Cd28 (Cd28 molecule) - Rat Genome Database
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Gene: Cd28 (Cd28 molecule) Rattus norvegicus
Analyze
Symbol: Cd28
Name: Cd28 molecule
RGD ID: 2299
Description: Exhibits identical protein binding activity. Involved in T cell activation and T cell costimulation. Localizes to membrane raft. Used to study lymphopenia. Human ortholog(s) of this gene implicated in multiple sclerosis and type 1 diabetes mellitus. Orthologous to human CD28 (CD28 molecule); PARTICIPATES IN allograft rejection pathway; autoimmune thyroiditis pathway; graft-versus-host disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose; aldehydo-D-glucosamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CD28 antigen; CD28RNA; T-cell-specific surface glycoprotein CD28
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
Rnor_6.0967,546,408 - 67,573,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl967,546,408 - 67,571,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0967,358,994 - 67,386,424 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4959,342,273 - 59,367,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1959,489,254 - 59,514,725 (+)NCBI
Celera959,589,124 - 59,614,592 (+)NCBICelera
Cytogenetic Map9q32NCBI
RH 3.4 Map9504.6RGD
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Arreaza GA, etal., J Clin Invest. 1997 Nov 1;100(9):2243-53.
2. Bachmaier K, etal., J Immunol. 1996 Aug 15;157(4):1752-7.
3. Bantsimba-Malanda C, etal., Am J Respir Crit Care Med. 2010 Aug 1;182(3):385-95. Epub 2010 Apr 15.
4. Barcelo B, etal., Eur Respir J. 2008 Mar;31(3):555-62. Epub 2007 Dec 5.
5. Beyersdorf N, etal., J Exp Med. 2005 Aug 1;202(3):445-55.
6. Botturi K, etal., Respir Res. 2011 Feb 28;12:25.
7. Chen X, etal., Blood. 2009 Apr 2;113(14):3226-34. Epub 2008 Dec 15.
8. Dolfi DV, etal., J Immunol. 2011 Apr 15;186(8):4599-608. Epub 2011 Mar 9.
9. Elflein K, etal., Blood. 2003 Sep 1;102(5):1764-70. Epub 2003 May 15.
10. Felonato M, etal., Infect Immun. 2010 Nov;78(11):4922-35. Epub 2010 Aug 16.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. GOA data from the GO Consortium
13. Haspot F, etal., Blood 2002 Mar 15;99(6):2228-34.
14. Heidema J, etal., J Immunol. 2007 Dec 15;179(12):8410-7.
15. Heron M, etal., Clin Exp Immunol. 2010 May;160(2):256-65. Epub 2009 Dec 17.
16. Ihara K, etal., Immunogenetics. 2001 Aug;53(6):447-54.
17. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
18. Lambers C, etal., Clin Exp Immunol. 2009 Mar;155(3):466-75.
19. Liu H, etal., Zhong Xi Yi Jie He Xue Bao. 2008 Jul;6(7):744-7.
20. Lorusso L, etal., Autoimmun Rev. 2009 Feb;8(4):287-91. Epub 2008 Sep 16.
21. Macphee IA, etal., Clin Exp Immunol 2002 Sep;129(3):405-10.
22. MGD data from the GO Consortium
23. Muller N, etal., J Clin Invest. 2008 Apr;118(4):1405-16.
24. Nakatsuji T Tohoku J Exp Med. 1999 Mar;187(3):215-25.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Nolan A, etal., Am J Respir Crit Care Med. 2008 Feb 1;177(3):301-8. Epub 2007 Nov 7.
27. Pawlowski P, etal., Endokrynol Diabetol Chor Przemiany Materii Wieku Rozw. 2004;10(2):81-5.
28. Pechhold K, etal., J Immunol. 2001 Feb 15;166(4):2531-9.
29. Pipeline to import KEGG annotations from KEGG into RGD
30. RGD automated data pipeline
31. RGD automated import pipeline for gene-chemical interactions
32. Sadra A, etal., Proc Natl Acad Sci U S A 2004 Aug 3;101(31):11422-7. Epub 2004 Jul 27.
33. Schmidt J, etal., J Neuroimmunol. 2003 Jul;140(1-2):143-52.
34. Tacke M, etal., J Immunol. 1995 May 15;154(10):5121-7.
35. Teutsch SM, etal., J Neuroimmunol 2004 Mar;148(1-2):218-30.
36. Wang S, etal., Cardiology. 2010;115(2):107-13. doi: 10.1159/000256660. Epub 2009 Nov 10.
Additional References at PubMed
PMID:1309509   PMID:3159820   PMID:3875683   PMID:7544393   PMID:7688139   PMID:7790813   PMID:8125140   PMID:8617933   PMID:9368605   PMID:10429671   PMID:10791997   PMID:11390434  
PMID:12707299   PMID:12777399   PMID:12867038   PMID:12874832   PMID:12925852   PMID:14973438   PMID:15067037   PMID:15240667   PMID:15491677   PMID:16809611   PMID:18089392   PMID:18337562  
PMID:18408588   PMID:18641304   PMID:18727698   PMID:19641626   PMID:19811406   PMID:21245484   PMID:21487638   PMID:21745657   PMID:22564625   PMID:23589618   PMID:23793062   PMID:23817958  
PMID:24043548  


Genomics

Candidate Gene Status
Cd28 is a candidate Gene for QTL Tspe1
Comparative Map Data
Cd28
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0967,546,408 - 67,573,858 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl967,546,408 - 67,571,871 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0967,358,994 - 67,386,424 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4959,342,273 - 59,367,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1959,489,254 - 59,514,725 (+)NCBI
Celera959,589,124 - 59,614,592 (+)NCBICelera
Cytogenetic Map9q32NCBI
RH 3.4 Map9504.6RGD
CD28
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2203,706,475 - 203,738,912 (+)EnsemblGRCh38hg38GRCh38
GRCh382203,706,509 - 203,739,756 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372204,571,198 - 204,603,635 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362204,279,443 - 204,310,801 (+)NCBINCBI36hg18NCBI36
Build 342204,396,703 - 204,428,062NCBI
Celera2198,326,049 - 198,357,410 (+)NCBI
Cytogenetic Map2q33.2NCBI
HuRef2196,418,462 - 196,450,899 (+)NCBIHuRef
CHM1_12204,577,787 - 204,610,219 (+)NCBICHM1_1
Cd28
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39160,785,547 - 60,812,521 (+)NCBIGRCm39mm39
GRCm38160,746,388 - 60,773,359 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl160,716,800 - 60,773,359 (+)EnsemblGRCm38mm10GRCm38
MGSCv37160,803,232 - 60,830,203 (+)NCBIGRCm37mm9NCBIm37
MGSCv36160,691,012 - 60,717,905 (+)NCBImm8
Celera161,261,669 - 61,288,639 (+)NCBICelera
Cytogenetic Map1C2NCBI
cM Map130.52NCBI
Cd28
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545711,162,282 - 11,192,991 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545711,159,769 - 11,253,099 (-)NCBIChiLan1.0ChiLan1.0
CD28
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B209,076,388 - 209,111,213 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B209,076,388 - 209,111,213 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B90,938,795 - 90,971,438 (+)NCBIMhudiblu_PPA_v0panPan3
CD28
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3712,503,811 - 12,532,854 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13712,503,849 - 12,536,362 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cd28
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936631335,411 - 363,407 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD28
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15107,128,208 - 107,162,943 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115107,128,103 - 107,155,431 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215118,472,553 - 118,502,433 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD28
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1089,471,730 - 89,500,387 (+)Ensembl
ChlSab1.11089,471,710 - 89,505,152 (+)NCBI
Cd28
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476512,650,092 - 12,667,168 (-)NCBI

Position Markers
RH94659  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0967,571,681 - 67,571,866NCBIRnor6.0
Rnor_5.0967,384,268 - 67,384,453UniSTSRnor5.0
RGSC_v3.4959,367,553 - 59,367,738UniSTSRGSC3.4
Celera959,614,402 - 59,614,587UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9504.6UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1598849Memor17Memory QTL 172.2exploratory 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)95488504176677636Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1578659Tspe1Trichinella spiralis expulsion QTL 14.8parasite quantity (VT:0010441)logarithm of the intestinal adult Trichinella spiralis count (CMO:0002024)96675744471010122Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:62
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000013701
Prediction methods: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 8 15
Low 2 24 13 6 4 6 8 9 16 25 23 11 8
Below cutoff 1 19 36 35 35 2 47 10 18

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013701   ⟹   ENSRNOP00000013701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl967,546,408 - 67,571,871 (+)Ensembl
RefSeq Acc Id: NM_013121   ⟹   NP_037253
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0967,546,408 - 67,571,871 (+)NCBI
Rnor_5.0967,358,994 - 67,386,424 (+)NCBI
RGSC_v3.4959,342,273 - 59,367,743 (+)RGD
Celera959,589,124 - 59,614,592 (+)RGD
Sequence:
RefSeq Acc Id: XM_008767078   ⟹   XP_008765300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0967,549,987 - 67,573,858 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767079   ⟹   XP_008765301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0967,549,993 - 67,573,858 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_037253 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765300 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765301 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA39003 (Get FASTA)   NCBI Sequence Viewer  
  EDL98926 (Get FASTA)   NCBI Sequence Viewer  
  P31042 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037253   ⟸   NM_013121
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008765300   ⟸   XM_008767078
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765301   ⟸   XM_008767079
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013701   ⟸   ENSRNOT00000013701
Protein Domains
Ig-like V-type   IGv

Transcriptome

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

Promoters
RGD ID:13696707
Promoter ID:EPDNEW_R7232
Type:initiation region
Name:Cd28_1
Description:Cd28 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_6.0967,546,375 - 67,546,435EPDNEW

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)
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)
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
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)
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
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:2299 AgrOrtholog
Ensembl Genes ENSRNOG00000010283 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013701 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013701 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CD28 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTLA4/CD28 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25660 UniProtKB/Swiss-Prot
NCBI Gene 25660 ENTREZGENE
PANTHER PTHR11494 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd28 PhenoGen
PRINTS CD28ANTIGEN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.10327 ENTREZGENE
UniProt CD28_RAT UniProtKB/Swiss-Prot
  G3V7C2_RAT UniProtKB/TrEMBL
  P31042 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Cd28  Cd28 molecule  Cd28  CD28 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Cd28  CD28 antigen      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function binds to B7-1 or B7-2 on Antigen Presenting Cells 634714
gene_process involved in initiation of the Th2-response; may be required to maintain basal IgE production during mercuric chloride (HgCl2)-induced autoimmunity 634715
gene_process costimulatory molecule for T-cell proliferation, particularly during T-cell mediated allograft responses 634714