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

    Gene ID: 5915, updated on 11-Apr-2024

    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
    NEW
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (24829321..25597932)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (24833434..25600779)
    105.20220307 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: 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
    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

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC97363, AC133680.1

    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-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 hormone-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in multicellular organism growth 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 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
    part_of 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

    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)

    NEW Try the new Transcript table

    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_2023_10

    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)