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

Summary

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Official Symbol: HTR3Aprovided by HGNC
Official Full Name: 5-hydroxytryptamine (serotonin) receptor 3A, ionotropicprovided by HGNC
Primary source: HGNC:5297
See related: Ensembl:ENSG00000166736; HPRD:08917; MIM:182139; Vega:OTTHUMG00000160494
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]

Genomic context

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Location :: 11q23.1

Sequence :: Chromosome: 11; NC_000011.9 (113845797..113861035)

See HTR3A in Epigenomics, MapViewer

Chromosome 11 - NC_000011.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

The association between HTR3A gene SNP and response to clozapine is influenced by various clinical predictors and by differing outcome definitions in patients with treatment-resistant schizophrenia.
Title: Outcome definitions and clinical predictors influence pharmacogenetic associations between HTR3A gene polymorphisms and response to clozapine in patients with schizophrenia.
HTR3A and HTR3B were detected in all investigated brain tissues with the exception of the cerebellum, and large differences in the A:B subunit ratio were observed.
Title: Replication of functional serotonin receptor type 3A and B variants in bipolar affective disorder: a European multicenter study.
Thus, rather than involving the 5-HT3-dependent pathway, the negative effect of ondansetron on platelet aggregation is instead manifested through the attenuation of agonist-induced IP3 production and MAPK (p38 and ERK2).
Title: The anti-aggregation effects of ondansetron on platelets involve IP3 signaling and MAP kinase pathway, but not 5-HT3-dependent pathway.
This study does not support the hypothesis that the 5-HT(3A) receptor plays a major role in the pathogenesis of schizophrenia.
Title: Lack of association of the 5-HT(3A) receptor with schizophrenia.
CC genotype of TPH2 rs2171363, GG genotype of TPH2 rs7305115, CC genotype of HTR2A rs2770304, and CC genotype of HTR2A rs6313 were associated with reduced internalizing scores for children born in the quartile above the birth weightmidpoint.
Title: Influence of birth weight on internalizing traits modulated by serotonergic genes.
The serotonin receptor 3A c.-42T allele is associated with severe dyspeptic symptoms. The stronger association among dyspeptic patients carrying the serotonin transporter L allele suggests an additive effect of the two polymorphisms.
Title: Serotonin receptor 3A polymorphism c.-42C > T is associated with severe dyspepsia.
Data show that 5-HTA/bungarotoxin binding sequence (BBS) receptors are constitutively internalized in the absence of an agonist and internalization as well as receptor function are inhibited by fluorescence.
Title: Fluorophore assisted light inactivation (FALI) of recombinant 5-HT₃A receptor constitutive internalization and function.
Report significant correlations of the HTR3A polymorphisms with amygdala responsiveness, anxiety, and irritable bowel syndrome symptom severity.
Title: The HTR3A polymorphism c. -42C>T is associated with amygdala responsiveness in patients with irritable bowel syndrome.
Rings of charge within the extracellular vestibule influence ion permeation of the 5-HT3A receptor.
Title: Rings of charge within the extracellular vestibule influence ion permeation of the 5-HT3A receptor.
findings indicate that HTR3A and HTR3B polymorphisms may not play a major role in the susceptibility to suicidal behavior in schizophrenia subjects.
Title: Are serotonin 3A and 3B receptor genes associated with suicidal behavior in schizophrenia subjects?

Submit: New GeneRIF Correction See all (66)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description
P46098	P27824	CANX		HPRD	PubMed
P46098	P11021	HSPA5		HPRD	PubMed

Pathways from BioSystems

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Ion channel transport, organism-specific biosystem (from REACTOME)
Ion channel transport, organism-specific biosystemIon channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore f...
Ligand-gated ion channel transport, organism-specific biosystem (from REACTOME)
Ligand-gated ion channel transport, organism-specific biosystemLigand-gated ion channels (LGICs) are a group of transmembrane ion channels that are opened or closed in response to the binding of a chemical messenger (Purves, 2001).
SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
Serotonergic synapse, organism-specific biosystem (from KEGG)
Serotonergic synapse, organism-specific biosystemSerotonin (5-Hydroxytryptamine, 5-HT) is a monoamine neurotransmitter that plays important roles in physiological functions such as learning and memory, emotion, sleep, pain, motor function and endoc...
Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
Transmembrane transport of small molecules, organism-specific biosystem
Transmembrane transport of small molecules

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

Homology

Homologs of the HTR3A gene: The HTR3A gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and zebrafish.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
extracellular ligand-gated ion channel activity	NAS Non-traceable Author Statement more info
receptor activity	TAS Traceable Author Statement more info	PubMed
serotonin binding	IDA Inferred from Direct Assay more info	PubMed
serotonin receptor activity	IDA Inferred from Direct Assay more info	PubMed
serotonin receptor activity	NAS Non-traceable Author Statement more info
serotonin-activated cation-selective channel activity	IEA Inferred from Electronic Annotation more info
voltage-gated potassium channel activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
cellular response to growth factor stimulus	IEA Inferred from Electronic Annotation more info
digestion	TAS Traceable Author Statement more info	PubMed
ion transmembrane transport	TAS Traceable Author Statement more info
response to cocaine	IEA Inferred from Electronic Annotation more info
serotonin receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
serotonin receptor signaling pathway	NAS Non-traceable Author Statement more info
synaptic transmission	TAS Traceable Author Statement more info	PubMed
transmembrane transport	TAS Traceable Author Statement more info
transport	NAS Non-traceable Author Statement more info

Component	Evidence Code	Pubs
axon	IEA Inferred from Electronic Annotation more info
cell junction	IEA Inferred from Electronic Annotation more info
cytoplasm	IEA Inferred from Electronic Annotation more info
integral to membrane	NAS Non-traceable Author Statement more info
integral to plasma membrane	TAS Traceable Author Statement more info	PubMed
neuronal cell body	IEA Inferred from Electronic Annotation more info
plasma membrane	TAS Traceable Author Statement more info
postsynaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: 5-hydroxytryptamine receptor 3A

Names: 5-hydroxytryptamine receptor 3A; 5-HT3-A; serotonin receptor 3A; 5HT3 serotonin receptor; 5-hydroxytryptamine receptor 3; 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

5001..20239

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000869.5 → NP_000860.2 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

CCDS8365.2

UniProtKB/TrEMBL

B4E398

UniProtKB/Swiss-Prot

P46098

Related

ENSP00000364648, ENST00000375498

Conserved Domains (3) summary

TIGR00860
Location:29 – 478
Blast Score: 1420

LIC; Cation transporter family protein

pfam02931
Location:42 – 248
Blast Score: 569

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:255 – 474
Blast Score: 424

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
NM_001161772.2 → NP_001155244.1 5-hydroxytryptamine receptor 3A isoform c

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/Swiss-Prot

P46098

Related

ENSP00000299961, OTTHUMP00000218319, ENST00000299961, OTTHUMT00000360824

Conserved Domains (3) summary

TIGR00860
Location:4 – 457
Blast Score: 1418

LIC; Cation transporter family protein

pfam02931
Location:21 – 227
Blast Score: 567

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:234 – 453
Blast Score: 422

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
NM_213621.3 → NP_998786.2 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

CCDS8366.2

UniProtKB/TrEMBL

B4E398

UniProtKB/Swiss-Prot

P46098

Related

ENSP00000347754, ENST00000355556

Conserved Domains (3) summary

TIGR00860
Location:29 – 510
Blast Score: 1392

LIC; Cation transporter family protein

pfam02931
Location:42 – 248
Blast Score: 577

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:255 – 506
Blast Score: 390

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

RNA

NR_046363.1 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000011.9 Reference GRCh37.p10 Primary Assembly

Range

113845797..113861035

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000143.1 Alternate HuRef

Range

109774553..109789782

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018922.1 Alternate CHM1_1.0

Range

113709146..113724383

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01039775.1 (34123..49352)	None
genomic	AJ005205.2	CAA06442.3
genomic	AMYH01004040.1 (148734..163971)	None
genomic	AP000908.4 (27714..40524)	None
genomic	CH471065.1	EAW67237.1
		EAW67238.1
		EAW67239.1
		EAW67240.1
genomic	U73443.1	AAB71736.1
mRNA	AF498984.1	AAM21131.1
mRNA	AJ003078.1	CAA05851.1
mRNA	AJ003079.1	CAA05852.1
mRNA	AJ003080.1	CAA05853.1
		CAA05854.1
mRNA	AK299973.1	BAG61798.1
mRNA	AK304630.1	BAG65410.1
mRNA	AK313896.1	BAG36619.1
mRNA	BC002354.2	AAH02354.1
mRNA	BC004453.1	AAH04453.2
mRNA	BT007204.1	AAP35868.1
mRNA	CD014118.1	None
mRNA	D49394.1	BAA08387.1
mRNA	S82612.1	AAB37533.2
other-genetic	BT008266.1	AAP36958.1
other-genetic	DQ892003.2	ABM82929.1
other-genetic	DQ895193.2	ABM86119.1