Cd40lg (CD40 ligand) - Rat Genome Database

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Gene: Cd40lg (CD40 ligand) Rattus norvegicus
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Symbol: Cd40lg
Name: CD40 ligand
RGD ID: 708418
Description: Enables CD40 receptor binding activity. Involved in several processes, including positive regulation of B cell proliferation; positive regulation of MHC class II biosynthetic process; and positive regulation of cytokine production. Located in several cellular components, including cell body; cell surface; and extracellular space. Used to study Ehrlich tumor carcinoma; artery disease (multiple); autoimmune disease (multiple); thrombosis; and vitamin B12 deficiency. Biomarker of atherosclerosis; coronary artery disease; perinatal necrotizing enterocolitis; periodontal disease; and pulmonary hypertension. Human ortholog(s) of this gene implicated in several diseases, including Kawasaki disease; autoimmune disease (multiple); combined T cell and B cell immunodeficiency (multiple); hematologic cancer (multiple); and lupus nephritis. Orthologous to human CD40LG (CD40 ligand); PARTICIPATES IN interleukin-4 signaling pathway; obesity pathway; allograft rejection pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 4-aminopyridine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CD40 ligand CD154; CD40-L; Cd40l; LOC84349; Tnfsf5; tumor necrosis factor (ligand) superfamily, member 5; tumor necrosis factor ligand superfamily member 5
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
mRatBN7.2X135,127,119 - 135,138,302 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX135,126,969 - 135,138,306 (+)Ensembl
Rnor_6.0X159,703,703 - 159,714,886 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX159,703,578 - 159,716,562 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X154,330,893 - 154,341,954 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,925,019 - 141,937,183 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X141,998,451 - 142,010,616 (+)NCBI
CeleraX143,160,596 - 143,171,765 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acquired immunodeficiency syndrome  (ISO)
Acute Coronary Syndrome  (ISO)
acute lymphoblastic leukemia  (ISO)
allergic disease  (ISO)
allergic rhinitis  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
anti-basement membrane glomerulonephritis  (IMP)
antiphospholipid syndrome  (ISO)
Aortic Valve, Calcification of  (IDA)
aplastic anemia  (ISO)
asthma  (ISO)
atherosclerosis  (IDA,IEP,ISO)
autistic disorder  (ISO)
autoimmune disease  (ISO)
autoimmune thrombocytopenic purpura  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
Behcet's disease  (ISO)
Brain Injuries  (IDA,IEP)
cardiovascular system disease  (ISO)
carotid artery disease  (ISO)
CD40 ligand deficiency  (ISO)
Cholangiofibrosis  (IDA)
Chromosome Breakage  (ISO)
Chromosome Xq26.3 Duplication Syndrome  (ISO)
Chronic Allograft Dysfunction  (IDA)
chronic lymphocytic leukemia  (ISO)
Colonic Neoplasms  (ISO)
combined T cell and B cell immunodeficiency  (ISO)
common variable immunodeficiency  (ISO)
congestive heart failure  (ISO)
coronary artery disease  (IEP,ISO)
Coronary Disease  (IDA)
crescentic glomerulonephritis  (ISO)
cutaneous lupus erythematosus  (ISO)
cystic fibrosis  (ISO)
dermatomyositis  (ISO)
diabetes mellitus  (ISO)
diabetic angiopathy  (ISO)
Diabetic Nephropathies  (ISO)
Discoid Lupus Erythematosus  (ISO)
dysgammaglobulinemia  (ISO)
Ehrlich tumor carcinoma  (IDA)
end stage renal disease  (ISO)
eosinophilic esophagitis  (ISO)
erythema multiforme  (ISO)
essential thrombocythemia  (ISO)
Experimental Arthritis  (IDA,IEP,ISO)
Experimental Autoimmune Myasthenia Gravis  (IMP)
Experimental Autoimmune Neuritis  (IEP)
Experimental Autoimmune Uveoretinitis  (ISO)
Experimental Diabetes Mellitus  (IEP,ISO)
Experimental Liver Neoplasms  (ISO)
factor VIII deficiency  (ISO)
familial hyperlipidemia  (ISO)
Fibrosis  (ISO)
follicular lymphoma  (ISO)
genetic disease  (ISO)
Graft vs Host Disease  (ISO)
granulomatosis with polyangiitis  (ISO)
Graves' disease  (ISO)
Hashimoto Disease  (ISO)
HELLP syndrome  (ISO)
hepatocellular carcinoma  (ISO)
herpes simplex  (ISO)
Hodgkin's lymphoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hyper IgM syndrome  (ISO)
Hypercholesterolemia  (IDA,IEP,ISO)
inflammatory bowel disease  (ISS)
Kawasaki disease  (ISO)
kidney disease  (ISO)
lichen planus  (ISO)
lupus nephritis  (ISO)
Lyme Neuroborreliosis  (ISO)
malaria  (ISO)
membranous glomerulonephritis  (ISO)
Metabolic Syndrome  (ISO)
Middle East respiratory syndrome  (ISO)
migraine  (ISO)
multiple myeloma  (ISO)
Murine Acquired Immunodeficiency Syndrome  (ISO)
myocardial infarction  (ISO)
Myocardial Ischemia  (IDA,IEP)
narcolepsy  (ISO)
Necrosis  (ISO)
nephrosis  (ISO)
obesity  (ISO)
ovarian disease  (ISO)
Ovarian Neoplasms  (ISO)
Overactive Urinary Bladder  (ISO)
pemphigus  (ISO)
perinatal necrotizing enterocolitis  (IEP)
periodontal disease  (IEP)
periodontitis  (ISO)
peritonitis  (ISO)
pneumonia  (ISO)
pre-eclampsia  (IMP,ISO)
Primary Graft Dysfunction  (ISO)
pulmonary hypertension  (IEP,ISO)
Reperfusion Injury  (IMP,ISO)
Sepsis  (IEP)
Shock  (ISO)
sickle cell anemia  (ISO)
Sjogren's syndrome  (ISO)
Subacute Combined Degeneration  (IDA,IEP)
syndromic X-linked intellectual disability Lubs type  (ISO)
systemic lupus erythematosus  (ISO)
thrombocytopenia  (ISO)
thrombosis  (IDA,ISO)
tick-borne encephalitis  (ISO)
transient cerebral ischemia  (ISO)
Transplant Rejection  (IMP,ISO)
type 1 diabetes mellitus  (IMP,ISO)
type 2 diabetes mellitus  (ISO)
urinary bladder cancer  (ISO)
Vascular Calcification  (ISO)
Viral Myocarditis  (IMP,ISO)
visceral leishmaniasis  (ISO)
vitamin B12 deficiency  (IDA)
Wounds, Penetrating  (IDA)
X-linked hyper IgM syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-mevalonic acid  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3'-diindolylmethane  (ISO)
4-aminopyridine  (EXP)
5-fluorouracil  (ISO)
acetylsalicylic acid  (ISO)
ADP  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asperentin  (ISO)
atorvastatin calcium  (ISO)
barium sulfate  (EXP)
benzo[a]pyrene  (EXP,ISO)
bezafibrate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
calcitriol  (ISO)
candesartan  (ISO)
carbon atom  (ISO)
ceric oxide  (EXP)
chlorpyrifos  (ISO)
cholesterol  (EXP)
cisplatin  (ISO)
clopidogrel  (ISO)
curcumin  (ISO)
DDE  (EXP)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
dioxygen  (ISO)
dipyridamole  (ISO)
doxorubicin  (ISO)
elemental carbon  (ISO)
eptifibatide  (ISO)
ethanol  (EXP)
etoposide  (ISO)
fenofibrate  (ISO)
fingolimod hydrochloride  (ISO)
furan  (EXP)
Fusarenone X  (ISO)
gemcitabine  (ISO)
glutathione  (ISO)
glyphosate  (ISO)
heparin  (ISO)
hydrogen peroxide  (ISO)
hydroxychloroquine  (ISO)
hydroxysafflor yellow A  (EXP)
ionomycin  (ISO)
isoflurane  (EXP)
lipopolysaccharide  (ISO)
medroxyprogesterone acetate  (ISO)
metformin  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
neoechinulin A  (ISO)
nickel dichloride  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
pentobarbital  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP)
rotenone  (EXP,ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sterigmatocystin  (ISO)
titanium dioxide  (ISO)
vemurafenib  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vinorelbine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
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Additional References at PubMed
PMID:7529792   PMID:8605945   PMID:8617933   PMID:9468137   PMID:9922218   PMID:12697681   PMID:12885753   PMID:12958312   PMID:14647274   PMID:15067037   PMID:15485634   PMID:15665763  
PMID:17082577   PMID:17976119   PMID:19164932   PMID:21410936   PMID:22017688   PMID:25511433   PMID:25993320   PMID:29155846   PMID:29843579   PMID:31331973  


Genomics

Comparative Map Data
Cd40lg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X135,127,119 - 135,138,302 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX135,126,969 - 135,138,306 (+)Ensembl
Rnor_6.0X159,703,703 - 159,714,886 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX159,703,578 - 159,716,562 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X154,330,893 - 154,341,954 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,925,019 - 141,937,183 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X141,998,451 - 142,010,616 (+)NCBI
CeleraX143,160,596 - 143,171,765 (+)NCBICelera
Cytogenetic MapXq37NCBI
CD40LG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX136,648,158 - 136,660,390 (+)EnsemblGRCh38hg38GRCh38
GRCh38X136,648,158 - 136,660,390 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X135,730,317 - 135,742,549 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X135,558,002 - 135,570,215 (+)NCBINCBI36hg18NCBI36
Build 34X135,455,855 - 135,468,068NCBI
CeleraX136,094,012 - 136,106,224 (+)NCBI
Cytogenetic MapXq26.3NCBI
HuRefX125,001,305 - 125,013,640 (+)NCBIHuRef
CHM1_1X135,641,985 - 135,654,211 (+)NCBICHM1_1
Cd40lg
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X56,257,503 - 56,269,402 (+)NCBIGRCm39mm39
GRCm39 EnsemblX56,257,503 - 56,269,402 (+)Ensembl
GRCm38X57,212,143 - 57,224,042 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX57,212,143 - 57,224,042 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X54,465,320 - 54,477,219 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X53,558,927 - 53,570,826 (+)NCBImm8
CeleraX43,689,623 - 43,701,548 (+)NCBICelera
Cytogenetic MapXA6NCBI
cM MapX31.21NCBI
Cd40lg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554898,465,164 - 8,477,746 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554898,465,571 - 8,477,714 (-)NCBIChiLan1.0ChiLan1.0
CD40LG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X136,042,849 - 136,055,158 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX136,042,849 - 136,058,202 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X125,776,138 - 125,788,820 (+)NCBIMhudiblu_PPA_v0panPan3
CD40LG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X107,001,421 - 107,023,007 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX107,010,890 - 107,023,006 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX92,832,126 - 92,844,241 (+)NCBI
ROS_Cfam_1.0X108,980,873 - 109,002,662 (+)NCBI
UMICH_Zoey_3.1X106,131,221 - 106,143,392 (+)NCBI
UNSW_CanFamBas_1.0X108,322,638 - 108,334,748 (+)NCBI
UU_Cfam_GSD_1.0X107,964,432 - 107,976,548 (+)NCBI
Cd40lg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X104,994,220 - 105,007,112 (+)NCBI
SpeTri2.0NW_00493651310,607,617 - 10,620,403 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD40LG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX111,778,493 - 111,789,711 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X111,778,666 - 111,788,901 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X127,636,797 - 127,647,035 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD40LG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X111,655,301 - 111,667,602 (+)NCBI
ChlSab1.1 EnsemblX111,655,397 - 111,666,639 (+)Ensembl
Vero_WHO_p1.0NW_02366606549,341,810 - 49,354,077 (+)NCBI
Cd40lg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480810,472,028 - 10,484,407 (-)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)X41052407146860749Rat
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)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
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)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:83
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000001162
Prediction methods:Microtar, 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

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
Low 2 17 1 19 1 1 1 8 9 8 11 1
Below cutoff 1 10 28 28 28 7 9 1 8 6 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001162   ⟹   ENSRNOP00000001162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX135,126,969 - 135,138,306 (+)Ensembl
Rnor_6.0 EnsemblX159,703,578 - 159,716,562 (+)Ensembl
RefSeq Acc Id: NM_053353   ⟹   NP_445805
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X135,127,119 - 135,138,302 (+)NCBI
Rnor_6.0X159,703,703 - 159,714,886 (+)NCBI
Rnor_5.0X154,330,893 - 154,341,954 (+)NCBI
RGSC_v3.4X141,925,019 - 141,937,183 (+)RGD
CeleraX143,160,596 - 143,171,765 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445805 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD09323 (Get FASTA)   NCBI Sequence Viewer  
  AAD22460 (Get FASTA)   NCBI Sequence Viewer  
  ABK59325 (Get FASTA)   NCBI Sequence Viewer  
  EDL75129 (Get FASTA)   NCBI Sequence Viewer  
  Q9Z2V2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445805   ⟸   NM_053353
- UniProtKB: Q9Z2V2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001162   ⟸   ENSRNOT00000001162
Protein Domains
TNF_2

Transcriptome

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

Promoters
RGD ID:13702074
Promoter ID:EPDNEW_R12598
Type:single initiation site
Name:Cd40lg_1
Description:CD40 ligand
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_6.0X159,703,637 - 159,703,697EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708418 AgrOrtholog
Ensembl Genes ENSRNOG00000000871 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001162 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001162 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CD40L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84349 UniProtKB/Swiss-Prot
NCBI Gene 84349 ENTREZGENE
PANTHER PTHR11471:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd40lg PhenoGen
PIRSF TNF_5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS CD40LIGAND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TNF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART TNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0SZW2_RAT UniProtKB/TrEMBL
  CD40L_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9R254 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Cd40lg  CD40 ligand  Tnfsf5  tumor necrosis factor (ligand) superfamily, member 5  Symbol and Name updated 1299863 APPROVED
2004-12-14 Tnfsf5  tumor necrosis factor (ligand) superfamily, member 5  LOC84349  CD40 ligand  Symbol and Name updated 1299863 APPROVED