Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HTR3D Gene

Aliases for HTR3D Gene

  • 5-Hydroxytryptamine Receptor 3D 2 3 5
  • 5-Hydroxytryptamine (Serotonin) Receptor 3 Family Member D 2 3
  • 5-Hydroxytryptamine (Serotonin) Receptor 3D, Ionotropic 2 3
  • Serotonin Receptor 3D 3 4
  • 5-Hydroxytryptamine Receptor 3 Subunit D 3
  • Serotonin 5-HT-3D Receptor 3
  • 5-HT3-D 4
  • 5-HT3D 4
  • 5HT3D 3

External Ids for HTR3D Gene

Previous GeneCards Identifiers for HTR3D Gene

  • GC03P185152
  • GC03P185070
  • GC03P185232
  • GC03P183749
  • GC03P181156

Summaries for HTR3D Gene

Entrez Gene Summary for HTR3D Gene

  • 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]

GeneCards Summary for HTR3D Gene

HTR3D (5-Hydroxytryptamine Receptor 3D) is a Protein Coding gene. Among its related pathways are Ligand-gated ion channel transport and CREB Pathway. Gene Ontology (GO) annotations related to this gene include extracellular ligand-gated ion channel activity and G-protein coupled serotonin receptor activity. An important paralog of this gene is HTR3E.

UniProtKB/Swiss-Prot for HTR3D 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. It is a cation-specific, but otherwise relatively nonselective, ion channel.

Tocris Summary for HTR3D Gene

  • Serotonin 5-HT3 receptors, are ligand-gated ion channels of the Cys-loop family. The receptor consists of four transmembrane domains that form an intrinsic cation-selective channel. So far five human 5-HT3 receptor subtypes have been identified (5-HT3A-E).

Gene Wiki entry for HTR3D Gene

Additional gene information for HTR3D Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HTR3D Gene

Genomics for HTR3D Gene

GeneHancer (GH) Regulatory Elements for HTR3D Gene

Promoters and enhancers for HTR3D Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I184005 Enhancer 1.1 Ensembl ENCODE 11.2 -25.2 -25157 1.6 PKNOX1 ARNT SIN3A FOS ATF7 DEK JUNB ZNF592 ATF4 MAFF ABCC5-AS1 ABCC5 EEF1A1P8 HTR3D HTR3C PARL RPSAP31 EIF2B5 CAMK2N2 MAP6D1
GH03I184002 Enhancer 0.6 Ensembl ENCODE 11.2 -27.6 -27644 2.8 CTCF ZBTB33 ABCC5 EEF1A1P8 HTR3D CAMK2N2 MAP6D1 ABCC5-AS1 PIR62380
GH03I184008 Enhancer 0.4 Ensembl 11.1 -23.4 -23443 0.2 GATA3 MNT FOXA1 ABCC5-AS1 ABCC5 HTR3D HTR3C EIF2B5 CAMK2N2
GH03I183532 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 2.4 -498.1 -498124 2.7 HDGF PKNOX1 ATF1 SMAD1 ARNT IRF4 NCOA2 POLR2B ZNF766 FOS KLHL6 ENSG00000199363 ENSG00000251730 ENSG00000253092 SNORA63D LINC00888 EIF4G1 YEATS2 B3GNT5 HTR3D
GH03I184472 Enhancer 0.8 FANTOM5 Ensembl ENCODE 1.4 +441.6 441625 1.7 MAX NR2F2 YY1 FAM131A LINC02054 LINC01840 EIF4G1 LINC01839 HTR3D LOC105374252
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HTR3D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HTR3D gene promoter:

Genomic Locations for HTR3D Gene

Genomic Locations for HTR3D Gene
7,826 bases
Plus strand

Genomic View for HTR3D Gene

Genes around HTR3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HTR3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HTR3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HTR3D Gene

Proteins for HTR3D Gene

  • Protein details for HTR3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    5-hydroxytryptamine receptor 3D
    Protein Accession:
    Secondary Accessions:
    • C9J2I6
    • J3QT78
    • Q495N5
    • Q495N6
    • Q7Z6B3

    Protein attributes for HTR3D Gene

    454 amino acids
    Molecular mass:
    50191 Da
    Quaternary structure:
    • Forms a pentaheteromeric complex with HTR3A. Not functional as a homomeric complex.

    Alternative splice isoforms for HTR3D Gene


neXtProt entry for HTR3D Gene

Post-translational modifications for HTR3D Gene

  • Glycosylation at posLast=6666
  • Modification sites at PhosphoSitePlus

Other Protein References for HTR3D Gene

No data available for DME Specific Peptides for HTR3D Gene

Domains & Families for HTR3D Gene

Gene Families for HTR3D Gene

Human Protein Atlas (HPA):
  • FDA approved drug targets
  • Predicted membrane proteins
  • Transporters

Suggested Antigen Peptide Sequences for HTR3D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ligand-gated ion channel (TC 1.A.9) family. 5-hydroxytryptamine receptor (TC 1.A.9.2) subfamily. HTR3D sub-subfamily.
  • Belongs to the ligand-gated ion channel (TC 1.A.9) family. 5-hydroxytryptamine receptor (TC 1.A.9.2) subfamily. HTR3D sub-subfamily.
genes like me logo Genes that share domains with HTR3D: view

Function for HTR3D Gene

Molecular function for HTR3D Gene

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

Phenotypes From GWAS Catalog for HTR3D Gene

Gene Ontology (GO) - Molecular Function for HTR3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity IEA --
GO:0005230 extracellular ligand-gated ion channel activity IEA --
GO:0005515 protein binding IPI 17392525
GO:0022850 serotonin-gated cation-selective channel activity IDA 17392525
genes like me logo Genes that share ontologies with HTR3D: view
genes like me logo Genes that share phenotypes with HTR3D: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HTR3D Gene

Localization for HTR3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for HTR3D Gene

Cell membrane; Multi-pass membrane protein. Note=Presumably retained within the endoplasmic reticulum unless complexed with HTR3A.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HTR3D gene
Compartment Confidence
plasma membrane 4
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for HTR3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with HTR3D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HTR3D Gene

Pathways & Interactions for HTR3D Gene

genes like me logo Genes that share pathways with HTR3D: view

Pathways by source for HTR3D Gene

Gene Ontology (GO) - Biological Process for HTR3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0007165 signal transduction IEA --
GO:0007268 chemical synaptic transmission TAS --
GO:0034220 ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with HTR3D: view

No data available for SIGNOR curated interactions for HTR3D Gene

Drugs & Compounds for HTR3D Gene

(86) Drugs for HTR3D Gene - From: DrugBank, ApexBio, DGIdb, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ethanol Approved Pharma Target 2326
Ergoloid mesylate Approved Pharma Target, antagonist 0
Setiptiline Approved Pharma Target, antagonist Serotonin receptor antagonist 0
Tiapride Approved, Investigational Pharma Target, antagonist 0
Asenapine Approved Pharma Antagonist Inhibits adrenergic receptor/5-HT receptor 55

(1) Additional Compounds for HTR3D Gene - From:

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(4) Tocris Compounds for HTR3D Gene

Compound Action Cas Number
2-Methyl-5-hydroxytryptamine hydrochloride 5-HT3 agonist/potent 5-HT6 ligand 845861-49-6
m-Chlorophenylbiguanide hydrochloride Potent and specific 5-HT3 agonist 2113-05-5
N-Methylquipazine dimaleate 5-HT3 agonist 171205-17-7
Zacopride hydrochloride Highly potent 5-HT3 receptor antagonist. Also 5-HT4 agonist 101303-98-4

(76) ApexBio Compounds for HTR3D Gene

Compound Action Cas Number
(±)-MDMA hydrochloride 92279-84-0
1-Phenylbiguanide hydrochloride 55-57-2
2-[1-(4-Piperonyl)piperazinyl]benzothiazole 155106-73-3
2-Methyl-5-hydroxytryptamine hydrochloride 845861-49-6
3-AQC 201216-42-4
Asenapine Inhibits adrenergic receptor/5-HT receptor 85650-56-2
Bilobalide Neuroprotective agent 33570-04-6
Blonanserin Atypical antipsychotic 132810-10-7
BTS 54-505 hydrochloride Potent SNRI,sibutramine metabolite 84484-78-6
Cisapride 81098-60-4
Clomipramine HCl SERT/NET dopamine transporter (DAT) blocker 17321-77-6
Clozapine N-oxide Metabolite of clozapine 34233-69-7
Dapoxetine HCl Selective serotonin reuptake inhibitor 129938-20-1
Desvenlafaxine 93413-62-8
Desvenlafaxine Succinate 386750-22-7
Dexfenfluramine hydrochloride 3239-45-0
Dihydroergotamine mesylate 6190-39-2
DOB hydrochloride 29705-96-2
DOI hydrochloride 42203-78-1
Duloxetine HCl 136434-34-9
Eltoprazine hydrochloride 98206-09-8
EMD 386088 hydrochloride 1171123-46-8
Escitalopram Oxalate Serotonin(5-HT) reuptake (SSRI) inhibitor 219861-08-2
Fenspiride HCl 5053-08-7
Fluoxetine HCl Serotonin reuptake inhibitor,selective 56296-78-7
Fluvoxamine maleate Serotonin reuptake inhibitor,selective,antidepressant 61718-82-9
GR 46611 185259-85-2
Ketanserin 74050-98-9
Lorcaserin HCl 846589-98-8
LY310762 192927-92-7
m-CPP hydrochloride 13078-15-4
Methysergide maleate 129-49-7
Milnacipran HCl 101152-94-7
Mosapride Citrate 5-HT receptor agonist 112885-42-4
MS 245 oxalate 275363-58-1
NAD 299 hydrochloride 184674-99-5
Naratriptan 143388-64-1
N-Methylquipazine dimaleate 171205-17-7
Olanzapine 132539-06-1
Ondansetron 99614-02-5
Palonosetron HCl 135729-62-3
Pizotifen Malate 5189-11-7
Psilocin 520-53-6
Quipazine dimaleate 150323-78-7
Risperidone SR-2A inhibitor 106266-06-2
Rizatriptan Benzoate 145202-66-0
RS 39604 hydrochloride 167710-87-4
RS 56812 hydrochloride 143339-12-2
RS 67333 hydrochloride 168986-60-5
RU 24969 66611-26-5
Sarpogrelate hydrochloride 135159-51-2
SB 200646 hydrochloride 143797-62-0
SB 203186 hydrochloride 207572-69-8
SB 204070 148688-01-1
SB 242084 1215566-78-1
SB 243213 dihydrochloride 200940-23-4
SB 258719 hydrochloride 1217674-10-6
SB271046 209481-20-9
SDZ 205-557 hydrochloride 1197334-02-3
SEA0400 Specific inhibitor of Na+/Ca2+ exchange 223104-29-8
Sertraline HCl 79559-97-0
SR 57227 hydrochloride 77145-61-0
Tandospirone Anxiolytic and antidepressant reagent 87760-53-0
Tianeptine sodium 5-HT uptake facilitator,selective,antidepressant 30123-17-2
Trazodone HCl Antidepressant 25332-39-2
Tropisetron 105826-92-4
Urapidil HCl 64887-14-5
Venlafaxine Dual serotonin/noradrenalin re-uptake inhibitor 99300-78-4
Vortioxetine 5-HT receptors antagonist 508233-74-7
Vortioxetine (Lu AA21004) HBr 5-HT receptor modulator, antidepressant and anxiolytic 960203-27-4
VUF 10166 155584-74-0
WY 45233 succinate 448904-47-0
Zacopride hydrochloride 101303-98-4
Ziprasidone HCl Serotonin and dopamine receptor antagonist 122883-93-6
Ziprasidone hydrochloride monohydrate 5-HT (serotonin)/dopamine receptor antagonist 138982-67-9
Zolmitriptan 139264-17-8
genes like me logo Genes that share compounds with HTR3D: view

Drug Products

Transcripts for HTR3D Gene

mRNA/cDNA for HTR3D Gene

(4) REFSEQ mRNAs :
(4) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HTR3D Gene

No ASD Table

Relevant External Links for HTR3D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HTR3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HTR3D Gene

Protein differential expression in normal tissues from HIPED for HTR3D Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HTR3D Gene

Protein tissue co-expression partners for HTR3D Gene

NURSA nuclear receptor signaling pathways regulating expression of HTR3D Gene:


SOURCE GeneReport for Unigene cluster for HTR3D Gene:


mRNA Expression by UniProt/SwissProt for HTR3D Gene:

Tissue specificity: Expressed in liver, as well as fetal and adult colon and kidney.
genes like me logo Genes that share expression patterns with HTR3D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HTR3D Gene

Orthologs for HTR3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for HTR3D Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HTR3D 34
  • 85 (a)
(Canis familiaris)
Mammalia HTR3D 34
  • 57 (a)
(Bos Taurus)
Mammalia HTR3D 34
  • 53 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 50 (a)
-- 34
  • 47 (a)
(Danio rerio)
Actinopterygii CU207281.1 34
  • 38 (a)
CU207281.2 34
  • 25 (a)
Species where no ortholog for HTR3D was found in the sources mined by GeneCards:
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for HTR3D Gene

Gene Tree for HTR3D (if available)
Gene Tree for HTR3D (if available)

Paralogs for HTR3D Gene

Paralogs for HTR3D Gene

(2) SIMAP similar genes for HTR3D Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HTR3D: view

Variants for HTR3D Gene

Sequence variations from dbSNP and Humsavar for HTR3D Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000011749 -- 184,032,274(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000524753 -- 184,032,811(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000588217 -- 184,037,534(+) A/G intron_variant
rs1000952 -- 184,038,034(+) G/A/T coding_sequence_variant, missense_variant
rs1001013167 -- 184,037,779(+) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HTR3D Gene

Variant ID Type Subtype PubMed ID
nsv4145 CNV insertion 18451855

Variation tolerance for HTR3D Gene

Residual Variation Intolerance Score: 94.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.83; 83.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HTR3D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HTR3D Gene

Disorders for HTR3D Gene

Additional Disease Information for HTR3D

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HTR3D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HTR3D Gene

Publications for HTR3D Gene

  1. Cloning, physical mapping and expression analysis of the human 5-HT3 serotonin receptor-like genes HTR3C, HTR3D and HTR3E. (PMID: 12801637) Niesler B … Rappold GA (Gene 2003) 2 3 4 58
  2. Two naturally occurring variants of the serotonin receptor gene HTR3C are associated with nausea in pregnancy. (PMID: 20021265) Goecke TW … Fasching PA (Acta obstetricia et gynecologica Scandinavica 2010) 3 44 58
  3. A candidate gene study of obstructive sleep apnea in European Americans and African Americans. (PMID: 20538960) Larkin EK … Redline S (American journal of respiratory and critical care medicine 2010) 3 44 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. Polymorphism in HTR3D shows different risks for acute chemotherapy-induced vomiting after anthracycline chemotherapy. (PMID: 20602613) Hammer C … Niesler B (Pharmacogenomics 2010) 3 44 58

Products for HTR3D Gene

Sources for HTR3D Gene

Loading form....