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

Gene ID: 30530, updated on 2-Nov-2024

Summary

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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, Nov 2024]
Orthologs
all
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Genomic context

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See rxrba in Genome Data Viewer
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_007130.7Genomic Context describing neighboring genes Neighboring gene hydroxysteroid (17-beta) dehydrogenase 8 Neighboring gene collagen, type XI, alpha 2 Neighboring gene succinate dehydrogenase complex, subunit A, flavoprotein (Fp) Neighboring gene coiled-coil domain containing 127b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile salts. Krasowski MD, et al. Mol Endocrinol, 2005 Jul. PMID 15718292, Free PMC Article
  2. Structure, linkage mapping and expression of the heart-type fatty acid-binding protein gene (fabp3 ) from zebrafish (Danio rerio). Liu RZ, et al. Eur J Biochem, 2003 Aug. PMID 12869198
  3. The orphan COUP-TF nuclear receptors are markers for neurogenesis from cnidarians to vertebrates. Gauchat D, et al. Dev Biol, 2004 Nov 1. PMID 15464576
  4. Retinoid requirements in the reproduction of zebrafish. Alsop D, et al. Gen Comp Endocrinol, 2008 Mar 1. PMID 18158153
  5. Identification and characterization of a novel retinoic acid response element in zebrafish cyp26a1 promoter. Li J, et al. Anat Rec (Hoboken), 2012 Feb. PMID 22190473

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

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)

  1. NM_001423448.1 → NP_001410377.1  retinoic acid receptor RXR-beta-A isoform 1

    Status: VALIDATED

    Source sequence(s)
    FP085394, FP101875
    UniProtKB/TrEMBL
    A0A8M3ASC4

  2. 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

  1. NC_007130.7 Reference GRCz11 Primary Assembly

    Range
    7244838..7273020 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. XM_068215026.1 → XP_068071127.1  retinoic acid receptor RXR-beta-A isoform X9

  8. XM_068215025.1 → XP_068071126.1  retinoic acid receptor RXR-beta-A isoform X8

  9. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7SYN5.1 GenPept UniProtKB/Swiss-Prot:Q7SYN5

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