Human Gene HTR3E (uc010hxq.3)
  Description: Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3E, ionotropic (HTR3E), transcript variant 4, mRNA.
RefSeq Summary (NM_001256613): This locus encodes a 5-hydroxytryptamine (serotonin) receptor subunit. The encoded protein, subunit E, may play a role in neurotransmission in myenteric neurons. Genes encoding subunits C, D and E form a cluster on chromosome 3. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Feb 2012].
Transcript (Including UTRs)
   Position: hg19 chr3:183,814,852-183,824,783 Size: 9,932 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr3:183,815,318-183,824,481 Size: 9,164 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:183,814,852-183,824,783)mRNA (may differ from genome)Protein (456 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: 5HT3E_HUMAN
DESCRIPTION: RecName: Full=5-hydroxytryptamine receptor 3E; Short=5-HT3-E; Short=5-HT3E; AltName: Full=Serotonin receptor 3E; Flags: Precursor;
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.
SUBUNIT: Forms a pentaheteromeric complex with HTR3A. Not functional as a homomeric complex.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Note=Presumably retained within the endoplasmic reticulum unless complexed with HTR3A.
TISSUE SPECIFICITY: Expressed in adult colon and intestine.
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family. 5-hydroxytryptamine receptor (TC 1.A.9.2) subfamily. HTR3E sub-subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HTR3E
CDC HuGE Published Literature: HTR3E

-  MalaCards Disease Associations
  MalaCards Gene Search: HTR3E
Diseases sorted by gene-association score: irritable bowel syndrome (7)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.34 RPKM in Small Intestine - Terminal Ileum
Total median expression: 0.71 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -106.70466-0.229 Picture PostScript Text
3' UTR -68.13302-0.226 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM
IPR018000 - Neurotransmitter_ion_chnl_CS

Pfam Domains:
PF02931 - Neurotransmitter-gated ion-channel ligand binding domain
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

SCOP Domains:
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore

ModBase Predicted Comparative 3D Structure on A5X5Y0
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0005515 protein binding
GO:0022850 serotonin-gated cation channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0007210 serotonin receptor signaling pathway
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  DQ644022 - Homo sapiens 5-HT3 receptor subunit E splice variant HTR3Ea mRNA, complete cds, alternatively spliced.
AY349352 - Homo sapiens 5-HT3c1 serotonin receptor-like protein mRNA, complete cds; alternatively spliced.
AY159813 - Homo sapiens 5-hydroxytryptamine serotonin receptor 3E (HTR3E) mRNA, complete cds.
BC101182 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3, family member E, mRNA (cDNA clone MGC:120034 IMAGE:40017961), complete cds.
BC101183 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3, family member E, mRNA (cDNA clone MGC:120035 IMAGE:40017962), complete cds.
BC101184 - Homo sapiens cDNA clone IMAGE:40017963, containing frame-shift errors.
BC101185 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3, family member E, mRNA (cDNA clone MGC:120037 IMAGE:40017964), complete cds.
KJ900580 - Synthetic construct Homo sapiens clone ccsbBroadEn_09974 HTR3E gene, encodes complete protein.
AY349353 - Homo sapiens 5-HT3c1 serotonin receptor-like protein mRNA, complete cds; alternatively spliced.
EU165354 - Homo sapiens serotonin receptor 3 subunit E splice variant 3 (HTR3E) mRNA, complete cds, alternatively spliced.
KJ904151 - Synthetic construct Homo sapiens clone ccsbBroadEn_13545 HTR3E gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein A5X5Y0 (Reactome details) participates in the following event(s):

R-HSA-975311 HTR3 pentamer:5HT transports Na+,K+, and Ca2+
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: 5HT3E_HUMAN, A5X5Y0, NM_001256613, NP_001243542, Q495G1, Q495G3, Q6V706, Q6V707, Q7Z6B2
UCSC ID: uc010hxq.3
RefSeq Accession: NM_001256613
Protein: A5X5Y0 (aka 5HT3E_HUMAN)
CCDS: CCDS58868.1, CCDS58869.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001256613.1
exon count: 9CDS single in 3' UTR: no RNA size: 2154
ORF size: 1371CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2249.00frame shift in genome: no % Coverage: 99.30
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.