Cd247 (Cd247 molecule) - Rat Genome Database

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Gene: Cd247 (Cd247 molecule) Rattus norvegicus
Analyze
Symbol: Cd247
Name: Cd247 molecule
RGD ID: 2305
Description: Predicted to enable identical protein binding activity and protein tyrosine kinase binding activity. Involved in cell surface receptor signaling pathway. Part of T cell receptor complex. Human ortholog(s) of this gene implicated in immunodeficiency 25. Orthologous to human CD247 (CD247 molecule); PARTICIPATES IN interleukin-12 signaling pathway; Chagas disease pathway; T cell receptor signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CD247 antigen; CD3 antigen, zeta polypeptide; Cd3z; T-cell receptor CD3 subunit zeta; T-cell receptor CD3, subunit zeta; T-cell surface glycoprotein CD3 zeta chain; TCRzeta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cd247em1Mcwi   Cd247em5Mcwi   Cd247em3Mcwi  
Genetic Models: SS-Cd247em3Mcwi SS-Cd247em1Mcwi SS-Cd247em5Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21378,043,302 - 78,118,437 (+)NCBI
Rnor_6.0 Ensembl1383,996,080 - 84,071,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01383,996,045 - 84,071,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01388,876,046 - 88,951,003 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41381,515,383 - 81,594,699 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11381,529,570 - 81,608,887 (+)NCBI
Celera1377,754,426 - 77,829,099 (+)NCBICelera
Cytogenetic Map13q23NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1390434   PMID:8176201   PMID:8417118   PMID:8681956   PMID:9064344   PMID:9208839   PMID:11390434   PMID:11435465   PMID:12477932   PMID:14967045   PMID:15184345   PMID:16940250  
PMID:17055436   PMID:18367546   PMID:21809042   PMID:24502978   PMID:28669876  


Genomics

Comparative Map Data
Cd247
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21378,043,302 - 78,118,437 (+)NCBI
Rnor_6.0 Ensembl1383,996,080 - 84,071,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01383,996,045 - 84,071,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01388,876,046 - 88,951,003 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41381,515,383 - 81,594,699 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11381,529,570 - 81,608,887 (+)NCBI
Celera1377,754,426 - 77,829,099 (+)NCBICelera
Cytogenetic Map13q23NCBI
CD247
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1167,430,640 - 167,518,610 (-)EnsemblGRCh38hg38GRCh38
GRCh381167,430,640 - 167,518,542 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371167,399,877 - 167,487,766 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361165,666,505 - 165,754,450 (-)NCBINCBI36hg18NCBI36
Build 341164,131,542 - 164,219,484NCBI
Celera1140,509,330 - 140,597,130 (-)NCBI
Cytogenetic Map1q24.2NCBI
HuRef1138,645,985 - 138,733,880 (-)NCBIHuRef
CHM1_11168,822,340 - 168,910,166 (-)NCBICHM1_1
Cd247
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391165,607,514 - 165,698,722 (+)NCBIGRCm39mm39
GRCm39 Ensembl1165,616,250 - 165,704,846 (+)Ensembl
GRCm381165,779,952 - 165,871,153 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1165,788,681 - 165,877,277 (+)EnsemblGRCm38mm10GRCm38
MGSCv371167,718,820 - 167,804,117 (+)NCBIGRCm37mm9NCBIm37
MGSCv361167,625,398 - 167,704,109 (+)NCBImm8
Celera1168,233,349 - 168,319,834 (+)NCBICelera
Cytogenetic Map1H2.3NCBI
cM Map173.14NCBI
Cd247
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554629,469,255 - 9,538,882 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554629,466,706 - 9,539,897 (+)NCBIChiLan1.0ChiLan1.0
CD247
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11146,648,733 - 146,736,071 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1146,648,733 - 146,736,071 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01142,863,860 - 142,951,851 (-)NCBIMhudiblu_PPA_v0panPan3
CD247
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1730,961,169 - 30,972,143 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha730,436,526 - 30,511,145 (+)NCBI
ROS_Cfam_1.0730,718,692 - 30,793,466 (+)NCBI
UMICH_Zoey_3.1730,557,903 - 30,632,136 (+)NCBI
UNSW_CanFamBas_1.0730,657,066 - 30,664,032 (+)NCBI
UU_Cfam_GSD_1.0730,828,331 - 30,902,528 (+)NCBI
Cd247
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344100,696,707 - 100,758,231 (+)NCBI
SpeTri2.0NW_00493648118,544,129 - 18,605,239 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD247
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl483,458,417 - 83,586,650 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1483,494,266 - 83,586,887 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2491,170,039 - 91,260,282 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD247
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12561,508,256 - 61,596,464 (+)NCBI
ChlSab1.1 Ensembl2561,508,283 - 61,595,414 (+)Ensembl
Vero_WHO_p1.0NW_02366605563,232,781 - 63,332,026 (+)NCBI
Cd247
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248265,504,676 - 5,574,037 (-)NCBI

Position Markers
RH94658  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21378,117,818 - 78,117,930 (+)MAPPER
Rnor_6.01384,070,787 - 84,070,898NCBIRnor6.0
Rnor_5.01388,950,382 - 88,950,493UniSTSRnor5.0
RGSC_v3.41381,594,104 - 81,594,215UniSTSRGSC3.4
Celera1377,828,481 - 77,828,592UniSTS
Cytogenetic Map13q23UniSTS
RH94479  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21378,117,588 - 78,117,758 (+)MAPPER
Rnor_6.01384,070,557 - 84,070,726NCBIRnor6.0
Rnor_5.01388,950,152 - 88,950,321UniSTSRnor5.0
RGSC_v3.41381,593,874 - 81,594,043UniSTSRGSC3.4
Celera1377,828,251 - 77,828,420UniSTS
Cytogenetic Map13q23UniSTS
PMC197251P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21378,117,282 - 78,117,765 (+)MAPPER
Rnor_6.01384,070,251 - 84,070,733NCBIRnor6.0
Rnor_5.01388,949,846 - 88,950,328UniSTSRnor5.0
RGSC_v3.41381,593,568 - 81,594,050UniSTSRGSC3.4
Celera1377,827,945 - 77,828,427UniSTS
Cytogenetic Map13q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136500824591629354Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137456837892916783Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137456837892916783Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137456837892916783Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
11530006Niddm72Non-insulin dependent diabetes mellitus QTL 720.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)137956708186833540Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)138040355991629354Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat


Genetic Models
This gene Cd247 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:459
Count of miRNA genes:193
Interacting mature miRNAs:219
Transcripts:ENSRNOT00000004403, ENSRNOT00000070958
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 2 8 19 6
Low 1 15 19 11 11 6 7 13 15 16 5 6
Below cutoff 16 24 24 24 2 4 37 14 20 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004403   ⟹   ENSRNOP00000004403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1383,996,080 - 84,071,400 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000070958   ⟹   ENSRNOP00000064534
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1383,996,080 - 84,071,400 (+)Ensembl
RefSeq Acc Id: NM_001205304   ⟹   NP_001192233
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21378,043,307 - 78,118,437 (+)NCBI
Rnor_6.01383,996,080 - 84,071,405 (+)NCBI
Rnor_5.01388,876,046 - 88,951,003 (+)NCBI
Celera1377,754,426 - 77,829,099 (+)NCBI
Sequence:
RefSeq Acc Id: NM_170789   ⟹   NP_740770
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21378,043,307 - 78,118,437 (+)NCBI
Rnor_6.01383,996,080 - 84,071,405 (+)NCBI
Rnor_5.01388,876,046 - 88,951,003 (+)NCBI
RGSC_v3.41381,515,383 - 81,594,699 (+)RGD
Celera1377,754,426 - 77,829,099 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250147   ⟹   XP_006250209
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21378,043,302 - 78,118,437 (+)NCBI
Rnor_6.01383,996,045 - 84,071,408 (+)NCBI
Rnor_5.01388,876,046 - 88,951,003 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_740770   ⟸   NM_170789
- Peptide Label: isoform 1 precursor
- UniProtKB: Q4V7G0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001192233   ⟸   NM_001205304
- Peptide Label: isoform 2 precursor
- UniProtKB: M0R576 (UniProtKB/TrEMBL),   Q4V7G0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250209   ⟸   XM_006250147
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000064534   ⟸   ENSRNOT00000070958
RefSeq Acc Id: ENSRNOP00000004403   ⟸   ENSRNOT00000004403

Transcriptome

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

Promoters
RGD ID:13698964
Promoter ID:EPDNEW_R9489
Type:multiple initiation site
Name:Cd247_1
Description:Cd247 molecule
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01383,996,126 - 83,996,186EPDNEW

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)
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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:2305 AgrOrtholog
Ensembl Genes ENSRNOG00000003298 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004403 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000064534 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004403 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000070958 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7384006 IMAGE-MGC_LOAD
InterPro CR3_zeta/IgE_Fc_rcpt_gamma UniProtKB/TrEMBL
  Phos_immunorcpt_sig_ITAM UniProtKB/TrEMBL
  T-cell_CD3_zeta/eta UniProtKB/TrEMBL
KEGG Report rno:25300 UniProtKB/TrEMBL
MGC_CLONE MGC:116047 IMAGE-MGC_LOAD
NCBI Gene 25300 ENTREZGENE
PANTHER PTHR10035 UniProtKB/TrEMBL
Pfam ITAM UniProtKB/TrEMBL
  TCR_zetazeta UniProtKB/TrEMBL
PhenoGen Cd247 PhenoGen
PROSITE ITAM_1 UniProtKB/TrEMBL
SMART ITAM UniProtKB/TrEMBL
TIGR TC216715
UniProt M0R576 ENTREZGENE, UniProtKB/TrEMBL
  Q4V7G0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Cd247  Cd247 molecule  Cd247  CD247 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Cd247  CD247 antigen  Cd3z  CD3 antigen, zeta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Cd3z  CD3 antigen, zeta polypeptide    T-cell receptor CD3, subunit zeta  Name updated 625702 APPROVED
2002-06-10 Cd3z  T-cell receptor CD3, subunit zeta      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function component of T cell receptor complex 634717
gene_process has a role in TCR assembly and TCR-mediated signaling 634717
gene_process does not promote surface expression of Fc gamma RIII, unlike human CD3 zeta chain 728653