Human Gene RARG (uc001scf.3) Description and Page Index
  Description: Homo sapiens retinoic acid receptor, gamma (RARG), transcript variant 1, mRNA.
RefSeq Summary (NM_000966): This gene encodes a retinoic acid receptor that belongs to the nuclear hormone receptor family. Retinoic acid receptors (RARs) act as ligand-dependent transcriptional regulators. When bound to ligands, RARs activate transcription by binding as heterodimers to the retinoic acid response elements (RARE) found in the promoter regions of the target genes. In their unbound form, RARs repress transcription of their target genes. RARs are involved in various biological processes, including limb bud development, skeletal growth, and matrix homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011].
Transcript (Including UTRs)
   Position: hg19 chr12:53,604,350-53,626,040 Size: 21,691 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr12:53,605,460-53,621,329 Size: 15,870 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:53,604,350-53,626,040)mRNA (may differ from genome)Protein (454 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RARG_HUMAN
DESCRIPTION: RecName: Full=Retinoic acid receptor gamma; Short=RAR-gamma; AltName: Full=Nuclear receptor subfamily 1 group B member 3;
FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors. Required for limb bud development. In concert with RARA or RARB, required for skeletal growth, matrix homeostasis and growth plate function (By similarity).
SUBUNIT: Homodimer (By similarity). Heterodimer with a RXR molecule (By similarity). Binds DNA preferentially as a RAR/RXR heterodimer (By similarity). Forms a complex with PUS1 and the SRA1 RNA in the nucleus (By similarity).
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
SEQUENCE CAUTION: Sequence=CAA40548.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=Wikipedia; Note=Retinoic acid receptor entry; URL="http://en.wikipedia.org/wiki/Retinoic_acid_receptor";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RARG
CDC HuGE Published Literature: RARG

-  MalaCards Disease Associations
  MalaCards Gene Search: RARG
Diseases sorted by gene-association score: paraneoplastic polyneuropathy (16), embryonal carcinoma (13), exfoliative ichthyosis (9), ichthyosis bullosa of siemens (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 56.98 RPKM in Esophagus - Mucosa
Total median expression: 569.85 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -243.70492-0.495 Picture PostScript Text
3' UTR -466.511110-0.420 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR003078 - Retinoic_acid_rcpt
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1EXA
- X-ray MuPIT

1EXX
- X-ray MuPIT

1FCX
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
1FCY - X-ray MuPIT 1FCZ - X-ray MuPIT 1FD0 - X-ray MuPIT
2LBD - X-ray MuPIT 3LBD - X-ray MuPIT 4LBD - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P13631
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003707 steroid hormone receptor activity
GO:0003708 retinoic acid receptor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
GO:0046965 retinoid X receptor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001843 neural tube closure
GO:0002063 chondrocyte development
GO:0002068 glandular epithelial cell development
GO:0003406 retinal pigment epithelium development
GO:0003417 growth plate cartilage development
GO:0003430 growth plate cartilage chondrocyte growth
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0008361 regulation of cell size
GO:0009952 anterior/posterior pattern specification
GO:0010468 regulation of gene expression
GO:0010628 positive regulation of gene expression
GO:0031076 embryonic camera-type eye development
GO:0031641 regulation of myelination
GO:0032331 negative regulation of chondrocyte differentiation
GO:0032526 response to retinoic acid
GO:0035116 embryonic hindlimb morphogenesis
GO:0035264 multicellular organism growth
GO:0043010 camera-type eye development
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0043068 positive regulation of programmed cell death
GO:0043401 steroid hormone mediated signaling pathway
GO:0045596 negative regulation of cell differentiation
GO:0045637 regulation of myeloid cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048048 embryonic eye morphogenesis
GO:0048384 retinoic acid receptor signaling pathway
GO:0048608 reproductive structure development
GO:0048732 gland development
GO:0060041 retina development in camera-type eye
GO:0060070 canonical Wnt signaling pathway
GO:0060173 limb development
GO:0060324 face development
GO:0060348 bone development
GO:0060349 bone morphogenesis
GO:0060429 epithelium development
GO:0060534 trachea cartilage development
GO:0060740 prostate gland epithelium morphogenesis
GO:0061037 negative regulation of cartilage development
GO:0070384 Harderian gland development
GO:0071300 cellular response to retinoic acid
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC019098 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone IMAGE:5013273), containing frame-shift errors.
BC098421 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone IMAGE:5442190), containing frame-shift errors.
BC064524 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone IMAGE:5738222), containing frame-shift errors.
BC072462 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone IMAGE:6473808), containing frame-shift errors.
M38258 - Human retinoic acid receptor gamma 1 mRNA, complete cds.
AK297023 - Homo sapiens cDNA FLJ59333 complete cds, highly similar to Retinoic acid receptor gamma-2.
AK297801 - Homo sapiens cDNA FLJ54463 complete cds, highly similar to Retinoic acid receptor gamma-2.
AK316259 - Homo sapiens cDNA, FLJ79158 complete cds, highly similar to Retinoic acid receptor gamma-2.
AK297277 - Homo sapiens cDNA FLJ54482 complete cds, highly similar to Retinoic acid receptor gamma-2.
AK297110 - Homo sapiens cDNA FLJ59338 complete cds, highly similar to Retinoic acid receptor gamma-2.
AK290588 - Homo sapiens cDNA FLJ75202 complete cds, highly similar to Homo sapiens, retinoic acid receptor, gamma.
M24857 - Human retinoic acid receptor gamma mRNA, complete cds.
L12060 - Homo sapiens retinoic acid receptor (gamma-7) mRNA.
BC093727 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone MGC:120762 IMAGE:7939572), complete cds.
BC093729 - Homo sapiens retinoic acid receptor, gamma, mRNA (cDNA clone MGC:120764 IMAGE:7939574), complete cds.
M57707 - Human retinoic acid receptor gamma mRNA, complete cds.
HQ692829 - Homo sapiens retinoic acid nuclear receptor gamma variant 2 (NR1B3) mRNA, complete cds.
AB307689 - Homo sapiens NR1B3 mRNA for retinoic acid receptor gamma, complete cds.
HQ692828 - Homo sapiens retinoic acid nuclear receptor gamma variant 1 (NR1B3) mRNA, complete cds.
KJ891983 - Synthetic construct Homo sapiens clone ccsbBroadEn_01377 RARG gene, encodes complete protein.
AB527503 - Synthetic construct DNA, clone: pF1KB5808, Homo sapiens RARG gene for retinoic acid receptor, gamma, without stop codon, in Flexi system.
AK301057 - Homo sapiens cDNA FLJ53545 complete cds, highly similar to Retinoic acid receptor gamma-B.
HQ229990 - Homo sapiens clone Such_081284 NUP98/RARG fusion protein mRNA, partial cds.
JD161289 - Sequence 142313 from Patent EP1572962.
JD273184 - Sequence 254208 from Patent EP1572962.
JD216645 - Sequence 197669 from Patent EP1572962.
JD392433 - Sequence 373457 from Patent EP1572962.
JD133858 - Sequence 114882 from Patent EP1572962.
JD324949 - Sequence 305973 from Patent EP1572962.
JD077281 - Sequence 58305 from Patent EP1572962.
JD445921 - Sequence 426945 from Patent EP1572962.
JD108364 - Sequence 89388 from Patent EP1572962.
JD157462 - Sequence 138486 from Patent EP1572962.
JD294477 - Sequence 275501 from Patent EP1572962.
JD535940 - Sequence 516964 from Patent EP1572962.
JD403556 - Sequence 384580 from Patent EP1572962.
JD233087 - Sequence 214111 from Patent EP1572962.
JD232937 - Sequence 213961 from Patent EP1572962.
JD360437 - Sequence 341461 from Patent EP1572962.
JD191728 - Sequence 172752 from Patent EP1572962.
JD252557 - Sequence 233581 from Patent EP1572962.
JD121544 - Sequence 102568 from Patent EP1572962.
JD352158 - Sequence 333182 from Patent EP1572962.
JD363310 - Sequence 344334 from Patent EP1572962.
JD260937 - Sequence 241961 from Patent EP1572962.
JD173066 - Sequence 154090 from Patent EP1572962.
JD471277 - Sequence 452301 from Patent EP1572962.
JD172910 - Sequence 153934 from Patent EP1572962.
JD420427 - Sequence 401451 from Patent EP1572962.
M32074 - Human retinoic acid receptor gamma 2 mRNA, 5' end.
JD107985 - Sequence 89009 from Patent EP1572962.
JD397433 - Sequence 378457 from Patent EP1572962.
JD141616 - Sequence 122640 from Patent EP1572962.
JD057588 - Sequence 38612 from Patent EP1572962.
JD415616 - Sequence 396640 from Patent EP1572962.
JD475436 - Sequence 456460 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity

Reactome (by CSHL, EBI, and GO)

Protein P13631 (Reactome details) participates in the following event(s):

R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-5334854 RAR:RXR binds SUMO-CRABP2:atRA
R-HSA-5634103 SUMO-CRABP2 dissociates from atRA:RAR:RXR
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-212436 Generic Transcription Pathway
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-162582 Signal Transduction
R-HSA-74160 Gene expression (Transcription)
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZAE4, NM_000966, NP_001230660, NR1B3, P13631, P22932, Q15281, Q52LZ8, Q9BYX8, Q9H1I3, Q9UJ38, RARG_HUMAN
UCSC ID: uc001scf.3
RefSeq Accession: NM_000966
Protein: P13631 (aka RARG_HUMAN)
CCDS: CCDS8850.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000966.5
exon count: 10CDS single in 3' UTR: no RNA size: 2992
ORF size: 1365CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2831.00frame shift in genome: no % Coverage: 99.16
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.