Human Gene GPR98 (uc003kjw.3) Description and Page Index
  Description: Homo sapiens G protein-coupled receptor 98 (GPR98), transcript variant 2, non-coding RNA.
RefSeq Summary (NM_032119): This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF435925.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN03267750, SAMN03267768 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000405460.9/ ENSP00000384582.2 RefSeq Select criteria :: based on conservation ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:90,076,898-90,460,033 Size: 383,136 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg19 chr5:90,077,182-90,459,717 Size: 382,536 Coding Exon Count: 26 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:90,076,898-90,460,033)mRNA (may differ from genome)Protein (1967 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHuman Cortex Gene ExpressionLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GPR98
CDC HuGE Published Literature: GPR98
Positive Disease Associations: Benzodiazepines , Body Weight , Bone Density , Calcium , Carotid Artery Diseases , Carotid Stenosis , Coronary Artery Disease , Hip , hip geometry , response to antipsychotic treatment
Related Studies:
  1. Benzodiazepines
    D E Adkins et al. Molecular psychiatry 2011, Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs., Molecular psychiatry. [PubMed 20195266]
  2. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Bone Density
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
           more ... click here to view the complete list

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.00 RPKM in Adrenal Gland
Total median expression: 80.39 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.00284-0.187 Picture PostScript Text
3' UTR -65.70316-0.208 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
  Pfam Domains:
PF00002 - 7 transmembrane receptor (Secretin family)
PF03160 - Calx-beta domain

ModBase Predicted Comparative 3D Structure on Q8WXG9-2
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF435925 - Homo sapiens very large G protein-coupled receptor 1b (VLGR1) mRNA, complete cds.
AF055084 - Homo sapiens very large G-protein coupled receptor-1 (VLGR1) mRNA, complete cds.
AK024416 - Homo sapiens cDNA FLJ14354 fis, clone Y79AA1001384, highly similar to Monogenic audiogenic seizure susceptibility protein 1 homolog precursor.
AB014586 - Homo sapiens mRNA for KIAA0686 protein, partial cds.
BC172212 - Synthetic construct Homo sapiens clone IMAGE:9094358 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
BC172210 - Synthetic construct Homo sapiens clone IMAGE:9094354 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
BC034748 - Homo sapiens G protein-coupled receptor 98, mRNA (cDNA clone IMAGE:5183306), with apparent retained intron.
BC172211 - Synthetic construct Homo sapiens clone IMAGE:9094356 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
JD288327 - Sequence 269351 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AF055084, KIAA0686, KIAA1943, MASS1, NM_032119, NP_115495, Q8WXG9-2, VLGR1
UCSC ID: uc003kjw.3
RefSeq Accession: NM_032119
Protein: Q8WXG9-2, splice isoform of Q8WXG9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF055084.1
exon count: 26CDS single in 3' UTR: no RNA size: 6503
ORF size: 5904CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 10233.50frame shift in genome: no % Coverage: 100.00
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: 349# 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.