Trpc5 (transient receptor potential cation channel, subfamily C, member 5) - Rat Genome Database

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Gene: Trpc5 (transient receptor potential cation channel, subfamily C, member 5) Rattus norvegicus
Analyze
Symbol: Trpc5
Name: transient receptor potential cation channel, subfamily C, member 5
RGD ID: 619787
Description: Exhibits ATPase binding activity; clathrin binding activity; and cytoskeletal protein binding activity. Involved in several processes, including generation of neurons; positive regulation of peptidyl-threonine phosphorylation; and regulation of membrane hyperpolarization. Localizes to several cellular components, including growth cone; membrane raft; and neuronal cell body. Orthologous to human TRPC5 (transient receptor potential cation channel subfamily C member 5); INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: short transient receptor potential channel 5; transient receptor protein 5; Trrp5
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
mRatBN7.2X107,946,163 - 108,230,978 (-)NCBI
Rnor_6.0 EnsemblX115,627,653 - 115,908,693 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X115,624,670 - 115,908,248 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X114,079,131 - 114,359,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X33,989,907 - 34,126,175 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X33,897,584 - 34,179,644 (+)NCBI
CeleraX107,338,307 - 107,473,426 (-)NCBICelera
Cytogenetic MapXq34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
1. Bush EW, etal., J Biol Chem. 2006 Nov 3;281(44):33487-96. Epub 2006 Sep 1.
2. Cvetkovic-Lopes V, etal., PLoS One. 2010 Dec 16;5(12):e15673. doi: 10.1371/journal.pone.0015673.
3. Davare MA, etal., J Neurosci. 2009 Aug 5;29(31):9794-808. doi: 10.1523/JNEUROSCI.1544-09.2009.
4. Fortin DA, etal., J Neurosci. 2012 Jun 13;32(24):8127-37. doi: 10.1523/JNEUROSCI.6034-11.2012.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Goel M, etal., Pflugers Arch. 2005 Oct;451(1):87-98. Epub 2005 Jul 16.
8. Greka A, etal., Nat Neurosci 2003 Aug;6(8):837-45.
9. He Z, etal., J Neurosci. 2012 Jul 4;32(27):9383-95. doi: 10.1523/JNEUROSCI.6363-11.2012.
10. Kumar S, etal., J Cell Physiol. 2012 Apr;227(4):1408-19. doi: 10.1002/jcp.22855.
11. Lee YM, etal., Am J Physiol Gastrointest Liver Physiol 2003 Apr;284(4):G604-16.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Schaldecker T, etal., J Clin Invest. 2013 Dec;123(12):5298-309. doi: 10.1172/JCI71165. Epub 2013 Nov 15.
18. Shin HY, etal., PLoS One. 2010 May 7;5(5):e10359. doi: 10.1371/journal.pone.0010359.
19. Strubing C, etal., J Biol Chem. 2003 Oct 3;278(40):39014-9. Epub 2003 Jul 11.
20. Xu SZ, etal., Toxicol Sci. 2012 Jan;125(1):56-68. doi: 10.1093/toxsci/kfr268. Epub 2011 Oct 9.
Additional References at PubMed
PMID:11301024   PMID:14505576   PMID:15199065   PMID:15334657   PMID:15689561   PMID:16469785   PMID:16635549   PMID:17593972   PMID:18247362   PMID:18250430   PMID:20164195   PMID:20865744  
PMID:21753024   PMID:22135323   PMID:22201561   PMID:23677990   PMID:25958233   PMID:27129253   PMID:27411851   PMID:31878108   PMID:32434348  


Genomics

Comparative Map Data
Trpc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X107,946,163 - 108,230,978 (-)NCBI
Rnor_6.0 EnsemblX115,627,653 - 115,908,693 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X115,624,670 - 115,908,248 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X114,079,131 - 114,359,862 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X33,989,907 - 34,126,175 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X33,897,584 - 34,179,644 (+)NCBI
CeleraX107,338,307 - 107,473,426 (-)NCBICelera
Cytogenetic MapXq34NCBI
TRPC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX111,768,011 - 112,082,776 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX111,774,315 - 112,082,776 (-)EnsemblGRCh38hg38GRCh38
GRCh38X111,768,011 - 112,082,943 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X111,011,239 - 111,326,004 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X110,904,198 - 111,212,660 (-)NCBINCBI36hg18NCBI36
Build 34X110,823,686 - 111,132,149NCBI
CeleraX111,497,049 - 111,805,514 (-)NCBI
Cytogenetic MapXq23NCBI
HuRefX100,639,095 - 100,946,273 (-)NCBIHuRef
CHM1_1X110,928,786 - 111,237,228 (-)NCBICHM1_1
Trpc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X143,160,323 - 143,471,176 (-)NCBIGRCm39mm39
GRCm39 EnsemblX143,164,667 - 143,471,176 (-)Ensembl
GRCm38X144,377,327 - 144,688,180 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX144,381,671 - 144,688,180 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X140,816,214 - 141,122,723 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X139,628,039 - 139,934,548 (-)NCBImm8
CeleraX128,337,325 - 128,644,030 (-)NCBICelera
Cytogenetic MapXF2NCBI
cM MapX65.49NCBI
Trpc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554903,860,909 - 4,057,275 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554903,777,756 - 4,057,275 (+)NCBIChiLan1.0ChiLan1.0
TRPC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X111,346,804 - 111,648,332 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX111,346,804 - 111,648,201 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X100,886,122 - 101,191,425 (-)NCBIMhudiblu_PPA_v0panPan3
TRPC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X84,835,130 - 84,989,609 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX84,801,096 - 85,116,625 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX70,936,399 - 71,117,033 (-)NCBI
ROS_Cfam_1.0X86,509,906 - 86,696,508 (-)NCBI
UMICH_Zoey_3.1X83,981,630 - 84,160,857 (-)NCBI
UNSW_CanFamBas_1.0X85,658,324 - 85,832,221 (-)NCBI
UU_Cfam_GSD_1.0X85,498,131 - 85,680,673 (-)NCBI
Trpc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X84,110,276 - 84,383,058 (-)NCBI
SpeTri2.0NW_0049364993,391,386 - 3,541,406 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRPC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX91,721,617 - 91,988,120 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X91,716,334 - 91,988,364 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X106,133,833 - 106,399,987 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRPC5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X99,546,923 - 99,856,971 (-)NCBI
ChlSab1.1 EnsemblX99,550,595 - 99,736,668 (-)Ensembl
Trpc5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248033,494,311 - 3,812,985 (+)NCBI

Position Markers
BF401448  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X115,642,629 - 115,642,777NCBIRnor6.0
Rnor_5.0X114,096,065 - 114,096,213UniSTSRnor5.0
RGSC_v3.4X34,111,718 - 34,111,866UniSTSRGSC3.4
CeleraX107,353,675 - 107,353,823UniSTS
RH 3.4 Map71130.32UniSTS
Cytogenetic MapXq14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:37
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000009400
Prediction methods:Microtar, Miranda, Pita, 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

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 32 1
Low 20 11 3 36 8 16 2
Below cutoff 17 20 15 13 15 6 6 6 27 24 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009400   ⟹   ENSRNOP00000009400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX115,627,852 - 115,764,217 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091423   ⟹   ENSRNOP00000071700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX115,627,653 - 115,908,693 (-)Ensembl
RefSeq Acc Id: NM_080898   ⟹   NP_543174
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,950,685 - 108,086,239 (-)NCBI
Rnor_6.0X115,627,852 - 115,764,217 (-)NCBI
Rnor_5.0X114,079,131 - 114,359,862 (-)NCBI
RGSC_v3.4X33,989,907 - 34,126,175 (+)RGD
CeleraX107,338,307 - 107,473,426 (-)RGD
Sequence:
RefSeq Acc Id: XM_017601900   ⟹   XP_017457389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,946,163 - 108,230,978 (-)NCBI
Rnor_6.0X115,624,670 - 115,908,248 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_543174 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457389 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL40872 (Get FASTA)   NCBI Sequence Viewer  
  ABS00942 (Get FASTA)   NCBI Sequence Viewer  
  EDL85183 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_543174   ⟸   NM_080898
- UniProtKB: Q8VD38 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457389   ⟸   XM_017601900
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071700   ⟸   ENSRNOT00000091423
RefSeq Acc Id: ENSRNOP00000009400   ⟸   ENSRNOT00000009400
Protein Domains
ANK_REP_REGION   Ion_trans   TRP_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)
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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:619787 AgrOrtholog
Ensembl Genes ENSRNOG00000027233 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009400 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071700 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009400 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091423 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  TRP_2 UniProtKB/TrEMBL
  TRPC5_channel UniProtKB/TrEMBL
  TRPC_channel UniProtKB/TrEMBL
KEGG Report rno:140933 UniProtKB/TrEMBL
NCBI Gene 140933 ENTREZGENE
PANTHER PTHR10117 UniProtKB/TrEMBL
  PTHR10117:SF76 UniProtKB/TrEMBL
Pfam Ank_2 UniProtKB/TrEMBL
  Ion_trans UniProtKB/TrEMBL
  TRP_2 UniProtKB/TrEMBL
PhenoGen Trpc5 PhenoGen
PRINTS TRNSRECEPTRP UniProtKB/TrEMBL
  TRPCHANNEL5 UniProtKB/TrEMBL
SMART ANK UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
UniProt A0A0G2K149_RAT UniProtKB/TrEMBL
  F1M176_RAT UniProtKB/TrEMBL
  Q8VD38 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Trpc5  transient receptor potential cation channel, subfamily C, member 5  Trrp5  transient receptor protein 5  Symbol and Name updated 1299863 APPROVED
2002-08-07 Trrp5  transient receptor protein 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with stathmin 2 1304405