Htr1f (5-hydroxytryptamine receptor 1F) - Rat Genome Database
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Gene: Htr1f (5-hydroxytryptamine receptor 1F) Rattus norvegicus
Analyze
Symbol: Htr1f
Name: 5-hydroxytryptamine receptor 1F
RGD ID: 71083
Description: Predicted to have G protein-coupled serotonin receptor activity; neurotransmitter receptor activity; and serotonin binding activity. Predicted to be involved in adenylate cyclase-inhibiting serotonin receptor signaling pathway and chemical synaptic transmission. Predicted to localize to dendrite and integral component of plasma membrane. Orthologous to human HTR1F (5-hydroxytryptamine receptor 1F); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 5-HT-1F; 5-HT1F; 5-hydroxytryptamine (serotonin) receptor 1F; 5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled; Htr1eb; serotonin receptor 1F; serotonin receptor gene (similar to Mm Htr1eb)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0111,982,113 - 1,983,513 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl111,982,113 - 1,983,513 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0111,960,208 - 1,961,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4112,260,587 - 2,261,687 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1112,260,586 - 2,261,687 (-)NCBI
Celera112,624,797 - 2,626,196 (-)NCBICelera
Cytogenetic Map11p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8380639   PMID:19077678   PMID:19735698   PMID:20833155   PMID:21422162   PMID:21653728  


Genomics

Comparative Map Data
Htr1f
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0111,982,113 - 1,983,513 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl111,982,113 - 1,983,513 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0111,960,208 - 1,961,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4112,260,587 - 2,261,687 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1112,260,586 - 2,261,687 (-)NCBI
Celera112,624,797 - 2,626,196 (-)NCBICelera
Cytogenetic Map11p12NCBI
HTR1F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl387,990,696 - 87,993,835 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl387,792,492 - 87,993,787 (+)EnsemblGRCh38hg38GRCh38
GRCh38387,792,706 - 87,994,856 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37387,841,929 - 88,043,964 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36388,114,416 - 88,125,609 (+)NCBINCBI36hg18NCBI36
Build 34388,122,589 - 88,123,690NCBI
Celera388,785,845 - 88,797,020 (+)NCBI
Cytogenetic Map3p11.2-p11.1NCBI
HuRef388,045,479 - 88,056,646 (+)NCBIHuRef
CHM1_1387,794,599 - 87,996,115 (+)NCBICHM1_1
Htr1f
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391664,745,092 - 64,926,147 (-)NCBIGRCm39mm39
GRCm381664,924,729 - 65,105,784 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1664,924,729 - 65,105,854 (-)EnsemblGRCm38mm10GRCm38
MGSCv371664,924,555 - 65,105,610 (-)NCBIGRCm37mm9NCBIm37
MGSCv361664,866,931 - 65,048,056 (-)NCBImm8
Celera1665,219,165 - 65,393,158 (-)NCBICelera
Cytogenetic Map16C1.3NCBI
cM Map1637.1NCBI
Htr1f
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554075,512,124 - 5,632,308 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554075,512,124 - 5,632,458 (-)NCBIChiLan1.0ChiLan1.0
HTR1F
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1390,045,663 - 90,244,207 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl390,241,126 - 90,242,226 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0387,933,394 - 88,196,379 (+)NCBIMhudiblu_PPA_v0panPan3
HTR1F
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl31273,493 - 427,622 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.131272,358 - 428,055 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Htr1f
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366101,735,939 - 1,737,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HTR1F
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13167,956,003 - 168,105,090 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113167,951,444 - 167,987,391 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213178,815,949 - 178,844,211 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HTR1F
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12288,933,841 - 89,098,040 (-)NCBI
Htr1f
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247894,381,022 - 4,382,271 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:27
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000000907
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium
Low 8 17 44 1 12 1
Below cutoff 2 26 4 3 2 3 22 33 16 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000907   ⟹   ENSRNOP00000000907
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl111,982,113 - 1,983,513 (-)Ensembl
RefSeq Acc Id: NM_021857   ⟹   NP_068629
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0111,982,113 - 1,983,513 (-)NCBI
Rnor_5.0111,960,208 - 1,961,608 (-)NCBI
RGSC_v3.4112,260,587 - 2,261,687 (-)RGD
Celera112,624,797 - 2,626,196 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_068629 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42133 (Get FASTA)   NCBI Sequence Viewer  
  EDL75903 (Get FASTA)   NCBI Sequence Viewer  
  P30940 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_068629   ⟸   NM_021857
- UniProtKB: G3V626 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000907   ⟸   ENSRNOT00000000907
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 1961443 1961444 G C snv SBN/Ygl (MCW), DOB/Oda (KyushuU), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), F344/Jcl (KyushuU), MHS/Gib (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 1983348 1983349 G C snv SBN/Ygl (MCW), CDR, F344/NRrrc (MCW), SBN/Ygl (RGD), F344/NCrl (RGD), MHS/Gib (RGD), WN/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 2261563 2261564 G C snv F344/NRrrc (KNAW), WN/N (KNAW), F344/NCrl (ICL), F344/NHsd (ICAHN), SBN/Ygl (ICL), LCR/2Mco (UMich), MHS/Gib (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:71083 AgrOrtholog
Ensembl Genes ENSRNOG00000000716 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000907 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000907 ENTREZGENE, UniProtKB/TrEMBL
InterPro 5HT1F_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  5HT_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60448 UniProtKB/TrEMBL
NCBI Gene 60448 ENTREZGENE
PANTHER PTHR24247:SF34 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Htr1f PhenoGen
PRINTS 5HTRECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART 7TM_GPCR_Srsx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.44301 ENTREZGENE
UniProt 5HT1F_RAT UniProtKB/Swiss-Prot
  G3V626 ENTREZGENE, UniProtKB/TrEMBL
  P30940 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Htr1f  5-hydroxytryptamine receptor 1F  Htr1f  5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-17 Htr1f  5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled  Htr1f  5-hydroxytryptamine (serotonin) receptor 1F  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Htr1f  5-hydroxytryptamine (serotonin) receptor 1F      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs binds 125I-labeled d-lysergic acid diethylamide (LSD) 70767
gene_protein 366 amino acids 70767