Htr5a (5-hydroxytryptamine receptor 5A) - Rat Genome Database

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Gene: Htr5a (5-hydroxytryptamine receptor 5A) Rattus norvegicus
Analyze
Symbol: Htr5a
Name: 5-hydroxytryptamine receptor 5A
RGD ID: 2851
Description: Enables G protein-coupled serotonin receptor activity. Involved in G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger; hippocampus development; and response to estradiol. Located in several cellular components, including Golgi apparatus; perikaryon; and rough endoplasmic reticulum. Is active in postsynaptic specialization membrane. Orthologous to human HTR5A (5-hydroxytryptamine receptor 5A); PARTICIPATES IN calcium/calcium-mediated signaling pathway; INTERACTS WITH (S)-amphetamine; 17alpha-ethynylestradiol; alendronic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 5-HT-5A; 5-HT5A; 5-hydroxytryptamine (serotonin) receptor 5A; 5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled; 5HT5A; MR22; REC17; serotonin receptor 5A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.247,444,968 - 7,454,651 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl47,444,968 - 7,454,651 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx412,455,005 - 12,464,692 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.048,269,250 - 8,278,935 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.046,615,442 - 6,625,127 (-)NCBIRnor_WKY
Rnor_6.04199,916 - 209,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4199,916 - 209,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04192,554 - 202,795 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,707,261 - 2,716,944 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.142,707,260 - 2,716,944 (-)NCBI
Celera42,826,290 - 2,835,975 (+)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 5-HT5A receptor localization in the rat spinal cord suggests a role in nociception and control of pelvic floor musculature. Doly S, etal., J Comp Neurol. 2004 Aug 30;476(4):316-29.
2. Pre- and postsynaptic localization of the 5-HT7 receptor in rat dorsal spinal cord: immunocytochemical evidence. Doly S, etal., J Comp Neurol. 2005 Sep 26;490(3):256-69.
3. Two members of a distinct subfamily of 5-hydroxytryptamine receptors differentially expressed in rat brain. Erlander MG, etal., Proc Natl Acad Sci U S A 1993 Apr 15;90(8):3452-6.
4. Ontogenetic distribution of 5-HT2C, 5-HT5A, and 5-HT7 receptors in the rat hippocampus. Garcia-Alcocer G, etal., Gene Expr. 2006;13(1):53-7.
5. Developmental expression of 5-HT 5A receptor mRNA in the rat brain. Garcia-Alcocer G, etal., Neurosci Lett. 2005 May 6;379(2):101-5.
6. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Localization of 5-HT2A, 5-HT3, 5-HT5A and 5-HT7 receptor-like immunoreactivity in the rat cerebellum. Geurts FJ, etal., J Chem Neuroanat 2002 Jun;24(1):65-74.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Estradiol induces expression of 5-hydroxytryptamine (5-HT) 4, 5-HT5, and 5-HT6 receptor messenger ribonucleic acid in rat anterior pituitary cell aggregates and allows prolactin release via the 5-HT4 receptor. Papageorgiou A and Denef C, Endocrinology. 2007 Mar;148(3):1384-95. Epub 2006 Nov 22.
12. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Pertussis toxin treatment prevents 5-HT(5a) receptor-mediated inhibition of cyclic AMP accumulation in rat C6 glioma cells. Thomas EA, etal., J Neurosci Res. 2000 Jul 1;61(1):75-81.
17. Serotonin 5-HT2A and 5-HT5A receptors are expressed by different motoneuron populations in rat Onuf's nucleus. Xu C, etal., J Comp Neurol. 2007 Jun 1;502(4):620-34.
Additional References at PubMed
PMID:7988681   PMID:11406289   PMID:20863873   PMID:26168890   PMID:33168874  


Genomics

Comparative Map Data
Htr5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.247,444,968 - 7,454,651 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl47,444,968 - 7,454,651 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx412,455,005 - 12,464,692 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.048,269,250 - 8,278,935 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.046,615,442 - 6,625,127 (-)NCBIRnor_WKY
Rnor_6.04199,916 - 209,599 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4199,916 - 209,599 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04192,554 - 202,795 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.442,707,261 - 2,716,944 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.142,707,260 - 2,716,944 (-)NCBI
Celera42,826,290 - 2,835,975 (+)NCBICelera
Cytogenetic Map4q11NCBI
HTR5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387155,070,324 - 155,087,392 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7155,070,324 - 155,087,392 (+)EnsemblGRCh38hg38GRCh38
GRCh377154,862,034 - 154,879,102 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367154,493,479 - 154,508,392 (+)NCBINCBI36Build 36hg18NCBI36
Build 347154,300,257 - 154,313,845NCBI
Celera7149,280,016 - 149,294,949 (+)NCBICelera
Cytogenetic Map7q36.2NCBI
HuRef7148,594,438 - 148,611,518 (+)NCBIHuRef
CHM1_17154,870,423 - 154,887,497 (+)NCBICHM1_1
T2T-CHM13v2.07156,245,922 - 156,263,037 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27154,090,358 - 154,107,446 (+)NCBI
Htr5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39528,046,714 - 28,060,084 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl528,047,147 - 28,060,086 (+)EnsemblGRCm39 Ensembl
GRCm38527,841,716 - 27,855,086 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl527,842,149 - 27,855,088 (+)EnsemblGRCm38mm10GRCm38
MGSCv37528,168,487 - 28,181,626 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36528,172,734 - 28,185,873 (+)NCBIMGSCv36mm8
Celera525,390,567 - 25,404,062 (+)NCBICelera
Cytogenetic Map5B1NCBI
cM Map513.24NCBI
Htr5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554918,257,698 - 8,267,817 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554918,258,032 - 8,266,503 (+)NCBIChiLan1.0ChiLan1.0
HTR5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17158,399,874 - 158,416,922 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7158,399,874 - 158,416,922 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07146,672,908 - 146,690,001 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
HTR5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11618,142,808 - 18,151,884 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1618,142,830 - 18,152,442 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1618,774,961 - 18,784,567 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01619,870,711 - 19,880,323 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1619,870,775 - 19,881,072 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11618,241,740 - 18,251,355 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01618,821,984 - 18,831,569 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01618,874,866 - 18,884,472 (+)NCBIUU_Cfam_GSD_1.0
Htr5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051183,356,644 - 3,369,173 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365279,534,903 - 9,543,574 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365279,534,723 - 9,547,235 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HTR5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1183,029,681 - 3,033,646 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2183,211,397 - 3,219,097 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HTR5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121123,229,239 - 123,244,360 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl21123,229,816 - 123,241,481 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607219,276,174 - 19,365,766 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Htr5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248002,618,973 - 2,625,559 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248002,616,861 - 2,625,907 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Htr5a
92 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:62
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000009317
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat

Markers in Region
RH94441  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.247,445,007 - 7,445,166 (-)MAPPERmRatBN7.2
Rnor_6.04209,401 - 209,559NCBIRnor6.0
Rnor_5.04202,597 - 202,755UniSTSRnor5.0
RGSC_v3.442,707,301 - 2,707,459UniSTSRGSC3.4
Celera42,835,777 - 2,835,935UniSTS
Cytogenetic Map4q11UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system nervous system reproductive system respiratory system
High
Medium 7
Low 51 5
Below cutoff 2 8 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009317   ⟹   ENSRNOP00000009317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl47,444,968 - 7,454,651 (-)Ensembl
Rnor_6.0 Ensembl4199,916 - 209,599 (+)Ensembl
RefSeq Acc Id: NM_013148   ⟹   NP_037280
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.247,444,968 - 7,454,651 (-)NCBI
Rnor_6.04199,916 - 209,599 (+)NCBI
Rnor_5.04192,554 - 202,795 (+)NCBI
RGSC_v3.442,707,261 - 2,716,944 (-)RGD
Celera42,826,290 - 2,835,975 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037280 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40615 (Get FASTA)   NCBI Sequence Viewer  
  EDL86411 (Get FASTA)   NCBI Sequence Viewer  
  P35364 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037280   ⟸   NM_013148
- UniProtKB: P35364 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009317   ⟸   ENSRNOT00000009317

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35364-F1-model_v2 AlphaFold P35364 1-357 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2851 AgrOrtholog
BioCyc Gene G2FUF-46128 BioCyc
Ensembl Genes ENSRNOG00000007066 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009317 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009317 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro 5HT5A_rcpt UniProtKB/Swiss-Prot
  5HT_rcpt UniProtKB/Swiss-Prot
  GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
KEGG Report rno:25689 UniProtKB/Swiss-Prot
NCBI Gene 25689 ENTREZGENE
PANTHER PTHR24247:SF108 UniProtKB/Swiss-Prot
Pfam 7tm_1 UniProtKB/Swiss-Prot
PharmGKB HTR5A RGD
PhenoGen Htr5a PhenoGen
PRINTS 5HT5ARECEPTR UniProtKB/Swiss-Prot
  5HTRECEPTOR UniProtKB/Swiss-Prot
  GPCRRHODOPSN UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
UniProt 5HT5A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Htr5a  5-hydroxytryptamine receptor 5A  Htr5a  5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-17 Htr5a  5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled  Htr5a  5-hydroxytryptamine (serotonin) receptor 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Htr5a  5-hydroxytryptamine (serotonin) receptor 5A      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in Purkinje cells, molecular layer interneurons and Golgi cells 727384