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HTR3D 5-hydroxytryptamine receptor 3D [ Homo sapiens (human) ]

Gene ID: 200909, updated on 13-Feb-2019

Summary

Official Symbol
HTR3Dprovided by HGNC
Official Full Name
5-hydroxytryptamine receptor 3Dprovided by HGNC
Primary source
HGNC:HGNC:24004
See related
Ensembl:ENSG00000186090 MIM:610122
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
5HT3D
Summary
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]
Orthologs

Genomic context

See HTR3D in Genome Data Viewer
Location:
3q27.1
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (184031544..184039369)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (183749332..183757157)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily C member 5 Neighboring gene ABCC5 antisense RNA 1 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 8 Neighboring gene uncharacterized LOC105374249 Neighboring gene 5-hydroxytryptamine receptor 3C Neighboring gene 5-hydroxytryptamine receptor 3C2, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A mega-analysis of genome-wide association studies for major depressive disorder.
NHGRI GWA Catalog
ABCC5, a gene that influences the anterior chamber depth, is associated with primary angle closure glaucoma.
NHGRI GWA Catalog

Pathways from BioSystems

  • 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).
  • 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...
  • Taste transduction, organism-specific biosystem (from KEGG)
    Taste transduction, organism-specific biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...
  • Taste transduction, conserved biosystem (from KEGG)
    Taste transduction, conserved biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119636, MGC119637

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to extracellular ligand-gated ion channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
serotonin-gated cation-selective channel activity IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemical synaptic transmission TAS
Traceable Author Statement
more info
 
ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nervous system process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
serotonin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
5-hydroxytryptamine receptor 3D
Names
5-hydroxytryptamine (serotonin) receptor 3 family member D
5-hydroxytryptamine (serotonin) receptor 3D, ionotropic
5-hydroxytryptamine receptor 3 subunit D
serotonin 5-HT-3D receptor
serotonin receptor 3D

NCBI Reference Sequences (RefSeq)

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

  1. NG_012750.1 RefSeqGene

    Range
    5001..12826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145143.1NP_001138615.1  5-hydroxytryptamine receptor 3D isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' coding region, compared to variant 3, resulting in an isoform (1) that is shorter than isoform 3.
    Source sequence(s)
    AC068644, AC131235, BK001746
    Consensus CDS
    CCDS46966.1
    UniProtKB/Swiss-Prot
    Q70Z44
    Related
    ENSP00000405409.2, ENST00000428798.6
    Conserved Domains (3) summary
    TIGR00860
    Location:27402
    LIC; Cation transporter family protein
    pfam02931
    Location:2369
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:189301
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
  2. NM_001163646.1NP_001157118.1  5-hydroxytryptamine receptor 3D isoform 3 precursor

    See identical proteins and their annotated locations for NP_001157118.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AC068644, AC131235, AJ437318, AY159812
    Consensus CDS
    CCDS54685.1
    UniProtKB/Swiss-Prot
    Q70Z44
    Related
    ENSP00000371929.3, ENST00000382489.3
    Conserved Domains (3) summary
    TIGR00860
    Location:92452
    LIC; Cation transporter family protein
    pfam02931
    Location:55130
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:237351
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
  3. NM_182537.2NP_872343.2  5-hydroxytryptamine receptor 3D isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the presence and absence of exons at its 5' end, and uses a downstream translational start codon, compared to variant 3. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 3.
    Source sequence(s)
    AC068644, AC131235, AY159812, BK001746
    Consensus CDS
    CCDS3249.1
    UniProtKB/Swiss-Prot
    Q70Z44
    UniProtKB/TrEMBL
    F6WC43
    Related
    ENSP00000334315.2, ENST00000334128.6
    Conserved Domains (1) summary
    pfam02932
    Location:64176
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    184031544..184039369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005854.1XP_016861343.1  5-hydroxytryptamine receptor 3D isoform X1

    UniProtKB/Swiss-Prot
    Q70Z44
    Related
    ENSP00000389268.1, ENST00000453435.1
    Conserved Domains (1) summary
    cl27321
    Location:2231
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
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