Human Gene HTR3D (uc011bqv.2)
  Description: Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3D, ionotropic (HTR3D), transcript variant 3, mRNA.
RefSeq Summary (NM_001163646): 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 chr3:183,750,619-183,757,157 Size: 6,539 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr3:183,750,619-183,756,763 Size: 6,145 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
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 (chr3:183,750,619-183,757,157)mRNA (may differ from genome)Protein (454 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
LynxMGIneXtProtOMIMPubMedReactome
TreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: 5HT3D_HUMAN
DESCRIPTION: RecName: Full=5-hydroxytryptamine receptor 3D; Short=5-HT3-D; Short=5-HT3D; AltName: Full=Serotonin receptor 3D; Flags: Precursor;
FUNCTION: This is one of the several different receptors for 5- hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor is a ligand-gated ion channel, which when activated causes fast, depolarizing responses. It is a cation-specific, but otherwise relatively nonselective, ion channel.
SUBUNIT: Forms a pentaheteromeric complex with HTR3A. Not functional as a homomeric complex.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Note=Presumably retained within the endoplasmic reticulum unless complexed with HTR3A.
TISSUE SPECIFICITY: Expressed in liver, as well as fetal and adult colon and kidney.
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family. 5-hydroxytryptamine receptor (TC 1.A.9.2) subfamily. HTR3D sub-subfamily.

-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
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
  InterPro Domains: Graphical view of domain structure
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM

Pfam Domains:
PF02931 - Neurotransmitter-gated ion-channel ligand binding domain
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

SCOP Domains:
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore

ModBase Predicted Comparative 3D Structure on Q70Z44
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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:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0005515 protein binding
GO:0022850 serotonin-gated cation channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0007210 serotonin receptor signaling pathway
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  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: 5HT3D_HUMAN, C9J2I6, NM_001163646, NP_001157118, Q495N5, Q495N6, Q70Z44, Q7Z6B3
UCSC ID: uc011bqv.2
RefSeq Accession: NM_001163646
Protein: Q70Z44 (aka 5HT3D_HUMAN)
CCDS: CCDS54685.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001163646.1
exon count: 8CDS single in 3' UTR: no RNA size: 1786
ORF size: 1365CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2642.00frame shift in genome: no % Coverage: 98.49
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.