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

Gene ID: 200909, updated on 26-Oct-2022

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; AllianceGenome:HGNC:24004
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
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Genomic context

See HTR3D in Genome Data Viewer
Location:
3q27.1
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184031544..184039369)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (186841085..186848924)
105.20220307 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 uncharacterized LOC124909468 Neighboring gene ABCC5 antisense RNA 1 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 8 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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119636, MGC119637

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in nervous system process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in serotonin receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
 
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
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)

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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

  1. NG_012750.1 RefSeqGene

    Range
    5199..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, ENST00000428798.7
    Conserved Domains (2) summary
    cd19063
    Location:182403
    LGIC_TM_5-HT3; transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor
    cl42365
    Location:27402
    LIC; Cation transporter family protein
  2. NM_001163646.2NP_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, Q7Z6B3
    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_001410851.1NP_001397780.1  5-hydroxytryptamine receptor 3D isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC068644, AC131235
    Consensus CDS
    CCDS93429.1
  4. NM_182537.3NP_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 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017005854.2XP_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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    186841085..186848924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)