Human Gene HTR3D (ENST00000334128.6) from GENCODE V44
  Description: Homo sapiens 5-hydroxytryptamine receptor 3D (HTR3D), transcript variant 2, mRNA. (from RefSeq NM_182537)
RefSeq Summary (NM_182537): 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].
Gencode Transcript: ENST00000334128.6
Gencode Gene: ENSG00000186090.11
Transcript (Including UTRs)
   Position: hg38 chr3:184,031,544-184,039,369 Size: 7,826 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr3:184,036,400-184,038,975 Size: 2,576 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:184,031,544-184,039,369)mRNA (may differ from genome)Protein (279 aa)
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HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F6WC43_HUMAN
DESCRIPTION: SubName: Full=5-hydroxytryptamine receptor 3D;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.03 RPKM in Testis
Total median expression: 0.03 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 -64.70225-0.288 Picture PostScript Text
3' UTR -94.40394-0.240 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
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM

Pfam Domains:
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

ModBase Predicted Comparative 3D Structure on F6WC43
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005216 ion channel activity

Biological Process:
GO:0006811 ion transport
GO:0007165 signal transduction
GO:0034220 ion transmembrane transport

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


-  Descriptions from all associated GenBank mRNAs
  AY159812 - Homo sapiens 5-hydroxytryptamine serotonin receptor 3D (HTR3D) mRNA, complete cds.
AJ437318 - Homo sapiens mRNA for 5-hydroxytryptamine 3-receptor subunit D (HTR3D gene).
BC101090 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3 family member D, mRNA (cDNA clone MGC:119636 IMAGE:40009594), complete cds.
BC101091 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 3 family member D, mRNA (cDNA clone MGC:119637 IMAGE:40009597), complete cds.
KJ903989 - Synthetic construct Homo sapiens clone ccsbBroadEn_13383 HTR3D gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000334128.1, ENST00000334128.2, ENST00000334128.3, ENST00000334128.4, ENST00000334128.5, F6WC43, F6WC43_HUMAN, NM_182537, uc003fmj.1, uc003fmj.2, uc003fmj.3
UCSC ID: ENST00000334128.6
RefSeq Accession: NM_182537
Protein: F6WC43 CCDS: CCDS3249.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.