Homo sapiens complex locus RARG, encoding retinoic acid receptor, gamma.
SUMMARY back to top
RefSeq annotates 2 representative transcripts (NM included in AceView variants .b and .d), 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 20 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 expressed at high level, 3.7 times the average gene in this release. The sequence of this gene is defined by 427 GenBank accessions from 383 cDNA clones, some from tongue, tumor tissue (seen 51 times), uterus (27), lung (22), brain (16), skin (12), trachea (9), amelanotic melanoma, cell line (8) and 103 other tissues. We annotate structural defects or features in 9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 26 distinct gt-ag introns. Transcription produces 21 different mRNAs, 20 alternatively spliced variants and 1 unspliced form. There are 4 probable alternative promotors, 5 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 12 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns.
5 variants were isolated in vivo, despite the fact that they are predicted targets 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 dAug10, gAug10, hAug10).
Function: There are 54 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Alcoholism; Attention Deficit Disorder with Hyperactivity; Autistic Disorder; Bipolar Disorder; Breast Neoplasms; Drug Toxicity; Edema; Genetic Predisposition to Disease; Mental Disorders; Schizophrenia) and proposed to participate in processes (anterior/posterior pattern formation, bone morphogenesis, embryonic eye morphogenesis, embryonic hindlimb morphogenesis, epithelium development, Harderian gland development, negative regulation of cell proliferation, negative regulation of transcription from RNA polymerase II promoter, positive regulation of apoptosis, positive regulation of programmed cell death, positive regulation of transcription from RNA polymerase II promoter, prostate gland epithelium morphogenesis, regulation of transcription, DNA-dependent, reproductive structure development, trachea cartilage development). Proteins are expected to have molecular functions (DNA binding, metal ion binding, retinoic acid receptor activity, retinoid X receptor binding, sequence-specific DNA binding, steroid hormone receptor activity, transcription factor activity, zinc ion binding) and to localize in various compartments (mitochondrion, nucleus, transcription factor complex). Putative protein interactors have been described (DMWDANDDMPK, HMGA1, ITGB1BP2, JUBANDHAUS4, MAP6, NCOA1, NCOA3, NCOR1, NCOR2, NR0B2, PNRC1, PNRC2, RXRA, RXRB, RXRG, SMAD3, SRF, USHBP1ANDNR2F6).
Protein coding potential: 18 spliced mRNAs putatively encode good proteins, altogether 18 different isoforms (12 complete, 4 COOH complete, 2 partial), some containing domains Ligand-binding domain of nuclear hormone receptor, Zinc finger, C4 type (two domains) [Pfam]. The remaining 3 mRNA variants (2 spliced, 1 unspliced; 1 partial) appear not to encode good proteins.
Isoform RARG.jAug10 is annotated using as Met a Kozak-compatible a..GTG. start, thereby gaining 149 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 12, links to other databases and other names
Map: This gene RARG maps on chromosome 12, at 12q13 according to Entrez Gene. In AceView, it covers 22.42 kb, from 53626764 to 53604346 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, PhosphoSite, the SNP view, gene overviews from Entrez Gene 5916, 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 RARG, RARC or NR1B3, LOC5916. It has been described as retinoic acid receptor gamma, RAR-gamma, OTTHUMP00000045736, nuclear receptor subfamily 1 group B member 3.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Rarg (e=3 10-26), Rara (e=3 10-24), Rarb (e=5 10-24).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes nhr-2 (e=4 10-13), nhr-101 (e=6 10-12), nhr-85 (e=7 10-12), nhr-23 (e=9 10-12), sex-1 (e=10-11), nhr-49 (e=2 10-11), unc-55 (e=2 10-11), nhr-41 (e=8 10-11), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G64600 (e=0.99), 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!.
          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.
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
Downstream sequence
aAug10 2852 bp 572 aa 381 bp 1106 bp 2kb including Promoter 21643 bp 1kb
bAug10 2955 bp 615 aa 484 bp 1106 bp 2kb including Promoter 21682 bp 1kb
cAug10 2966 bp 607 aa 487 bp 1114 bp 2kb including Promoter 21690 bp 1kb
dAug10 2708 bp 443 aa 270 bp 1106 bp 21 bp 2kb including Promoter 9801 bp 1kb
eAug10 1828 bp 432 aa 246 bp 283 bp 2kb possibly including promoter 9070 bp 1kb
fAug10 1559 bp 413 aa 178 bp 139 bp 2kb possibly including promoter 7151 bp 1kb
gAug10 2097 bp 382 aa 323 bp 625 bp 69 bp 2kb including Promoter 21147 bp 1kb
hAug10 2435 bp 333 aa 356 bp 1077 bp 69 bp 2kb including Promoter 21634 bp 1kb
iAug10 1368 bp 201 aa 310 bp 452 bp 2kb including Promoter 18590 bp 1kb
jAug10 991 bp 179 aa 454 bp 54 bp 2kb possibly including promoter 5528 bp 1kb
kAug10 812 bp 137 aa 161 bp 237 bp 2kb including Promoter 17644 bp 1kb
lAug10 577 bp 126 aa 25 bp 171 bp 2kb including Promoter 5367 bp 1kb
mAug10 550 bp 135 aa 141 bp 2kb including Promoter 4605 bp 1kb
nAug10 553 bp 124 aa 180 bp 2kb including Promoter 763 bp 1kb
oAug10 556 bp 121 aa 188 bp 2kb 4711 bp 1kb
pAug10 588 bp 128 aa 200 bp 2kb including Promoter 4664 bp 1kb
qAug10 591 bp 130 aa 196 bp 2kb including Promoter 4670 bp 1kb
rAug10 543 bp 116 aa 9 bp 183 bp 2kb including Promoter 4553 bp 1kb
sAug10 902 bp 135 aa 382 bp 112 bp 2kb including Promoter 16846 bp 1kb
tAug10-unspliced 823 bp 53 aa 584 bp 77 bp 2kb 823 bp 1kb
uAug10 563 bp 176 aa 376 bp 2kb including Promoter 16848 bp 1kb

Gene neighbors and Navigator on chromosome 12q13 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               54 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q, .r, .s, .t-u, .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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !