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

Gene ID: 5915, updated on 4-Jan-2025

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
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Genomic context

See RARB in Genome Data Viewer
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_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:24839678-24840178 Neighboring gene uncharacterized LOC124909355 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:24993785-24994373 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:24996287-24996461 Neighboring gene RNA, 7SL, cytoplasmic 216, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 125 Neighboring gene Sharpr-MPRA regulatory region 14202 Neighboring gene Sharpr-MPRA regulatory region 8133 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:25288369-25288948 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:25332905-25333494 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:25335344-25336543 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:25365148-25365656 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:25365657-25366165 Neighboring gene U7 small nuclear RNA Neighboring gene RNA, 5S ribosomal pseudogene 126 Neighboring gene cofilin 1 pseudogene 7 Neighboring gene Sharpr-MPRA regulatory region 14684 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:25461538-25462319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:25468815-25469652 Neighboring gene RARB antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:25491906-25492406 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:25495987-25496611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:25496710-25497250 Neighboring gene uncharacterized LOC124909356 Neighboring gene H3 histone pseudogene 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:25609805-25610306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:25614420-25614948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:25614949-25615476 Neighboring gene NUP98-TOP2B recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19608 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:25705465-25705653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:25706135-25706698 Neighboring gene DNA topoisomerase II beta Neighboring gene microRNA 4442 Neighboring gene cysteine rich protein 1 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

EBI GWAS Catalog

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

General gene information

Clone Names

  • MGC97363, AC133680.1

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in apoptotic process  
involved_in cell differentiation  
involved_in embryonic digestive tract development PubMed 
involved_in embryonic eye morphogenesis  
involved_in embryonic hindlimb morphogenesis  
involved_in glandular epithelial cell development  
involved_in growth plate cartilage development  
involved_in multicellular organism growth  
involved_in negative regulation of apoptotic process  
involved_in negative regulation of chondrocyte differentiation  
involved_in negative regulation of stem cell proliferation  
involved_in negative regulation of transcription by RNA polymerase II  
involved_in neural precursor cell proliferation  
involved_in neurogenesis  
involved_in outflow tract septum morphogenesis  
involved_in positive regulation of apoptotic process  
involved_in positive regulation of transcription by RNA polymerase II  
involved_in regulation of myelination  
involved_in retinoic acid receptor signaling pathway  
involved_in signal transduction PubMed 
involved_in stem cell proliferation  
involved_in striatum development  
involved_in ureteric bud development  
involved_in ventricular cardiac muscle cell differentiation  
Component Evidence Code Pubs
located_in chromatin  
located_in cytoplasm  
located_in nucleoplasm  
located_in nucleoplasm  
is_active_in nucleus  
located_in nucleus PubMed 

General protein information

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

  1. NG_029013.3 RefSeqGene

    Range
    603941..773610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000965.5NP_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:179409
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:75159
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  2. NM_001290216.3NP_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:186416
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:82166
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  3. NM_001290217.2NP_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:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:147
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  4. NM_001290266.2NP_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:130360
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:26110
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  5. NM_001290276.2NP_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:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:147
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
  6. NM_001290277.1NP_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:75159
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
    cl11397
    Location:179363
    NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators
  7. NM_001290300.2NP_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:136366
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cd06964
    Location:32116
    NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers
  8. NM_016152.4NP_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:67297
    NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
    cl02596
    Location:147
    NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

RNA

  1. 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
  2. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    24829321..25597932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    24833434..25600779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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