HTR3A 5-hydroxytryptamine receptor 3A [Homo sapiens (human)] - Gene

Summary

Official Symbol: HTR3Aprovided by HGNC
Official Full Name: 5-hydroxytryptamine receptor 3Aprovided by HGNC
Primary source: HGNC:HGNC:5297
See related: Ensembl:ENSG00000166736 MIM:182139; AllianceGenome:HGNC:5297
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HTR3; 5HT3R; 5-HT-3; 5-HT3A; 5-HT3R
Summary: 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]
Expression: Biased expression in lymph node (RPKM 3.0), appendix (RPKM 1.1) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q23.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (113975108..113990313)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (113985458..114000652)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (113845830..113861035)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression Patterns of Serotonin Receptors 5-HT1A, 5-HT2A, and 5-HT3A during Human Fetal Lung Development.
Title: Expression Patterns of Serotonin Receptors 5-HT1A, 5-HT2A, and 5-HT3A during Human Fetal Lung Development.
Serotonin type 3 receptor subunit gene polymorphisms associated with psychosomatic symptoms in irritable bowel syndrome: A multicenter retrospective study.
Title: Serotonin type 3 receptor subunit gene polymorphisms associated with psychosomatic symptoms in irritable bowel syndrome: A multicenter retrospective study.
Fear reacquisition and symptoms of combat-related PTSD: Specificity and preliminary examination of the influence of the 5-HT3A receptor gene.
Title: Fear reacquisition and symptoms of combat-related PTSD: Specificity and preliminary examination of the influence of the 5-HT3A receptor gene.
5'UTR polymorphism in the serotonergic receptor HTR3A gene is differently associated with striatal Dopamine D2/D3 receptor availability in the right putamen in Fibromyalgia patients and healthy controls-Preliminary evidence.
Title: 5'UTR polymorphism in the serotonergic receptor HTR3A gene is differently associated with striatal Dopamine D2/D3 receptor availability in the right putamen in Fibromyalgia patients and healthy controls-Preliminary evidence.
5-HT3 Signaling Alters Development of Sacral Neural Crest Derivatives That Innervate the Lower Urinary Tract.
Title: 5-HT3 Signaling Alters Development of Sacral Neural Crest Derivatives That Innervate the Lower Urinary Tract.
Orthosteric and Allosteric Activation of Human 5-HT3A Receptors.
Title: Orthosteric and Allosteric Activation of Human 5-HT(3)A Receptors.
High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition.
Title: High-resolution structures of multiple 5-HT(3A)R-setron complexes reveal a novel mechanism of competitive inhibition.
HTR3A is correlated with unfavorable histology and promotes proliferation through ERK phosphorylation in lung adenocarcinoma.
Title: HTR3A is correlated with unfavorable histology and promotes proliferation through ERK phosphorylation in lung adenocarcinoma.
Voltage-gated fluorometry was used to characterize conformational changes in the extracellular domain of the 5-HT3A receptor.
Title: Conformational Changes in the 5-HT(3A) Receptor Extracellular Domain Measured by Voltage-Clamp Fluorometry.
This study demonstrated that the C and E subunits when assembled as simple or complex heteromeric 5-HT3 receptors may alter efficacies of serotonin and clinically used antagonists.
Title: The C and E subunits of the serotonin 5-HT(3) receptor subtly modulate electrical properties of the receptor.

Submit: New GeneRIF Correction See all GeneRIFs (105)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-D49394 (e-PCR)
- UniSTS:26632

RH36483 (e-PCR)
- UniSTS:79165

SHGC-31530 (e-PCR)
- UniSTS:19519

D11S1786 (e-PCR), detects polymorphism
- UniSTS:13696

5HT3R (e-PCR)
- UniSTS:44676

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables excitatory extracellular ligand-gated monoatomic ion channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serotonin binding	IDA Inferred from Direct Assay more info	PubMed
enables serotonin-gated monoatomic cation channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables serotonin-gated monoatomic cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in excitatory postsynaptic potential	IEA Inferred from Electronic Annotation more info
involved_in inorganic cation transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in monoatomic ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of membrane potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in serotonin receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in serotonin-gated cation-selective signaling pathway	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cleavage furrow	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
part_of serotonin-activated cation-selective channel complex	IDA Inferred from Direct Assay more info	PubMed
part_of serotonin-activated cation-selective channel complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
part_of transmembrane transporter complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: 5-hydroxytryptamine receptor 3A

Names: 5-hydroxytryptamine (serotonin) receptor 3A, ionotropic; 5-hydroxytryptamine receptor 3; 5HT3 serotonin receptor; serotonin receptor 3A; serotonin-gated ion channel receptor

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_013058.1 RefSeqGene

Range

5034..20239

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000869.6 → NP_000860.3 5-hydroxytryptamine receptor 3A isoform b precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (b), that is missing an internal segment compared to isoform a.

Source sequence(s)

AK304630, AP000908, BC002354

Consensus CDS

CCDS8365.3

UniProtKB/Swiss-Prot

B4DSY6, G5E986, O60854, P46098, Q7KZM7, Q99918, Q9BSZ9

UniProtKB/TrEMBL

B2R9S2

Related

ENSP00000424189.2, ENST00000504030.7

Conserved Domains (1) summary

TIGR00860
Location:23 → 472

LIC; Cation transporter family protein
NM_001161772.3 → NP_001155244.1 5-hydroxytryptamine receptor 3A isoform c

See identical proteins and their annotated locations for NP_001155244.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an alternate 5' exon and lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (c), that has a different N-terminus and is missing an internal segment compared to isoform a.

Source sequence(s)

AK299973, AP000908, BC002354

Consensus CDS

CCDS53710.1

UniProtKB/TrEMBL

B2R9S2

Related

ENSP00000299961.4, ENST00000299961.5

Conserved Domains (3) summary

TIGR00860
Location:4 → 457

LIC; Cation transporter family protein

pfam02931
Location:21 → 227

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:234 → 453

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
NM_213621.4 → NP_998786.3 5-hydroxytryptamine receptor 3A isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as h5-HT3RL, represents the longest transcript, and encodes the longest isoform (a).

Source sequence(s)

AJ003078, AK304630, AP000908, CD014118

Consensus CDS

CCDS8366.3

UniProtKB/TrEMBL

B2R9S2

Related

ENSP00000347754.2, ENST00000355556.6

Conserved Domains (1) summary

TIGR00860
Location:23 → 504

LIC; Cation transporter family protein

RNA

NR_046363.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate segment and an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AJ003080, AK304630, AP000908, BC002354