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 negative regulation of thymocyte apoptotic process. Predicted to be located in 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8921,716,522 - 21,726,751 (+)NCBIGRCr8
mRatBN7.2914,218,907 - 14,229,141 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0916,528,970 - 16,539,383 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,529,579 - 16,539,472 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,436,852 - 15,445,993 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1910,095,697 - 10,098,251 (+)NCBI
Celera911,966,527 - 11,977,493 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

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 (+)NCBIGRCr8
mRatBN7.2914,218,907 - 14,229,141 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0916,528,970 - 16,539,383 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl916,529,579 - 16,539,472 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0915,436,852 - 15,445,993 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1910,095,697 - 10,098,251 (+)NCBI
Celera911,966,527 - 11,977,493 (+)NCBICelera
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37642,883,791 - 42,893,576 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36642,991,705 - 43,001,554 (+)NCBINCBI36Build 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 Ensembl
GRCm381746,755,663 - 46,763,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,755,663 - 46,763,712 (-)EnsemblGRCm38mm10GRCm38
MGSCv371746,892,612 - 46,900,661 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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
ChiLan1.0NW_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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,495,933 - 11,502,247 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01211,950,108 - 11,956,422 (+)NCBIROS_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_1.0
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ptcra
109 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat

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
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 7 7
Low 1 1 10 17 5
Below cutoff 5 16 14 2 14 2 2 4 12 25 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067894   ⟹   ENSRNOP00000059713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,218,802 - 14,229,235 (+)Ensembl
Rnor_6.0 Ensembl916,529,579 - 16,539,063 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091565   ⟹   ENSRNOP00000069313
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl914,219,671 - 14,229,235 (+)Ensembl
Rnor_6.0 Ensembl916,530,074 - 16,539,472 (+)Ensembl
RefSeq 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
  ENSRNOP00000059713.3
  ENSRNOP00000069313.1
  ENSRNOP00000083966.1
GenBank Protein P0C6B3 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000059713   ⟸   ENSRNOT00000067894
RefSeq Acc Id: ENSRNOP00000069313   ⟸   ENSRNOT00000091565
RefSeq Acc Id: ENSRNOP00000083966   ⟸   ENSRNOT00000104384
RefSeq Acc Id: NP_001400550   ⟸   NM_001413621
- Peptide Label: precursor
- UniProtKB: 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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067894 ENTREZGENE
  ENSRNOT00000067894.4 UniProtKB/TrEMBL
  ENSRNOT00000091565.2 UniProtKB/TrEMBL
  ENSRNOT00000104384.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTCRA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116462 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 116462 ENTREZGENE
PANTHER PRE T-CELL ANTIGEN RECEPTOR ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR37866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PTCRA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptcra PhenoGen
RatGTEx ENSRNOG00000042581 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JV15_RAT UniProtKB/TrEMBL
  A0A8I6A0C4_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