Human Gene HTR3A (ENST00000299961.5_5) from GENCODE V47lift37
  Description: 5-hydroxytryptamine receptor 3A, transcript variant 3 (from RefSeq NM_001161772.3)
Gencode Transcript: ENST00000299961.5_5
Gencode Gene: ENSG00000166736.12_12
Transcript (Including UTRs)
   Position: hg19 chr11:113,848,222-113,861,032 Size: 12,811 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr11:113,848,277-113,860,485 Size: 12,209 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:113,848,222-113,861,032)mRNA (may differ from genome)Protein (463 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: HTR3A
Diseases sorted by gene-association score: serotonin syndrome (26), motion sickness (25), irritable bowel syndrome (20), rumination disorder (15), social phobia (14), cyclic vomiting syndrome (13), constipation (13), dyspepsia (12), cocaine abuse (11), bulimia nervosa (10), generalized anxiety disorder (9), panic disorder (8), amnestic disorder (8), obsessive-compulsive disorder (8), premature ejaculation (8), anxiety disorder (8), hodgkin's lymphoma, mixed cellularity (7), sudden infant death syndrome (7), gastroparesis (7), sialadenitis (7), superior mesenteric artery syndrome (7), migraine with or without aura 1 (6), functional gastric disease (6), carcinoid syndrome (5), functional diarrhea (5), mucositis (5), early-onset schizophrenia (4), brunner syndrome (4), alcohol dependence (3), diarrhea (3), cholera (3), schizophrenia (3), gilles de la tourette syndrome (2), psychotic disorder (2), autistic disorder (2)

-  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: 1.41 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 11.28 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 -4.3055-0.078 Picture PostScript Text
3' UTR -161.20547-0.295 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
IPR008132 - 5HT3_rcpt
IPR008133 - 5HT3_rcpt_A
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 Q9UEP2
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0015276 ligand-gated ion channel activity

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

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK304630 - Homo sapiens cDNA FLJ61569 complete cds, highly similar to 5-hydroxytryptamine 3 receptor precursor.
D49394 - Homo sapiens mRNA for serotonin 5-HT3 receptor, complete cds.
AK313896 - Homo sapiens cDNA, FLJ94532, highly similar to Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3A (HTR3A),mRNA.
BC004453 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3A, mRNA (cDNA clone MGC:4303 IMAGE:2819400), complete cds.
BC002354 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3A, mRNA (cDNA clone MGC:8469 IMAGE:2821710), complete cds.
AJ003078 - Homo sapiens mRNA for 5-HT3 serotonin receptor (long isoform).
AJ003079 - Homo sapiens mRNA for 5-hydroxytryptamine3 receptor.
AJ003080 - Homo sapiens mRNA for serotonin receptor (short isoform).
BT007204 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3A mRNA, complete cds.
S82612 - Homo sapiens 5-hydroxytryptamine type 3AS receptor subunit mRNA, complete cds.
AB587356 - Synthetic construct DNA, clone: pF1KB0465, Homo sapiens HTR3A gene for 5-hydroxytryptamine (serotonin) receptor 3A, without stop codon, in Flexi system.
CU677922 - Synthetic construct Homo sapiens gateway clone IMAGE:100018334 5' read HTR3A mRNA.
DQ892003 - Synthetic construct clone IMAGE:100004633; FLH182223.01X; RZPDo839D11138D 5-hydroxytryptamine (serotonin) receptor 3A (HTR3A) gene, encodes complete protein.
DQ895193 - Synthetic construct Homo sapiens clone IMAGE:100009653; FLH182219.01L; RZPDo839D11137D 5-hydroxytryptamine (serotonin) receptor 3A (HTR3A) gene, encodes complete protein.
KJ901501 - Synthetic construct Homo sapiens clone ccsbBroadEn_10895 HTR3A gene, encodes complete protein.
KR709873 - Synthetic construct Homo sapiens clone CCSBHm_00007056 HTR3A (HTR3A) mRNA, encodes complete protein.
KR709874 - Synthetic construct Homo sapiens clone CCSBHm_00007058 HTR3A (HTR3A) mRNA, encodes complete protein.
KR709875 - Synthetic construct Homo sapiens clone CCSBHm_00007059 HTR3A (HTR3A) mRNA, encodes complete protein.
KR709876 - Synthetic construct Homo sapiens clone CCSBHm_00007060 HTR3A (HTR3A) mRNA, encodes complete protein.
AF498984 - Homo sapiens 5-hydroxytryptamine receptor 3A (HTR3A) mRNA, complete cds.
AK299973 - Homo sapiens cDNA FLJ54916 complete cds, highly similar to 5-hydroxytryptamine 3 receptor precursor.
JD498873 - Sequence 479897 from Patent EP1572962.
JD552127 - Sequence 533151 from Patent EP1572962.
JD103017 - Sequence 84041 from Patent EP1572962.
JD163289 - Sequence 144313 from Patent EP1572962.
JD429111 - Sequence 410135 from Patent EP1572962.
JD507720 - Sequence 488744 from Patent EP1572962.
JD327379 - Sequence 308403 from Patent EP1572962.
JD474939 - Sequence 455963 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000299961.1, ENST00000299961.2, ENST00000299961.3, ENST00000299961.4, NM_001161772, Q9UEP2, Q9UEP2_HUMAN, uc317mmn.1
UCSC ID: ENST00000299961.5_5
RefSeq Accession: NM_001161772.3
Protein: Q9UEP2

-  Gene Model Information
  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.