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

Gene ID: 5915, updated on 24-May-2020

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
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; 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

Genomic context

See RARB in Genome Data Viewer
Location:
3p24.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (24829323..25597932)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (25215638..25639423)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit K pseudogene 2 Neighboring gene uncharacterized LOC107986070 Neighboring gene RNA, 7SL, cytoplasmic 216, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 125 Neighboring gene uncharacterized LOC105376998 Neighboring gene RNA, 5S ribosomal pseudogene 126 Neighboring gene cofilin 1 pseudogene 7 Neighboring gene RARB antisense RNA 1 Neighboring gene H3 histone pseudogene 10 Neighboring gene NUP98-TOP2B recombination region Neighboring gene DNA topoisomerase II beta Neighboring gene microRNA 4442

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Microphthalmia, syndromic 12 Compare labs

NHGRI GWAS Catalog

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC97363, AC133680.1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
drug binding IEA
Inferred from Electronic Annotation
more info
 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
retinoid X receptor binding IEA
Inferred from Electronic Annotation
more info
 
signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
embryonic digestive tract development IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic eye morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
glandular epithelial cell development IEA
Inferred from Electronic Annotation
more info
 
growth plate cartilage development IEA
Inferred from Electronic Annotation
more info
 
hormone-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
outflow tract septum morphogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of myelination IEA
Inferred from Electronic Annotation
more info
 
retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
striatum development IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
ureteric bud development IEA
Inferred from Electronic Annotation
more info
 
ventricular cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
host cell nucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
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)

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/Swiss-Prot
    P10826
    UniProtKB/TrEMBL
    F1D8S6, Q86UC5
    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_001290216.2NP_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
    UniProtKB/Swiss-Prot
    P10826
    Related
    ENSP00000373282.4, ENST00000383772.8
    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_001290217.1NP_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/Swiss-Prot
    P10826
    UniProtKB/TrEMBL
    Q5QHG3
    Related
    ENSP00000391391.1, ENST00000458646.1
    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_001290266.1NP_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/Swiss-Prot
    P10826
    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_001290276.1NP_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/Swiss-Prot
    P10826
    UniProtKB/TrEMBL
    Q5QHG3, Q86UC5
    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
    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_001290300.1NP_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
    F1D8S6, Q3SB16
    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_016152.3NP_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/Swiss-Prot
    P10826
    UniProtKB/TrEMBL
    Q5QHG3
    Related
    ENSP00000398840.2, ENST00000437042.6
    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_110892.1 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
  2. NR_110893.1 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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    24829323..25597932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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