RARB retinoic acid receptor beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: RARBprovided by HGNC
Official Full Name: retinoic acid receptor betaprovided by HGNC
Primary source: HGNC:HGNC:9865
See related: Ensembl:ENSG00000077092 MIM:180220; AllianceGenome:HGNC:9865
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HAP; RRB2; NR1B2; MCOPS12; RARbeta; RARbeta1
Summary: This gene encodes retinoic acid receptor beta, a member of the thyroid-steroid hormone receptor superfamily of nuclear transcriptional regulators. This receptor localizes to the cytoplasm and to subnuclear compartments. It binds retinoic acid, the biologically active form of vitamin A which mediates cellular signalling in embryonic morphogenesis, cell growth and differentiation. It is thought that this protein limits growth of many cell types by regulating gene expression. The gene was first identified in a hepatocellular carcinoma where it flanks a hepatitis B virus integration site. Alternate promoter usage and differential splicing result in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression: Ubiquitous expression in placenta (RPKM 7.0), urinary bladder (RPKM 5.7) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p24.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (24829321..25597932)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (24833434..25600779)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (24870812..25639423)

Chromosome 3 - NC_000003.12 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A De Novo Noncoding RARB Variant Associated with Complex Microphthalmia Alters a Putative Regulatory Element.
Title: A De Novo Noncoding RARB Variant Associated with Complex Microphthalmia Alters a Putative Regulatory Element.
RARB associated with MSI, affects progression and prognosis of gastric cancer.
Title: RARB associated with MSI, affects progression and prognosis of gastric cancer.
Promoter hypermethylation of RARB and GSTP1 genes in plasma cell-free DNA as breast cancer biomarkers in Peruvian women.
Title: Promoter hypermethylation of RARB and GSTP1 genes in plasma cell-free DNA as breast cancer biomarkers in Peruvian women.
Retinoic Acid Receptor beta Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease.
Title: Retinoic Acid Receptor β Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease.
Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta.
Title: Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta.
Hepatocyte Nuclear Factor 4alpha (HNF4alpha) Plays a Controlling Role in Expression of the Retinoic Acid Receptor beta (RARbeta) Gene in Hepatocytes.
Title: Hepatocyte Nuclear Factor 4α (HNF4α) Plays a Controlling Role in Expression of the Retinoic Acid Receptor β (RARβ) Gene in Hepatocytes.
Epigenetic regulation of RARB overcomes the radio-resistance of colorectal carcinoma cells via cancer stem cells.
Title: Epigenetic regulation of RARB overcomes the radio-resistance of colorectal carcinoma cells via cancer stem cells.
DNA hypermethylation of CADM1, PAX5, WT1, RARbeta, and PAX6 genes in oropharyngeal cancer associated with human papillomavirus.
Title: DNA hypermethylation of CADM1, PAX5, WT1, RARβ, and PAX6 genes in oropharyngeal cancer associated with human papillomavirus.
Aberrant epigenetic regulation of RARbeta by TET2 is involved in cutaneous squamous cell carcinoma resistance to retinoic acid.
Title: Aberrant epigenetic regulation of RARβ by TET2 is involved in cutaneous squamous cell carcinoma resistance to retinoic acid.
Polymorphisms in Vitamin A-Related Genes and Their Functions in Autoimmune Thyroid Disease.
Title: Polymorphisms in Vitamin A-Related Genes and Their Functions in Autoimmune Thyroid Disease.

Submit: New GeneRIF Correction See all GeneRIFs (198)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Microphthalmia, syndromic 12 MedGen: C3809803 OMIM: 615524 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Common body mass index-associated variants confer risk of extreme obesity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of retinoic acid receptor, beta (RARB) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef induces loss of F-actin assembly and inhibits retinoid receptor-mediated transcription	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC17571P1 (e-PCR)
- UniSTS:271637

Rarb (e-PCR), detects polymorphism
- UniSTS:470565

PMC139866P1 (e-PCR)
- UniSTS:270900

RARB-707F (e-PCR)
- UniSTS:20814

RH121389 (e-PCR)
- UniSTS:134235

RH123921 (e-PCR)
- UniSTS:136296

D3S2327 (e-PCR)
- UniSTS:149354

RH120953 (e-PCR)
- UniSTS:134030

RARB (e-PCR)
- UniSTS:505233

RARB_245.2 (e-PCR)
- UniSTS:277660

PMC113761P1 (e-PCR)
- UniSTS:270252

D3S1583 (e-PCR), detects polymorphism
- UniSTS:14289

D3S3335 (e-PCR)
- UniSTS:36064

SHGC-3675 (e-PCR)
- UniSTS:85224

RARB (e-PCR)
- UniSTS:266481

SHGC-76778 (e-PCR)
- UniSTS:38897

SGC31578 (e-PCR)
- UniSTS:48625

D3S4231 (e-PCR)
- UniSTS:38898

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables heterocyclic compound binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear retinoid X receptor binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryonic digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic eye morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in glandular epithelial cell development	IEA Inferred from Electronic Annotation more info
involved_in growth plate cartilage development	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in outflow tract septum morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic process	IEA Inferred from Electronic Annotation 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 myelination	IEA Inferred from Electronic Annotation more info
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in striatum development	IEA Inferred from Electronic Annotation more info
involved_in ureteric bud development	IEA Inferred from Electronic Annotation more info
involved_in ventricular cardiac muscle cell differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: retinoic acid receptor beta

Names: HBV-activated protein; RAR-beta; RAR-epsilon; hepatitis B virus activated protein; nuclear receptor subfamily 1 group B member 2; retinoic acid receptor, beta polypeptide

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.

Genomic

NG_029013.3 RefSeqGene

Range

603941..773610

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000965.5 → NP_000956.2 retinoic acid receptor beta isoform 1

See identical proteins and their annotated locations for NP_000956.2

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as beta-2, is a predominant transcript. This variant can initiate translation from an upstream AUG site and also from a downstream, in-frame AUG site (PMID: 12118004). The isoform (1) represented in this RefSeq is derived from the upstream AUG start codon.

Source sequence(s)

AC093416, AC098477, AC133141

Consensus CDS

CCDS2642.1

UniProtKB/TrEMBL

A8K7L7, B6ZGR8, F1D8S6

Related

ENSP00000332296.4, ENST00000330688.9

Conserved Domains (2) summary

cd06937
Location:179 → 409

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:75 → 159

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001290216.3 → NP_001277145.1 retinoic acid receptor beta isoform 3

See identical proteins and their annotated locations for NP_001277145.1

Status: REVIEWED

Description

Transcript Variant: This variant (3, also known as beta-1) initiates from an upstream promoter and differs in the 5' UTR and 5' coding region compared to variant 1. The resulting isoform (3) has a longer and different N-terminus compared to isoform 1.

Source sequence(s)

AC092422, AC133680, AF157483, BC030234, DA240288, DC376623

Consensus CDS

CCDS93227.1

UniProtKB/Swiss-Prot

P10826, P12891, Q00989, Q15298, Q9UN48

UniProtKB/TrEMBL

B4DSI3

Related

ENSP00000510650.1, ENST00000688892.1

Conserved Domains (2) summary

cd06937
Location:186 → 416

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:82 → 166

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001290217.2 → NP_001277146.1 retinoic acid receptor beta isoform 2

See identical proteins and their annotated locations for NP_001277146.1

Status: REVIEWED

Description

Transcript Variant: This variant (4, also known as beta-5) has an alternate 5' exon, compared to variant 1. The resulting isoform (2, also known as beta', formerly, beta-4) has a shorter N-terminus, compared to isoform 1. Three variants in this gene encode the same isoform 2.

Source sequence(s)

AY501390, BC030234, DA882771

Consensus CDS

CCDS46775.1

UniProtKB/TrEMBL

Q5QHG3, Q6FHY0

Related

ENSP00000391391.1, ENST00000458646.2

Conserved Domains (2) summary

cd06937
Location:67 → 297

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cl02596
Location:1 → 47

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
NM_001290266.2 → NP_001277195.1 retinoic acid receptor beta isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as beta-4) has an alternate splice site in the 5' region, compared to variant 1. This variant can initiate translation from a non-AUG (CUG) site and also from a downstream, in-frame AUG site (PMID: 12118004). The isoform (4, also known as beta-4) represented in this RefSeq is derived from the CUG start codon, and has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC098477, AF157483, BC030234

UniProtKB/TrEMBL

A8K7L7, B6ZGR8

Conserved Domains (2) summary

cd06937
Location:130 → 360

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:26 → 110

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_001290276.2 → NP_001277205.1 retinoic acid receptor beta isoform 2

See identical proteins and their annotated locations for NP_001277205.1

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as beta-2) is a predominant transcript. This variant can initiate translation from an upstream AUG site and also from a downstream, in-frame AUG site (PMID: 12118004). The isoform (2, also known as beta', formerly, beta-4) represented in this RefSeq is derived from the downstream AUG start codon, and has a shorter N-terminus, compared to isoform 1. Three variants in this gene encode the same isoform 2.

Source sequence(s)

AC098477, BC030234, BC050415

Consensus CDS

CCDS46775.1

UniProtKB/TrEMBL

Q5QHG3, Q6FHY0

Conserved Domains (2) summary

cd06937
Location:67 → 297

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cl02596
Location:1 → 47

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
NM_001290277.1 → NP_001277206.1 retinoic acid receptor beta isoform 5

See identical proteins and their annotated locations for NP_001277206.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) has an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (5) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AC098477, BC030234, CD014022

Consensus CDS

CCDS93228.1

UniProtKB/TrEMBL

A0A8I5KWP3, A8K7L7, B6ZGR8

Related

ENSP00000510520.1, ENST00000691912.1

Conserved Domains (2) summary

cd06964
Location:75 → 159

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

cl11397
Location:179 → 363

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
NM_001290300.2 → NP_001277229.1 retinoic acid receptor beta isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (8, also known as beta1') has an alternate 5' exon, compared to variant 1. The resulting isoform (6) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

BC030234, DQ083391, HQ692864

UniProtKB/TrEMBL

A8K7L7, B6ZGR8

Conserved Domains (2) summary

cd06937
Location:136 → 366

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cd06964
Location:32 → 116

NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
NM_016152.4 → NP_057236.1 retinoic acid receptor beta isoform 2

See identical proteins and their annotated locations for NP_057236.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as beta-4) has an alternate splice site in the 5' region, compared to variant 1. This variant can initiate translation from a non-AUG (CUG) site and also from a downstream, in-frame AUG site (PMID: 12118004). The isoform (2, also known as beta', formerly, beta-4) represented in this RefSeq is derived from the AUG start codon, and has a shorter N-terminus, compared to isoform 1. Three variants in this gene encode the same isoform 2.

Source sequence(s)

AC093416, AC098477, AF157483, BC030234

Consensus CDS

CCDS46775.1

UniProtKB/TrEMBL

Q5QHG3, Q6FHY0

Related

ENSP00000398840.2, ENST00000437042.7

Conserved Domains (2) summary

cd06937
Location:67 → 297

NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

cl02596
Location:1 → 47

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

RNA

NR_110892.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC098477, BC030234, CD014021

Related

ENST00000685523.1
NR_110893.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC098477, BC030234, CD014020

Related

ENST00000480001.6