Homo sapiens complex locus RARB, encoding retinoic acid receptor, beta.
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SUMMARY back to top
RefSeq summary
[RARB] 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. The gene expresses at least two transcript variants; one additional transcript has been described, but its full length nature has not been determined. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is well expressed, 1.3 times the average gene in this release. The sequence of this gene is defined by 159 GenBank accessions from 132 cDNA clones, some from kidney (seen 9 times), eye (8), hepatocellular carcinoma (8), tongue, tumor tissue (7), lung (6), placenta cot 25-normalized (5), brain (4) and 62 other tissues. We annotate structural defects or features in 31 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 14 distinct gt-ag introns. Transcription produces 9 different mRNAs, 8 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, presence or absence of 4 cassette exons, overlapping exons with different boundaries.
Note that mRNA .fAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant bAug10, gAug10).
Function: There are 122 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Adenocarcinoma; Alcoholism; Attention Deficit Disorder with Hyperactivity; Autistic Disorder; Bipolar Disorder; Brain Neoplasms; Breast Neoplasms; Carcinoma, Small Cell; Carcinoma, Squamous Cell and 18 others), proposed to participate in pathways (Non-small cell lung cancer, Pathways in cancer, Small cell lung cancer) and processes (signal transduction, embryonic eye morphogenesis, embryonic hindlimb morphogenesis, negative regulation of cell proliferation, negative regulation of transcription from RNA polymerase II promoter, neurogenesis, positive regulation of apoptosis, positive regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-dependent, striatum development, ureteric bud development, ventricular cardiac muscle cell differentiation). Proteins are expected to have molecular functions (DNA binding, protein binding, metal ion binding, retinoic acid receptor activity, sequence-specific DNA binding, steroid hormone receptor activity, transcription activator activity, transcription factor activity, zinc ion binding) and to localize in various compartments (nucleus, membrane, cytoplasm). Putative protein interactors have been described (CEBPA, CEBPB, DNMT3A, DNMT3B, HDAC1, HIST4H4, MAP6, NCOA1, NCOA3, NCOR2, NR4A2, PNRC1, RXRA, RXRB, RXRG, S1PR2ANDDNMT1, SMAD2).
Protein coding potential: 8 spliced mRNAs putatively encode good proteins, altogether 8 different isoforms (7 complete, 1 partial), some containing domains Ligand-binding domain of nuclear hormone receptor, Zinc finger, C4 type (two domains) [Pfam], some transmembrane domains, a coiled coil stretch [Psort2]. The remaining mRNA variant (unspliced) appears not to encode a good protein.
3 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 62 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 3, links to other databases and other names
Map: This gene RARB maps on chromosome 3, at 3p24 according to Entrez Gene. In AceView, it covers 423.61 kb, from 25215823 to 25639428 (NCBI 37, August 2010), on the direct strand.
Links to: , manual annotations from GAD, KEGG_05200, KEGG_05222, KEGG_05223, the SNP view, gene overviews from Entrez Gene 5915, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as RARB, HAP, RRB2 or NR1B2, LOC5915. It has been described as retinoic acid receptor beta, RAR-beta, RAR-epsilon, OTTHUMP00000208326, HBV-activated protein, retinoic acid receptor beta 2, retinoic acid receptor beta 4, retinoic acid receptor beta 5, hepatitis B virus activated protein, retinoic acid receptor, beta polypeptide, nuclear receptor subfamily 1 group B member 2.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Rara (e=3 10-54), Rarb (e=4 10-48).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes nhr-23 (e=4 10-25), sex-1 (e=10-23), nhr-85 (e=4 10-23), nhr-41 (e=2 10-22), nhr-91 (e=10-21), nhr-2 (e=4 10-25), nhr-6 (e=5 10-21), nhr-14 (e=5 10-21), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene ATMRP14 (e=0.54), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 2775 bp 453 aa 97 bp 1316 bp 2kb possibly including promoter 169670 bp 1kb
bAug10 4862 bp 448 aa 2202 bp 1313 bp 90 bp 2kb possibly including promoter 171400 bp 1kb
cAug10 1258 bp 402 aa 16 bp 33 bp 2kb probably including promoter 167934 bp 1kb
dAug10 2561 bp 397 aa 54 bp 1313 bp 2kb possibly including promoter 139594 bp 1kb
eAug10 1235 bp 272 aa 383 bp 33 bp 2kb probably including promoter 167934 bp 1kb
fAug10 1191 bp 272 aa 16 bp 356 bp 2kb probably including promoter 167934 bp 1kb
gAug10 564 bp 166 aa 66 bp 33 bp 2kb possibly including promoter 395455 bp 1kb
hAug10 1689 bp 107 aa 30 bp 1335 bp 2kb including Promoter 34960 bp 1kb
iAug10-unspliced 398 bp 82 aa 145 bp 4 bp 2kb 398 bp 1kb

Gene neighbors and Navigator on chromosome 3p24 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               122 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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