Human Gene GABRB1 (uc011bzd.1)
  Description: Homo sapiens gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1), mRNA.
RefSeq Summary (NM_000812): The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes GABA A receptor, beta 1 subunit. It is mapped to chromosome 4p12 in a cluster comprised of genes encoding alpha 4, alpha 2 and gamma 1 subunits of the GABA A receptor. Alteration of this gene is implicated in the pathogenetics of schizophrenia. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr4:47,033,295-47,035,635 Size: 2,341 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr4:47,033,669-47,034,816 Size: 1,148 Coding Exon Count: 3 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:47,033,295-47,035,635)mRNA (may differ from genome)Protein (184 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCHuman Cortex Gene ExpressionLynxMalacardsMGIPubMed
TreefamUniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GABRB1
CDC HuGE Published Literature: GABRB1
Positive Disease Associations: alcohol dependence , Body Height , Creatinine , Echocardiography , epilepsy , manic-depressive illness , Waist Circumference
Related Studies:
  1. alcohol dependence
    Parsian A et al. 1999, Human chromosomes 11p15 and 4p12 and alcohol dependence: possible association with the GABRB1 gene., American journal of medical genetics. 1999 Oct;88(5):533-8. [PubMed 10490712]
    Results with TH and DRD4 genes indicate that these two genes may not play major roles in the development of alcoholism.
  2. Body Height
    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. Body Height
    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.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: GABRB1
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 45* (1230), schizoaffective disorder (6), schizophrenia (5), alcohol dependence (2)
* = Manually curated disease association

-  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: 1.88 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 14.60 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 -102.70374-0.275 Picture PostScript Text
3' UTR -252.54819-0.308 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
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel

SCOP Domains:
63712 - Nicotinic receptor ligand binding domain-like

ModBase Predicted Comparative 3D Structure on B4DJD0
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK225686 - Homo sapiens mRNA for Gamma-aminobutyric-acid receptor beta-1 subunit precursor variant, clone: SYN05435.
BC022449 - Homo sapiens gamma-aminobutyric acid (GABA) A receptor, beta 1, mRNA (cDNA clone MGC:25991 IMAGE:4797401), complete cds.
AK225167 - Homo sapiens mRNA for Gamma-aminobutyric-acid receptor beta-1 subunit precursor (GABA(A) receptor) variant, clone: CBR02137.
X14767 - Human mRNA for GABA-A receptor, beta 1 subunit.
AK312720 - Homo sapiens cDNA, FLJ93124, highly similar to Homo sapiens gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1), mRNA.
AK293691 - Homo sapiens cDNA FLJ57719 complete cds, highly similar to Gamma-aminobutyric-acid receptor beta-1 subunit precursor.
AB385048 - Synthetic construct DNA, clone: pF1KB5121, Homo sapiens GABRB1 gene for gamma-aminobutyric-acid receptor subunit beta-1 precursor, complete cds, without stop codon, in Flexi system.
KJ534841 - Homo sapiens clone GABRB1_iso-A_adult-A03 gamma-aminobutyric acid A receptor beta 1 isoform A (GABRB1) mRNA, partial cds, alternatively spliced.
KJ535054 - Homo sapiens clone GABRB1_iso-B_fetal-F13 gamma-aminobutyric acid A receptor beta 1 isoform B (GABRB1) mRNA, complete cds, alternatively spliced.
DQ892357 - Synthetic construct clone IMAGE:100004987; FLH185502.01X; RZPDo839B11148D gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1) gene, encodes complete protein.
DQ893370 - Synthetic construct clone IMAGE:100006000; FLH196710.01X; RZPDo839H02156D gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1) gene, encodes complete protein.
DQ895564 - Synthetic construct Homo sapiens clone IMAGE:100010024; FLH185498.01L; RZPDo839B11147D gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1) gene, encodes complete protein.
DQ896690 - Synthetic construct Homo sapiens clone IMAGE:100011150; FLH263663.01L; RZPDo839H01155D gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1) gene, encodes complete protein.
DQ896691 - Synthetic construct Homo sapiens clone IMAGE:100011151; FLH196706.01L; RZPDo839H02155D gamma-aminobutyric acid (GABA) A receptor, beta 1 (GABRB1) gene, encodes complete protein.
CU692622 - Synthetic construct Homo sapiens gateway clone IMAGE:100019567 5' read GABRB1 mRNA.
AK296023 - Homo sapiens cDNA FLJ60591 complete cds, moderately similar to Gamma-aminobutyric-acid receptor beta-1 subunit precursor.
AK307120 - Homo sapiens cDNA, FLJ97068.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04080 - Neuroactive ligand-receptor interaction

-  Other Names for This Gene
  Alternate Gene Symbols: AK296023, B4DJD0, B4DJD0_HUMAN
UCSC ID: uc011bzd.1
RefSeq Accession: NM_000812
Protein: B4DJD0

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK296023.1
exon count: 3CDS single in 3' UTR: no RNA size: 1641
ORF size: 555CDS single in intron: no Alignment % ID: 99.88
txCdsPredict score: 1035.00frame 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: 1134# 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.