Trpa1 (transient receptor potential cation channel, subfamily A, member 1) - Rat Genome Database

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Gene: Trpa1 (transient receptor potential cation channel, subfamily A, member 1) Rattus norvegicus
Analyze
Symbol: Trpa1
Name: transient receptor potential cation channel, subfamily A, member 1
RGD ID: 1303284
Description: Exhibits osmolarity-sensing cation channel activity and voltage-gated calcium channel activity. Involved in several processes, including cellular response to caffeine; cellular response to carbon dioxide; and regulation of nervous system process. Localizes to apical plasma membrane and axon. Used to study diabetic neuropathy. Human ortholog(s) of this gene implicated in familial episodic pain syndrome 1. Orthologous to human TRPA1 (transient receptor potential cation channel subfamily A member 1); INTERACTS WITH 3-phenylprop-2-enal; 4-hydroxynon-2-enal; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ANKTM1; ankyrin-like with transmembrane domains protein 1; transient receptor potential cation channel subfamily A member 1; wasabi receptor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Trpa1em1Kcrd  
Genetic Models: W-Trpa1em1Kcrd
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.254,379,999 - 4,433,243 (+)NCBI
Rnor_6.0 Ensembl53,783,247 - 3,836,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.053,783,247 - 3,836,485 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.053,764,339 - 3,818,781 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.453,531,163 - 3,584,401 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.153,531,162 - 3,584,401 (+)NCBI
Celera53,971,809 - 4,024,939 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dibutyrin  (ISO)
1,2-dichloroethane  (ISO)
1,2-naphthoquinone  (ISO)
1-naphthol  (ISO)
1-nitronaphthalene  (ISO)
2,4-di-tert-butylphenol  (ISO)
2,4-Dimethylphenol  (ISO)
2-ethylhexan-1-ol  (ISO)
2-Ethylphenol  (ISO)
2-Methoxy-4-methylphenol  (ISO)
3,4-xylenol  (ISO)
3,5-xylenol  (ISO)
3-Ethylphenol  (ISO)
3-phenylprop-2-enal  (EXP,ISO)
4-ethylphenol  (ISO)
4-hydroxynon-2-enal  (EXP,ISO)
8-Br-cAMP  (ISO)
acetophenone  (ISO)
aconitine  (EXP)
acrolein  (EXP,ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
allicin  (EXP,ISO)
allyl isothiocyanate  (EXP,ISO)
amiloride  (ISO)
arachidonic acid  (ISO)
atenolol  (ISO)
atropine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
Cannabichromene  (ISO)
cannabidiol  (EXP,ISO)
cannabidiolic acid  (ISO)
Cannabinol  (ISO)
capsaicin  (EXP,ISO)
carbon dioxide  (EXP)
carvacrol  (EXP,ISO)
cisplatin  (ISO)
citronellal  (ISO)
coniferyl aldehyde  (ISO)
crotonaldehyde  (EXP,ISO)
cyclophosphamide  (EXP)
deoxynivalenol  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
edelfosine  (ISO)
entinostat  (ISO)
eugenol  (EXP)
fluorescein 5-isothiocyanate  (ISO)
folic acid  (ISO)
formaldehyde  (EXP,ISO)
gadolinium atom  (ISO)
gentamycin  (ISO)
glutathione  (ISO)
hydrogen sulfide  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
isocyanates  (ISO)
isopentenyl diphosphate  (ISO)
Lasiocarpine  (ISO)
lidocaine  (EXP,ISO)
linalool  (ISO)
menadione  (ISO)
methylglyoxal  (ISO)
N(gamma)-nitro-L-arginine methyl ester  (ISO)
N-acetyl-1,4-benzoquinone imine  (EXP,ISO)
N-acetyl-L-cysteine  (ISO)
naphthalene  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
p-methoxybenzaldehyde  (ISO)
paracetamol  (ISO)
picrocrocin  (ISO)
resiniferatoxin  (EXP)
ruthenium red  (ISO)
safranal  (ISO)
SB 431542  (ISO)
serotonin  (ISO)
styrene  (ISO)
tributyrin  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
U-73122  (ISO)
valproic acid  (ISO)
WIN 55212-2  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Andrade EL, etal., Am J Physiol Renal Physiol. 2011 May;300(5):F1223-34. doi: 10.1152/ajprenal.00535.2010. Epub 2011 Mar 2.
2. Bianchi BR, etal., J Pharmacol Exp Ther. 2012 May;341(2):360-8. doi: 10.1124/jpet.111.189902. Epub 2012 Feb 7.
3. Cao DS, etal., PLoS One. 2012;7(5):e38005. doi: 10.1371/journal.pone.0038005. Epub 2012 May 31.
4. del Camino D, etal., J Neurosci. 2010 Nov 10;30(45):15165-74. doi: 10.1523/JNEUROSCI.2580-10.2010.
5. Eid SR, etal., Mol Pain. 2008 Oct 27;4:48. doi: 10.1186/1744-8069-4-48.
6. Ji G, etal., Neuroscience. 2008 Jun 26;154(3):1054-66. doi: 10.1016/j.neuroscience.2008.04.039. Epub 2008 May 2.
7. Jordt SE, etal., Nature 2004 Jan 15;427(6971):260-5. Epub 2004 Jan 07.
8. Kaji I, etal., Am J Physiol Gastrointest Liver Physiol. 2012 Apr;302(7):G690-701. doi: 10.1152/ajpgi.00289.2011. Epub 2011 Dec 29.
9. Koivisto A, etal., Pharmacol Res. 2012 Jan;65(1):149-58. doi: 10.1016/j.phrs.2011.10.006. Epub 2011 Nov 23.
10. Kojima R, etal., Eur J Pharmacol. 2014 Jan 15;723:288-93. doi: 10.1016/j.ejphar.2013.11.020. Epub 2013 Nov 28.
11. Krimon S, etal., Pharmacol Biochem Behav. 2013 Nov;112:49-55. doi: 10.1016/j.pbb.2013.09.017. Epub 2013 Oct 9.
12. McGaraughty S, etal., Mol Pain. 2010 Mar 5;6:14. doi: 10.1186/1744-8069-6-14.
13. MGD data from the GO Consortium
14. OMIM Disease Annotation Pipeline
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Staruschenko A, etal., J Biol Chem. 2010 May 14;285(20):15167-77. doi: 10.1074/jbc.M110.106153. Epub 2010 Mar 15.
19. Vermeulen W, etal., Eur J Pharmacol. 2013 Jan 5;698(1-3):404-12. doi: 10.1016/j.ejphar.2012.10.014. Epub 2012 Oct 23.
20. Wang S, etal., Mol Pain. 2012 Mar 29;8:22. doi: 10.1186/1744-8069-8-22.
21. Wang YY, etal., J Neurosci. 2010 Sep 29;30(39):12958-63. doi: 10.1523/JNEUROSCI.2715-10.2010.
22. Zhang XF, etal., Eur J Neurosci. 2008 Feb;27(3):605-11. doi: 10.1111/j.1460-9568.2008.06030.x.
Additional References at PubMed
PMID:12654248   PMID:15483558   PMID:15843607   PMID:16110328   PMID:16304633   PMID:16546170   PMID:16564016   PMID:16595689   PMID:16630838   PMID:16675144   PMID:16831854   PMID:17329204  
PMID:17517374   PMID:17571167   PMID:17584831   PMID:17588549   PMID:17943255   PMID:18272293   PMID:18297068   PMID:18398506   PMID:18463259   PMID:18598259   PMID:19158342   PMID:19211797  
PMID:19237591   PMID:19299646   PMID:19348834   PMID:19371346   PMID:19419422   PMID:19464796   PMID:19491712   PMID:19629446   PMID:19812688   PMID:19961905   PMID:20034057   PMID:20133428  
PMID:20167675   PMID:20182791   PMID:20497466   PMID:20547126   PMID:20588026   PMID:20717636   PMID:21076024   PMID:21316356   PMID:21619614   PMID:21653898   PMID:21868092   PMID:22588108  
PMID:22721614   PMID:22740698   PMID:22809691   PMID:22865090   PMID:22928941   PMID:23098993   PMID:23133534   PMID:23222658   PMID:23293814   PMID:23384628   PMID:23521647   PMID:23603259  
PMID:23707800   PMID:23784920   PMID:23832015   PMID:23842678   PMID:23846257   PMID:23873754   PMID:23916509   PMID:23918657   PMID:23959730   PMID:24071625   PMID:24358160   PMID:24607781  
PMID:24780252   PMID:25484020   PMID:25605129   PMID:25639234   PMID:25765567   PMID:25855297   PMID:25858491   PMID:25884403   PMID:25889103   PMID:25896791   PMID:26046936   PMID:26172081  
PMID:26274042   PMID:26393428   PMID:26567040   PMID:26643912   PMID:26888187   PMID:26922555   PMID:26935999   PMID:27236325   PMID:27411353   PMID:27497709   PMID:27589700   PMID:27748654  
PMID:27752892   PMID:27904941   PMID:28017670   PMID:28032561   PMID:28103292   PMID:28370084   PMID:28640016   PMID:28698251   PMID:28710476   PMID:29428952   PMID:29537196   PMID:29777700  
PMID:30236550   PMID:30510606   PMID:31016687   PMID:31144562   PMID:31257266   PMID:31531184   PMID:31969645   PMID:32708653  


Genomics

Comparative Map Data
Trpa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.254,379,999 - 4,433,243 (+)NCBI
Rnor_6.0 Ensembl53,783,247 - 3,836,485 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.053,783,247 - 3,836,485 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.053,764,339 - 3,818,781 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.453,531,163 - 3,584,401 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.153,531,162 - 3,584,401 (+)NCBI
Celera53,971,809 - 4,024,939 (+)NCBICelera
Cytogenetic Map5q11NCBI
TRPA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl872,019,917 - 72,075,584 (-)EnsemblGRCh38hg38GRCh38
GRCh38872,021,250 - 72,094,885 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37872,933,485 - 72,987,819 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36873,096,040 - 73,150,373 (-)NCBINCBI36hg18NCBI36
Build 34873,096,039 - 73,150,373NCBI
Celera868,932,963 - 68,987,289 (-)NCBI
Cytogenetic Map8q21.11NCBI
HuRef868,428,222 - 68,482,529 (-)NCBIHuRef
CHM1_1872,986,840 - 73,041,189 (-)NCBICHM1_1
Trpa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39114,942,868 - 14,989,086 (-)NCBIGRCm39mm39
GRCm39 Ensembl114,942,872 - 14,989,086 (-)Ensembl
GRCm38114,872,644 - 14,918,862 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl114,872,648 - 14,918,862 (-)EnsemblGRCm38mm10GRCm38
MGSCv37114,862,729 - 14,908,943 (-)NCBIGRCm37mm9NCBIm37
MGSCv36114,857,862 - 14,904,076 (-)NCBImm8
Celera114,822,489 - 14,871,741 (-)NCBICelera
Cytogenetic Map1A3NCBI
Trpa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554447,876,429 - 7,921,372 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554447,876,284 - 7,922,010 (+)NCBIChiLan1.0ChiLan1.0
TRPA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1870,208,697 - 70,262,802 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl870,210,352 - 70,262,627 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0868,551,685 - 68,605,336 (-)NCBIMhudiblu_PPA_v0panPan3
TRPA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12920,951,736 - 21,000,956 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2920,951,716 - 21,001,208 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2921,214,374 - 21,266,355 (-)NCBI
ROS_Cfam_1.02921,050,161 - 21,102,458 (-)NCBI
UMICH_Zoey_3.12921,102,449 - 21,154,677 (-)NCBI
UNSW_CanFamBas_1.02921,151,285 - 21,203,541 (-)NCBI
UU_Cfam_GSD_1.02921,431,610 - 21,483,919 (-)NCBI
Trpa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530358,307,190 - 58,354,763 (+)NCBI
SpeTri2.0NW_0049366481,094,460 - 1,141,394 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRPA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl463,306,738 - 63,558,485 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1463,493,374 - 63,558,486 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2469,132,584 - 69,265,553 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TRPA1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1867,698,067 - 67,754,407 (-)NCBI
ChlSab1.1 Ensembl867,698,786 - 67,751,885 (-)Ensembl
Trpa1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474418,997,273 - 19,042,838 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)516665875533324Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat


Genetic Models
This gene Trpa1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:104
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000009874
Prediction methods:Microtar, 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 integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 1 20 22 12 8
Below cutoff 2 21 6 2 11 2 1 1 50 11 19 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009874   ⟹   ENSRNOP00000009874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl53,783,247 - 3,836,485 (+)Ensembl
RefSeq Acc Id: NM_207608   ⟹   NP_997491
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,379,999 - 4,433,243 (+)NCBI
Rnor_6.053,783,247 - 3,836,485 (+)NCBI
Rnor_5.053,764,339 - 3,818,781 (+)NCBI
RGSC_v3.453,531,163 - 3,584,401 (+)RGD
Celera53,971,809 - 4,024,939 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_997491 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAS78661 (Get FASTA)   NCBI Sequence Viewer  
  EDM11520 (Get FASTA)   NCBI Sequence Viewer  
  Q6RI86 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_997491   ⟸   NM_207608
- UniProtKB: Q6RI86 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009874   ⟸   ENSRNOT00000009874
Protein Domains
ANK_REP_REGION

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303284 AgrOrtholog
Ensembl Genes ENSRNOG00000007354 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009874 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009874 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:312896 UniProtKB/Swiss-Prot
NCBI Gene 312896 ENTREZGENE
Pfam Ank_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Trpa1 PhenoGen
PRINTS ANKYRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ANK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48403 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LRH9_RAT UniProtKB/TrEMBL
  Q6RI86 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Trpa1  transient receptor potential cation channel, subfamily A, member 1    transient receptor potential cation channel subfamily A member 1  Name updated 1299863 APPROVED
2005-07-14 Trpa1  transient receptor potential cation channel subfamily A member 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains member of the transient receptor ion channel family 1303969
gene_drugs activated by tetrahydrocannabinol and cannabinol; but does not appear to be activated by endocannabinoids 1303969
gene_expression expressed in trigeminal ganglial neurons 1303969