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Aliases for HTR3A Gene

Aliases for HTR3A Gene

  • 5-Hydroxytryptamine (Serotonin) Receptor 3A, Ionotropic 2 3
  • HTR3 3 4 6
  • Serotonin-Gated Ion Channel Receptor 3 4
  • 5-Hydroxytryptamine Receptor 3 3 4
  • Serotonin Receptor 3A 3 4
  • 5-HT3-A 3 4
  • 5-HT-3 3 4
  • 5-HT3A 3 4
  • 5-HT3R 3 4
  • 5HT3R 3 4
  • 5-Hydroxytryptamine (Serotonin) Receptor 3A 2
  • 5-Hydroxytryptamine Receptor 3A 3
  • 5HT3 Serotonin Receptor 3

External Ids for HTR3A Gene

Previous HGNC Symbols for HTR3A Gene

  • HTR3

Previous GeneCards Identifiers for HTR3A Gene

  • GC11P116198
  • GC11P115357
  • GC11P113879
  • GC11P113383
  • GC11P113351
  • GC11P109774

Summaries for HTR3A Gene

Entrez Gene Summary for HTR3A Gene

  • The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit A of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor causes fast, depolarizing responses in neurons after activation. It appears that the heteromeric combination of A and B subunits is necessary to provide the full functional features of this receptor, since either subunit alone results in receptors with very low conductance and response amplitude. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for HTR3A Gene

HTR3A (5-Hydroxytryptamine (Serotonin) Receptor 3A, Ionotropic) is a Protein Coding gene. Diseases associated with HTR3A include hypochondriasis and fibromyalgia. Among its related pathways are CREB Pathway and SIDS Susceptibility Pathways. GO annotations related to this gene include receptor activity and serotonin receptor activity. An important paralog of this gene is HTR3D.

UniProtKB/Swiss-Prot for HTR3A Gene

  • 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 in neurons. It is a cation-specific, but otherwise relatively nonselective, ion channel.

Tocris Summary for HTR3A Gene

  • Serotonin 5-HT3 receptors, are ligand-gated ion channels of the Cys-loop family. The receptor consists of 4-transmembrane domains that form an intrinsic cation-selective channel. So far five human 5-HT3 receptor subtypes have been identified (5-HT3A-E). The 5-HT3B-E subtypes do not form functional homo-oligomeric complexes like the 5-HT3A subtypes, but co-assemble with 5-HT3A to influence its functional expression.

Gene Wiki entry for HTR3A Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HTR3A Gene

Genomics for HTR3A Gene

Regulatory Elements for HTR3A Gene

Genomic Location for HTR3A Gene

113,974,881 bp from pter
113,990,313 bp from pter
15,433 bases
Plus strand

Genomic View for HTR3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HTR3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HTR3A Gene

Proteins for HTR3A Gene

  • Protein details for HTR3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    5-hydroxytryptamine receptor 3A
    Protein Accession:
    Secondary Accessions:
    • B4DSY6
    • G5E986
    • O60854
    • Q7KZM7
    • Q99918
    • Q9BSZ9

    Protein attributes for HTR3A Gene

    478 amino acids
    Molecular mass:
    55280 Da
    Quaternary structure:
    • Forms pentahomomeric complex as well as pentaheteromeric complex with HTR3B or HTR3C or HTR3D or HTR3E; homomeric complex is functional but exhibits low conductance with modified voltage dependence, and decreased agonist and antagonist affinity. Interacts with RIC3.
    • The HA-stretch region of HTR3A seems to be responsible for the low conductance of HTR3A homomers compared to that of HTR3A/HTR3B heteromers

    Alternative splice isoforms for HTR3A Gene


neXtProt entry for HTR3A Gene

Proteomics data for HTR3A Gene at MOPED

Post-translational modifications for HTR3A Gene

  • Glycosylation at Asn28, Asn104, Asn170, and Asn186
  • Modification sites at PhosphoSitePlus

Other Protein References for HTR3A Gene

No data available for DME Specific Peptides for HTR3A Gene

Domains for HTR3A Gene

Gene Families for HTR3A Gene

  • HTR :5-HT (serotonin) receptors
  • HTR3 :Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic

Graphical View of Domain Structure for InterPro Entry



  • P46098
  • Belongs to the ligand-gated ion channel (TC 1.A.9) family. 5-hydroxytryptamine receptor (TC 1.A.9.2) subfamily. HTR3A sub-subfamily.
genes like me logo Genes that share domains with HTR3A: view

Function for HTR3A Gene

Molecular function for HTR3A Gene

GENATLAS Biochemistry: 5-hydroxytryptamine (serotonin) receptor,subtype 3a,coexpressed with HTR3B in the amygdala,caudate and hyppocampus,also expressed in other tissues,component of HTR3 receptor,mediating rapid excitatory responses
UniProtKB/Swiss-Prot 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 in neurons. It is a cation-specific, but otherwise relatively nonselective, ion channel.

Gene Ontology (GO) - Molecular Function for HTR3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity TAS 9950429
GO:0004993 serotonin receptor activity IDA 7565620
GO:0005230 extracellular ligand-gated ion channel activity --
GO:0005232 serotonin-activated cation-selective channel activity IEA --
GO:0005249 voltage-gated potassium channel activity IEA --
genes like me logo Genes that share ontologies with HTR3A: view
genes like me logo Genes that share phenotypes with HTR3A: view

Animal Models for HTR3A Gene

MGI Knock Outs for HTR3A:

miRNA for HTR3A Gene

miRTarBase miRNAs that target HTR3A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for HTR3A Gene

Localization for HTR3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HTR3A Gene

Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for HTR3A Gene COMPARTMENTS Subcellular localization image for HTR3A gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
endoplasmic reticulum 1
golgi apparatus 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HTR3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 7565620
GO:0016020 membrane --
GO:0016021 integral component of membrane --
genes like me logo Genes that share ontologies with HTR3A: view

Pathways for HTR3A Gene

genes like me logo Genes that share pathways with HTR3A: view

Pathways by source for HTR3A Gene

1 Qiagen pathway for HTR3A Gene
1 BioSystems pathway for HTR3A Gene
1 KEGG pathway for HTR3A Gene

Gene Ontology (GO) - Biological Process for HTR3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 7565620
GO:0006811 ion transport --
GO:0006812 cation transport --
GO:0007210 serotonin receptor signaling pathway IDA 7565620
GO:0007268 synaptic transmission TAS 7565620
genes like me logo Genes that share ontologies with HTR3A: view

Compounds for HTR3A Gene

(5) Tocris Compounds for HTR3A Gene

Compound Action Cas Number
Dexfenfluramine hydrochloride 5-HT re-uptake inhibitor. Also stimulates 5-HT release [3239-45-0]
Granisetron hydrochloride 5-HT3 antagonist [107007-99-8]
Ondansetron hydrochloride Selective 5-HT3 antagonist [99614-01-4]
SR 57227 hydrochloride Potent, selective 5-HT3 agonist [77145-61-0]
Y-25130 hydrochloride Potent, selective 5-HT3 antagonist [123040-16-4]

(2) HMDB Compounds for HTR3A Gene

Compound Synonyms Cas Number PubMed IDs
  • Ondansetron
  • 3-(2-Aminoethyl)-1H-indol-5-ol

(18) Drugbank Compounds for HTR3A Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
122852-42-0 target antagonist
  • OPC 31
129722-12-9 target antagonist
  • Chloroprocain
133-16-4 target antagonist
81098-60-4 target agonist
5786-21-0 target antagonist

(132) Novoseek inferred chemical compound relationships for HTR3A Gene

Compound -log(P) Hits PubMed IDs
ondansetron 92.8 119
granisetron 92.2 93
5-hydroxytryptamine 90.6 130
tropisetron 90.2 59
2-methyl-5-ht 88.6 26

(1) PharmGKB related drug/compound annotations for HTR3A Gene

Drug/compound Annotation
clozapine CA
genes like me logo Genes that share compounds with HTR3A: view

Transcripts for HTR3A Gene

Unigene Clusters for HTR3A Gene

5-hydroxytryptamine (serotonin) receptor 3A, ionotropic:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HTR3A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b
SP1: - -
SP2: - -
SP3: - - - -
SP4: -

Relevant External Links for HTR3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HTR3A Gene

mRNA expression in normal human tissues for HTR3A Gene

mRNA differential expression in normal tissues according to GTEx for HTR3A Gene

This gene is overexpressed in Minor Salivary Gland (14.4), Pancreas (4.8), and Brain - Caudate (basal ganglia) (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for HTR3A Gene

SOURCE GeneReport for Unigene cluster for HTR3A Gene Hs.413899

mRNA Expression by UniProt/SwissProt for HTR3A Gene

Tissue specificity: Expressed in cerebral cortex, amygdala, hippocampus, and testis. Detected in monocytes of the spleen and tonsil, in small and large intestine, uterus, prostate, ovary and placenta.
genes like me logo Genes that share expressions with HTR3A: view

Orthologs for HTR3A Gene

This gene was present in the common ancestor of animals.

Orthologs for HTR3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HTR3A 35
  • 98.97 (n)
  • 98.76 (a)
HTR3A 36
  • 99 (a)
(Bos Taurus)
Mammalia HTR3A 35
  • 87.17 (n)
  • 87.24 (a)
HTR3A 36
  • 86 (a)
(Canis familiaris)
Mammalia HTR3A 35
  • 87.94 (n)
  • 88.08 (a)
HTR3A 36
  • 83 (a)
(Mus musculus)
Mammalia Htr3a 35
  • 83.92 (n)
  • 86.62 (a)
Htr3a 16
Htr3a 36
  • 83 (a)
(Monodelphis domestica)
Mammalia HTR3A 36
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia HTR3A 36
  • 76 (a)
(Rattus norvegicus)
Mammalia Htr3a 35
  • 83.84 (n)
  • 86.24 (a)
(Gallus gallus)
Aves HTR3A 35
  • 73.85 (n)
  • 73.33 (a)
HTR3A 36
  • 69 (a)
(Anolis carolinensis)
Reptilia HTR3A 36
  • 67 (a)
(Danio rerio)
Actinopterygii htr3a 36
  • 73 (a)
htr3a 36
  • 65 (a)
LOC571641 35
  • 67.79 (n)
  • 68.54 (a)
(Caenorhabditis elegans)
Secernentea Y57G11C.2 37
  • 27 (a)
C04C3.2 37
  • 27 (a)
acr-18 37
  • 22 (a)
acr-22 37
  • 28 (a)
acr-17 37
  • 29 (a)
Species with no ortholog for HTR3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for HTR3A Gene

Gene Tree for HTR3A (if available)
Gene Tree for HTR3A (if available)

Paralogs for HTR3A Gene

Paralogs for HTR3A Gene

genes like me logo Genes that share paralogs with HTR3A: view

Variants for HTR3A Gene

Sequence variations from dbSNP and Humsavar for HTR3A Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs8236 -- 113,990,122(+) TGCTT(C/T)TCTTT utr-variant-3-prime, nc-transcript-variant
rs897686 -- 113,985,208(-) AACTC(A/G)TAAAG intron-variant
rs897687 -- 113,985,089(-) AACTC(C/T)TGTTG intron-variant
rs909411 -- 113,983,560(-) ATATA(C/T)GCACA intron-variant
rs909412 -- 113,983,843(-) GAATC(A/G)CAAAT intron-variant

Relevant External Links for HTR3A Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for HTR3A Gene

Disorders for HTR3A Gene

MalaCards: The human disease database

MalaCards: The human disease database. (21) Diseases for HTR3A Gene including...

Search for HTR3A Gene in MalaCards »

(93) Novoseek inferred disease relationships for HTR3A Gene

Disease -log(P) Hits PubMed IDs
migraine 63.7 47
serotonin syndrome 62 8
schizophrenia 58.2 34
functional gastrointestinal disorder 56.7 2
functional dyspepsia 55.1 1

Relevant External Links for HTR3A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with HTR3A: view

No data available for UniProtKB/Swiss-Prot for HTR3A Gene

Publications for HTR3A Gene

  1. Mutational analysis of serotonin receptor genes: HTR3A and HTR3B in fibromyalgia patients. (PMID: 15293096) Frank B. … Rappold G. (Clin. Rheumatol. 2004) 3 4 23 48
  2. A cytoplasmic region determines single-channel conductance in 5-HT3 receptors. (PMID: 12867984) Kelley S.P. … Peters J.A. (Nature 2003) 2 3 4 23
  3. A polymorphism in the serotonin receptor 3A (HTR3A) gene and its association with harm avoidance in women. (PMID: 14557147) Melke J. … Eriksson E. (Arch. Gen. Psychiatry 2003) 3 23 48
  4. Functional variants of the serotonin receptor type 3A and B gene are associated with eating disorders. (PMID: 19741568) Hammer C. … Niesler B. (Pharmacogenet. Genomics 2009) 3 23 48
  5. Distinguishable haplotype blocks in the HTR3A and HTR3B region in the Japanese reveal evidence of association of HTR3B with female major depression. (PMID: 16487942) Yamada K. … Yoshikawa T. (Biol. Psychiatry 2006) 3 4 48

Products for HTR3A Gene

Sources for HTR3A Gene

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