Human Gene HTR6 (ENST00000289753.2_4) from GENCODE V47lift37
  Description: 5-hydroxytryptamine receptor 6 (from RefSeq NM_000871.3)
Gencode Transcript: ENST00000289753.2_4
Gencode Gene: ENSG00000158748.4_7
Transcript (Including UTRs)
   Position: hg19 chr1:19,991,368-20,007,459 Size: 16,092 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr1:19,992,247-20,005,861 Size: 13,615 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:19,991,368-20,007,459)mRNA (may differ from genome)Protein (440 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: 5HT6R_HUMAN
DESCRIPTION: RecName: Full=5-hydroxytryptamine receptor 6; Short=5-HT-6; Short=5-HT6; AltName: Full=Serotonin receptor 6;
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. The activity of this receptor is mediated by G proteins that stimulate adenylate cyclase. It has a high affinity for tricyclic psychotropic drugs.
INTERACTION: P06241:FYN; NbExp=7; IntAct=EBI-1182222, EBI-515315;
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in several human brain regions, most prominently in the caudate nucleus.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: HTR6
Diseases sorted by gene-association score: acute stress disorder (7), amnestic disorder (6), schizophrenia (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 2.71 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 10.10 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 -397.80879-0.453 Picture PostScript Text
3' UTR -629.701598-0.394 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
IPR000276 - 7TM_GPCR_Rhodpsn
IPR017452 - GPCR_Rhodpsn_supfam

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)

SCOP Domains:
81321 - Family A G protein-coupled receptor-like

ModBase Predicted Comparative 3D Structure on P50406
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004930 G-protein coupled receptor activity
GO:0004969 histamine receptor activity
GO:0004993 G-protein coupled serotonin receptor activity
GO:0005515 protein binding
GO:0030594 neurotransmitter receptor activity

Biological Process:
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007187 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0007268 chemical synaptic transmission
GO:0021795 cerebral cortex cell migration
GO:0032008 positive regulation of TOR signaling

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005929 cilium
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  L41147 - Homo sapiens 5-HT6 serotonin receptor mRNA, complete cds.
JD458837 - Sequence 439861 from Patent EP1572962.
JD146940 - Sequence 127964 from Patent EP1572962.
JD128758 - Sequence 109782 from Patent EP1572962.
JD379843 - Sequence 360867 from Patent EP1572962.
JD485666 - Sequence 466690 from Patent EP1572962.
JD484692 - Sequence 465716 from Patent EP1572962.
BC074995 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 6, mRNA (cDNA clone MGC:103988 IMAGE:30915396), complete cds.
BC074996 - Homo sapiens 5-hydroxytryptamine (serotonin) receptor 6, mRNA (cDNA clone MGC:104148 IMAGE:30915608), complete cds.
JD431667 - Sequence 412691 from Patent EP1572962.
AB528973 - Synthetic construct DNA, clone: pF1KB6634, Homo sapiens HTR6 gene for 5-hydroxytryptamine (serotonin) receptor 6, without stop codon, in Flexi system.
KJ891413 - Synthetic construct Homo sapiens clone ccsbBroadEn_00807 HTR6 gene, encodes complete protein.
AY429105 - Homo sapiens 5-hydroxytryptamine/serotonin receptor 6 mRNA, complete cds.
Z49119 - H.sapiens mRNA for serotonin 6 receptor (5-HT6; partial).
AB209129 - Homo sapiens mRNA for 5-hydroxytryptamine (serotonin) receptor 6 variant protein.
AF007141 - Homo sapiens clone 23925 mRNA sequence.
JD068010 - Sequence 49034 from Patent EP1572962.
JD329439 - Sequence 310463 from Patent EP1572962.
JD198757 - Sequence 179781 from Patent EP1572962.
JD400148 - Sequence 381172 from Patent EP1572962.
JD042142 - Sequence 23166 from Patent EP1572962.
JD281819 - Sequence 262843 from Patent EP1572962.
JD403975 - Sequence 384999 from Patent EP1572962.
JD358552 - Sequence 339576 from Patent EP1572962.
JD123377 - Sequence 104401 from Patent EP1572962.
JD538628 - Sequence 519652 from Patent EP1572962.
JD206491 - Sequence 187515 from Patent EP1572962.
JD247980 - Sequence 229004 from Patent EP1572962.
JD090527 - Sequence 71551 from Patent EP1572962.
JD275088 - Sequence 256112 from Patent EP1572962.
JD199893 - Sequence 180917 from Patent EP1572962.
JD155722 - Sequence 136746 from Patent EP1572962.
JD534612 - Sequence 515636 from Patent EP1572962.
JD452108 - Sequence 433132 from Patent EP1572962.
JD322966 - Sequence 303990 from Patent EP1572962.
JD425064 - Sequence 406088 from Patent EP1572962.
JD277275 - Sequence 258299 from Patent EP1572962.
JD481159 - Sequence 462183 from Patent EP1572962.
JD137715 - Sequence 118739 from Patent EP1572962.
JD271659 - Sequence 252683 from Patent EP1572962.
JD500806 - Sequence 481830 from Patent EP1572962.
JD378834 - Sequence 359858 from Patent EP1572962.
JD193621 - Sequence 174645 from Patent EP1572962.
JD123034 - Sequence 104058 from Patent EP1572962.
JD120790 - Sequence 101814 from Patent EP1572962.
JD054540 - Sequence 35564 from Patent EP1572962.
JD423034 - Sequence 404058 from Patent EP1572962.
JD343937 - Sequence 324961 from Patent EP1572962.
JD526818 - Sequence 507842 from Patent EP1572962.
JD135230 - Sequence 116254 from Patent EP1572962.
JD426414 - Sequence 407438 from Patent EP1572962.
JD486048 - Sequence 467072 from Patent EP1572962.

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

Protein P50406 (Reactome details) participates in the following event(s):

R-HSA-390931 5-HT4, 6 and 7 receptors can bind serotonin
R-HSA-744886 The Ligand:GPCR:Gs complex dissociates
R-HSA-744887 Liganded Gs-activating GPCRs bind inactive heterotrimeric Gs
R-HSA-379044 Liganded Gs-activating GPCR acts as a GEF for Gs
R-HSA-390666 Serotonin receptors
R-HSA-418555 G alpha (s) signalling events
R-HSA-375280 Amine ligand-binding receptors
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: 5HT6R_HUMAN, ENST00000289753.1, NM_000871, P50406, Q13640, Q5TGZ1, uc317ksu.1, uc317ksu.2
UCSC ID: ENST00000289753.2_4
RefSeq Accession: NM_000871.3
Protein: P50406 (aka 5HT6R_HUMAN or 5H6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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