Ptcra (pre T-cell antigen receptor alpha) - Rat Genome Database

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Gene: Ptcra (pre T-cell antigen receptor alpha) Rattus norvegicus
Analyze
Symbol: Ptcra
Name: pre T-cell antigen receptor alpha
RGD ID: 621388
Description: Predicted to be involved in alpha-beta T cell differentiation and negative regulation of thymocyte apoptotic process. Predicted to be located in plasma membrane. Orthologous to human PTCRA (pre T cell antigen receptor alpha); PARTICIPATES IN Notch signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 1,2-dichloroethane (ortholog); 1-chloro-2,4-dinitrobenzene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: pT-alpha; pT-alpha-TCR; pTa
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,716,522 - 21,726,751 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,716,522 - 21,726,751 (+)EnsemblGRCr8
mRatBN7.2914,218,907 - 14,229,141 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)EnsemblmRatBN7.2
Rnor_6.0916,528,970 - 16,539,383 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,529,579 - 16,539,472 (+)Ensemblrn6Rnor6.0
Rnor_5.0915,436,852 - 15,445,993 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera911,966,527 - 11,977,493 (+)NCBICelera
RGSC_v3.1910,095,697 - 10,098,251 (+)NCBI
Cytogenetic Map9q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
plasma membrane  (IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Early T cell development can be traced in rat fetal liver. Alonso-C LM, etal., Eur J Immunol 2000 Dec;30(12):3604-13.
2. 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.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Analysis and expression of a cloned pre-T cell receptor gene. Saint-Ruf C, etal., Science 1994 Nov 18;266(5188):1208-12.
Additional References at PubMed
PMID:15728238  


Genomics

Comparative Map Data
Ptcra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,716,522 - 21,726,751 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl921,716,522 - 21,726,751 (+)EnsemblGRCr8
mRatBN7.2914,218,907 - 14,229,141 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)EnsemblmRatBN7.2
Rnor_6.0916,528,970 - 16,539,383 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,529,579 - 16,539,472 (+)Ensemblrn6Rnor6.0
Rnor_5.0915,436,852 - 15,445,993 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera911,966,527 - 11,977,493 (+)NCBICelera
RGSC_v3.1910,095,697 - 10,098,251 (+)NCBI
Cytogenetic Map9q12NCBI
PTCRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38642,916,053 - 42,925,838 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl642,915,989 - 42,925,838 (+)Ensemblhg38GRCh38
GRCh37642,883,791 - 42,893,576 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36642,991,705 - 43,001,554 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34642,991,704 - 43,001,551NCBI
Celera644,435,989 - 44,445,838 (+)NCBICelera
Cytogenetic Map6p21.1NCBI
HuRef642,601,262 - 42,611,014 (+)NCBIHuRef
CHM1_1642,886,198 - 42,896,045 (+)NCBICHM1_1
T2T-CHM13v2.0642,744,769 - 42,754,903 (+)NCBIT2T-CHM13v2.0
Ptcra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,066,589 - 47,074,659 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1747,066,589 - 47,074,638 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381746,755,663 - 46,763,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,755,663 - 46,763,712 (-)Ensemblmm10GRCm38
MGSCv371746,892,612 - 46,900,661 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361746,218,852 - 46,226,903 (-)NCBIMGSCv36mm8
Celera1750,191,264 - 50,199,524 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Ptcra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,920,712 - 8,927,409 (+)Ensembl
ChiLan1.0NW_0049554378,920,997 - 8,927,354 (+)NCBIChiLan1.0ChiLan1.0
PTCRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2557,412,241 - 57,422,701 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1653,282,249 - 53,292,717 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0642,504,369 - 42,514,837 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1643,799,778 - 43,809,790 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,799,778 - 43,811,882 (+)EnsemblpanPan2panpan1.1
PTCRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,468,882 - 11,475,234 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,472,103 - 11,473,394 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1211,495,933 - 11,502,247 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01211,950,108 - 11,956,422 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11211,478,014 - 11,484,344 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01211,562,466 - 11,568,789 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01211,656,338 - 11,662,670 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ptcra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494646,963,945 - 46,971,111 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647616,989,281 - 16,996,065 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTCRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,006,050 - 38,012,193 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1738,006,074 - 38,012,193 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,454,440 - 43,460,558 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7q11-q12NCBI
PTCRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11729,229,095 - 29,237,665 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604442,980,384 - 42,983,844 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptcra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475416,542,741 - 16,547,428 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ptcra
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1483,103,882 - 83,112,599 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ptcra
137 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:114
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000067894
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9671488829567695Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat

Markers in Region
RH135276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2914,228,803 - 14,229,003 (+)MAPPERmRatBN7.2
Rnor_6.0916,539,041 - 16,539,240NCBIRnor6.0
Rnor_5.0915,445,656 - 15,445,855UniSTSRnor5.0
RGSC_v3.4910,101,015 - 10,101,214UniSTSRGSC3.4
Celera911,977,151 - 11,977,350UniSTS
RH 3.4 Map955.4UniSTS
Cytogenetic Map9q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
4 2 11 27 43 49 23 75 23 2 170 92 3 19 49 55 26 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000067894   ⟹   ENSRNOP00000059713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl921,716,522 - 21,726,751 (+)Ensembl
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)Ensembl
Rnor_6.0 Ensembl916,529,579 - 16,539,063 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000091565   ⟹   ENSRNOP00000069313
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl921,717,251 - 21,726,751 (+)Ensembl
mRatBN7.2 Ensembl914,219,671 - 14,229,235 (+)Ensembl
Rnor_6.0 Ensembl916,530,074 - 16,539,472 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104384   ⟹   ENSRNOP00000083966
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,225,522 - 14,229,235 (+)Ensembl
RefSeq Acc Id: NM_001413621   ⟹   NP_001400550
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8921,716,522 - 21,726,751 (+)NCBI
mRatBN7.2914,218,907 - 14,229,141 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001400550 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG16904 (Get FASTA)   NCBI Sequence Viewer  
  EDM18861 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059713
GenBank Protein P0C6B3 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Acc Id: ENSRNOP00000059713   ⟸   ENSRNOT00000067894
Ensembl Acc Id: ENSRNOP00000069313   ⟸   ENSRNOT00000091565
Ensembl Acc Id: ENSRNOP00000083966   ⟸   ENSRNOT00000104384
RefSeq Acc Id: NP_001400550   ⟸   NM_001413621
- Peptide Label: precursor
- UniProtKB: P0C6B3 (UniProtKB/Swiss-Prot),   A0A9M1XLL3 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C6B3-F1-model_v2 AlphaFold P0C6B3 1-199 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:621388 AgrOrtholog
BioCyc Gene G2FUF-28244 BioCyc
Ensembl Genes ENSRNOG00000042581 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000067894 ENTREZGENE
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
InterPro Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  PTCRA UniProtKB/Swiss-Prot
NCBI Gene 116462 ENTREZGENE
PANTHER PRE T-CELL ANTIGEN RECEPTOR ALPHA UniProtKB/Swiss-Prot
  PTHR37866 UniProtKB/Swiss-Prot
Pfam PTCRA UniProtKB/Swiss-Prot
PhenoGen Ptcra PhenoGen
RatGTEx ENSRNOG00000042581 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt A0A0G2JV15_RAT UniProtKB/TrEMBL
  A0A9M1XLL3 ENTREZGENE, UniProtKB/TrEMBL
  P0C6B3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Ptcra  pre T-cell antigen receptor alpha      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Ptcra  pre T-cell antigen receptor alpha      Symbol and Name status set to provisional 70820 PROVISIONAL