-templated transcription. Predicted to be located in nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including blastoderm; digestive system; eye; gonad; and tail bud. Orthologous to human RXRB (retinoid X receptor beta). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 19

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (7244838..7273020, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	19	NC_007130.6 (7325913..7354127, complement)

Chromosome 19 - NC_007130.7 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
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?

Submit: New GeneRIF Correction

General gene information

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Markers

RXRE (e-PCR)
- UniSTS:205416

rxre (e-PCR)
- UniSTS:205513

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
contributes_to DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info
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 steroid receptor activity	IEA Inferred from Electronic Annotation more info
enables retinoic acid-responsive element binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	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: retinoic acid receptor RXR-beta-A

Names: nuclear receptor subfamily 2 group B member 2-A; retinoid X receptor beta-A; retinoid receptor-epsilon; retinoid x receptor, epsilon

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_001423448.1 → NP_001410377.1 retinoic acid receptor RXR-beta-A isoform 1

Status: VALIDATED

Source sequence(s)

FP085394, FP101875

UniProtKB/TrEMBL

A0A8M3ASC4
NM_131275.2 → NP_571350.1 retinoic acid receptor RXR-beta-A isoform 2

See identical proteins and their annotated locations for NP_571350.1

Status: VALIDATED

Source sequence(s)

FP085394, FP101875

UniProtKB/TrEMBL

Q1LV96

Related

ENSDARP00000119017.2, ENSDART00000136528.4

Conserved Domains (3) summary

cd06943
Location:193 → 416

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:91 → 166

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:1 → 84

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

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_007130.7 Reference GRCz11 Primary Assembly

Range

7244838..7273020 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005159412.4 → XP_005159469.1 retinoic acid receptor RXR-beta-A isoform X6

UniProtKB/TrEMBL

A0A8M2B5Y2

Conserved Domains (3) summary

cd06943
Location:218 → 427

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:124 → 199

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 117

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_005159411.4 → XP_005159468.1 retinoic acid receptor RXR-beta-A isoform X4

UniProtKB/TrEMBL

A0A8M2B632

Conserved Domains (3) summary

cd06943
Location:218 → 441

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:124 → 199

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 117

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_005159410.4 → XP_005159467.1 retinoic acid receptor RXR-beta-A isoform X2

See identical proteins and their annotated locations for XP_005159467.1

UniProtKB/Swiss-Prot

O42556, Q1LV98, Q7SYN5, Q8AW18, Q90418

Related

ENSDARP00000125725.1, ENSDART00000102075.6

Conserved Domains (3) summary

cd06943
Location:226 → 449

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:124 → 199

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 117

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_009294025.3 → XP_009292300.1 retinoic acid receptor RXR-beta-A isoform X5

UniProtKB/TrEMBL

A0A8M3B3B9

Conserved Domains (3) summary

cd06943
Location:227 → 436

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:133 → 208

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 126

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_009294024.3 → XP_009292299.1 retinoic acid receptor RXR-beta-A isoform X3

UniProtKB/TrEMBL

A0A8M3AK00

Conserved Domains (3) summary

cd06943
Location:235 → 444

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:133 → 208

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 126

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_009294022.3 → XP_009292297.1 retinoic acid receptor RXR-beta-A isoform X1

UniProtKB/TrEMBL

A0A8M3AVB4

Conserved Domains (3) summary

cd06943
Location:235 → 458

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:133 → 208

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:21 → 126

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
XM_068215026.1 → XP_068071127.1 retinoic acid receptor RXR-beta-A isoform X9
XM_068215025.1 → XP_068071126.1 retinoic acid receptor RXR-beta-A isoform X8
XM_021467983.2 → XP_021323658.1 retinoic acid receptor RXR-beta-A isoform X7

UniProtKB/TrEMBL

A0A8M9PAS6

Conserved Domains (3) summary

cd06943
Location:202 → 425

NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

cd06956
Location:100 → 175

NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

pfam11825
Location:1 → 93

Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1