Human Gene HTR3D (uc010hxp.3)
  Description: Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3D, ionotropic (HTR3D), transcript variant 2, mRNA.
RefSeq Summary (NM_182537): The protein encoded this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit D of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a mitogen and a hormone. This hormone has been linked to neuropsychiatric disorders, including anxiety, depression, and migraine. Serotonin receptors causes fast and depolarizing responses in neurons following activation. The genes encoding subunits C, D and E of this type 3 receptor form a cluster on chromosome 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009].
Transcript (Including UTRs)
   Position: hg19 chr3:183,752,845-183,757,157 Size: 4,313 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr3:183,753,008-183,756,763 Size: 3,756 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:183,752,845-183,757,157)mRNA (may differ from genome)Protein (233 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCLynxMGIOMIMPubMedReactome
TreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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): HTR3D
CDC HuGE Published Literature: HTR3D

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 0.03 RPKM in Testis
Total median expression: 0.03 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 -53.20163-0.326 Picture PostScript Text
3' UTR -99.83394-0.253 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:
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

SCOP Domains:
90112 - Neurotransmitter-gated ion-channel transmembrane pore

ModBase Predicted Comparative 3D Structure on Q70Z44-3
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AY159812 - Homo sapiens 5-hydroxytryptamine serotonin receptor 3D (HTR3D) mRNA, complete cds.
AJ437318 - Homo sapiens mRNA for 5-hydroxytryptamine 3-receptor subunit D (HTR3D gene).
BC101090 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3 family member D, mRNA (cDNA clone MGC:119636 IMAGE:40009594), complete cds.
BC101091 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3 family member D, mRNA (cDNA clone MGC:119637 IMAGE:40009597), complete cds.
KJ903989 - Synthetic construct Homo sapiens clone ccsbBroadEn_13383 HTR3D gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q70Z44 (Reactome details) participates in the following event(s):

R-HSA-975311 HTR3 pentamer:5HT transports Na+,K+, and Ca2+
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: BC101090, NM_182537, NP_872343, Q70Z44-3
UCSC ID: uc010hxp.3
RefSeq Accession: NM_182537
Protein: Q70Z44-3, splice isoform of Q70Z44

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC101090.2
exon count: 4CDS single in 3' UTR: no RNA size: 1043
ORF size: 702CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1103.50frame 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: 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.