Braf (B-Raf proto-oncogene, serine/threonine kinase) - Rat Genome Database

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Gene: Braf (B-Raf proto-oncogene, serine/threonine kinase) Rattus norvegicus
Analyze
Symbol: Braf
Name: B-Raf proto-oncogene, serine/threonine kinase
RGD ID: 619908
Description: Enables MAP kinase kinase kinase activity; mitogen-activated protein kinase kinase binding activity; and small GTPase binding activity. Involved in several processes, including cellular response to nerve growth factor stimulus; positive regulation of ERK1 and ERK2 cascade; and response to cAMP. Located in neuron projection; nucleus; and plasma membrane. Used to study bile duct adenoma; cholangiocarcinoma; intrahepatic cholangiocarcinoma; and thyroid gland papillary carcinoma. Human ortholog(s) of this gene implicated in several diseases, including Noonan syndrome 7; carcinoma (multiple); cardiofaciocutaneous syndrome (multiple); central nervous system benign neoplasm (multiple); and melanoma (multiple). Orthologous to human BRAF (B-Raf proto-oncogene, serine/threonine kinase); PARTICIPATES IN the extracellular signal-regulated Raf/Mek/Erk signaling pathway; adenosine signaling pathway; altered extracellular signal-regulated Raf/Mek/Erk signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: MODEL
Also known as: B-Raf; serine/threonine-protein kinase B-raf; v-raf murine sarcoma viral oncogene homolog B; v-raf murine sarcoma viral oncogene homolog B1
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
mRatBN7.2468,375,484 - 68,510,652 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl468,384,649 - 68,510,463 (-)Ensembl
Rnor_6.0467,389,331 - 67,520,549 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl467,396,192 - 67,520,356 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0467,196,477 - 67,327,649 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4467,117,759 - 67,243,058 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1467,405,110 - 67,426,026 (-)NCBI
Celera463,383,337 - 63,515,499 (-)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adrenocortical carcinoma  (ISO)
ameloblastoma  (ISO)
Aortic Aneurysm, Giant Congenital  (ISO)
arteriovenous malformations of the brain  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
bile duct adenoma  (IAGP)
bladder urothelial carcinoma  (ISO)
Brain Neoplasms  (ISO)
Breast Neoplasms  (ISO)
cancer  (ISO)
Carcinogenesis  (ISO)
cardiofaciocutaneous syndrome  (ISO)
cardiofaciocutaneous syndrome 1  (ISO)
cardiomyopathy  (ISO)
cholangiocarcinoma  (IAGP)
chronic lymphocytic leukemia  (ISO)
chronic myeloid leukemia  (ISO)
colon cancer  (ISO)
colon carcinoma  (ISO)
Colonic Neoplasms  (ISO)
colorectal adenocarcinoma  (ISO)
colorectal cancer  (ISO)
Colorectal Neoplasms  (ISO)
Costello syndrome  (ISO)
craniopharyngioma  (ISO)
Cutaneous Malignant Melanoma, Susceptibility To, 1  (ISO)
cutaneous T cell lymphoma  (ISO)
Dandy Walker Cyst  (ISO)
Dandy-Walker syndrome  (ISO)
Developmental Disabilities  (ISO)
disease of cellular proliferation  (ISO)
dysembryoplastic neuroepithelial tumor  (ISO)
endometrial carcinoma  (ISO)
Experimental Melanoma  (ISO)
Experimental Neoplasms  (ISO)
Follicular Thyroid Cancer  (ISO)
gallbladder cancer  (ISO)
ganglioglioma  (ISO)
gastric adenocarcinoma  (ISO)
gastrointestinal stromal tumor  (ISO)
genetic disease  (ISO)
germinoma  (ISO)
glioblastoma  (ISO)
head and neck squamous cell carcinoma  (ISO)
hepatocellular carcinoma  (ISO)
high grade glioma  (ISO)
hypertrophic cardiomyopathy  (ISO)
hypertrophic cardiomyopathy 4  (ISO)
intrahepatic cholangiocarcinoma  (IAGP)
Kidney Neoplasms  (ISO)
Langerhans-cell histiocytosis  (ISS)
Liver Metastasis  (IAGP)
Liver Neoplasms  (ISO)
lung adenocarcinoma  (ISO)
lung cancer  (ISO,ISS)
lung carcinoma  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
Lymphatic Metastasis  (ISO)
malignant astrocytoma  (ISO)
Mandibular Neoplasms  (ISO)
melanoma  (ISO)
Microsatellite Instability  (ISO)
multiple myeloma  (ISO)
Neoplasm Metastasis  (ISO)
nephroblastoma  (ISO)
neuroendocrine tumor  (ISO)
Nevus  (ISO)
newborn respiratory distress syndrome  (ISO)
non-Hodgkin lymphoma  (ISO)
Nonseminomatous Germ Cell Tumor  (ISO)
Noonan syndrome  (ISO)
Noonan syndrome 1  (ISO,ISS)
Noonan syndrome 7  (ISO)
Noonan syndrome with multiple lentigines  (ISO)
Noonan syndrome with multiple lentigines 3  (ISO)
Ovarian Neoplasms  (ISO)
ovarian serous cystadenocarcinoma  (ISO)
pancreatic acinar cell adenocarcinoma  (ISO)
pancreatic cancer  (ISO)
papillary renal cell carcinoma  (ISO)
Paraproteinemias  (ISO)
PHACE Association  (ISO)
plasma cell neoplasm  (ISO)
plasmacytoma  (ISO)
pleomorphic xanthoastrocytoma  (ISO)
Premature Birth  (ISO)
prostate adenocarcinoma  (ISO)
Prostatic Neoplasms  (ISO)
pulmonary valve stenosis  (ISO)
RASopathy  (ISO)
Sezary's disease  (ISO)
skin melanoma  (ISO)
Sporadic Papillary Renal Cell Carcinoma  (ISO)
thyroid gland papillary carcinoma  (IMP,ISO)
Thyroid Neoplasms  (ISO)
transitional cell carcinoma  (ISO)
type 2 diabetes mellitus  (ISO)
uterine cancer  (ISO)
ventricular septal defect  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
3',5'-cyclic AMP  (EXP,ISO)
4-hydroxynon-2-enal  (ISO)
4-vinylcyclohexene dioxide  (ISO)
ABT-737  (ISO)
afimoxifene  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
betulin  (ISO)
Biflorin  (ISO)
bisphenol A  (EXP)
cadmium atom  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cobimetinib  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
dabrafenib  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
endosulfan  (EXP)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
famotidine  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gemcitabine  (ISO)
hexadecanoic acid  (ISO)
hydrogen cyanide  (ISO)
icariside II  (ISO)
isotretinoin  (ISO)
ketamine  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
lycopene  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (ISO)
paracetamol  (ISO)
Pentoxifylline  (EXP)
phenobarbital  (ISO)
Pirarubicin  (EXP)
pirinixic acid  (ISO)
ponatinib  (ISO)
potassium cyanide  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
rutin  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sorafenib  (EXP,ISO)
succimer  (ISO)
tamoxifen  (ISO)
tanespimycin  (EXP,ISO)
tert-butyl hydroperoxide  (ISO)
theophylline  (EXP)
trametinib  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vemurafenib  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
alpha-beta T cell differentiation  (ISO)
CD4-positive or CD8-positive, alpha-beta T cell lineage commitment  (ISO)
CD4-positive, alpha-beta T cell differentiation  (ISO)
cell differentiation  (ISO)
cellular response to calcium ion  (ISO)
cellular response to nerve growth factor stimulus  (IEP)
cellular response to xenobiotic stimulus  (ISO)
epidermal growth factor receptor signaling pathway  (ISO)
establishment of protein localization to membrane  (ISO)
face development  (ISO)
head morphogenesis  (ISO)
long-term synaptic potentiation  (ISO)
MAPK cascade  (ISO)
myeloid progenitor cell differentiation  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of endothelial cell apoptotic process  (ISO)
negative regulation of fibroblast migration  (ISO)
negative regulation of neuron apoptotic process  (IMP,ISO)
negative regulation of synaptic vesicle exocytosis  (ISO)
positive regulation of axon regeneration  (ISO)
positive regulation of axonogenesis  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IMP,ISO)
positive regulation of gene expression  (ISO)
positive regulation of glucose transmembrane transport  (ISO)
positive regulation of peptidyl-serine phosphorylation  (ISO)
positive regulation of stress fiber assembly  (ISO)
positive regulation of substrate adhesion-dependent cell spreading  (ISO)
positive T cell selection  (ISO)
protein phosphorylation  (IDA,IMP,ISO)
regulation of axon regeneration  (ISO)
regulation of cell population proliferation  (ISO)
regulation of T cell differentiation  (ISO)
response to cAMP  (IMP)
response to peptide hormone  (IMP)
somatic stem cell population maintenance  (ISO)
T cell receptor signaling pathway  (ISO)
thymus development  (ISO)
thyroid gland development  (ISO)
trehalose metabolism in response to stress  (ISO)
visual learning  (ISO)

Cellular Component

References

References - curated
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9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Gruppuso PA and Boylan JM, FEBS Lett. 2000 Jan 21;466(1):200-4.
12. Hoeflich KP, etal., Cancer Res. 2006 Jan 15;66(2):999-1006.
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23. MGD data from the GO Consortium
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25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
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28. OMIM Disease Annotation Pipeline
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32. Pipeline to import KEGG annotations from KEGG into RGD
33. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
34. Pipeline to import SMPDB annotations from SMPDB into RGD
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38. RGD automated data pipeline
39. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
40. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:9207797   PMID:9679960   PMID:9837904   PMID:10704835   PMID:10854065   PMID:11698596   PMID:12194967   PMID:12650640   PMID:15199148   PMID:15736129   PMID:15782137   PMID:15784729  
PMID:15886202   PMID:16116448   PMID:16157584   PMID:16342120   PMID:16818623   PMID:16858395   PMID:16980614   PMID:17380122   PMID:17563371   PMID:18228248   PMID:18567582   PMID:18952847  
PMID:19667065   PMID:19727074   PMID:21203559   PMID:22065586   PMID:22169110   PMID:22510884   PMID:22628551   PMID:22891351   PMID:22892241   PMID:23010278   PMID:23022482   PMID:23334952  
PMID:23616533   PMID:24492844   PMID:24733831   PMID:25155755   PMID:25437913   PMID:26333016   PMID:27658714   PMID:29225069   PMID:29433126  


Genomics

Comparative Map Data
Braf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2468,375,484 - 68,510,652 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl468,384,649 - 68,510,463 (-)Ensembl
Rnor_6.0467,389,331 - 67,520,549 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl467,396,192 - 67,520,356 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0467,196,477 - 67,327,649 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4467,117,759 - 67,243,058 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1467,405,110 - 67,426,026 (-)NCBI
Celera463,383,337 - 63,515,499 (-)NCBICelera
Cytogenetic Map4q22NCBI
BRAF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7140,719,327 - 140,924,929 (-)EnsemblGRCh38hg38GRCh38
GRCh387140,713,328 - 140,924,929 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377140,413,128 - 140,624,729 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367140,080,751 - 140,271,033 (-)NCBINCBI36hg18NCBI36
Build 347139,887,462 - 140,077,748NCBI
Celera7135,155,867 - 135,346,614 (-)NCBI
Cytogenetic Map7q34NCBI
HuRef7134,729,459 - 134,920,529 (-)NCBIHuRef
CHM1_17140,368,045 - 140,559,148 (-)NCBICHM1_1
CRA_TCAGchr7v27139,771,989 - 139,962,886 (-)NCBI
Braf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39639,580,171 - 39,702,592 (-)NCBIGRCm39mm39
GRCm39 Ensembl639,580,171 - 39,702,397 (-)Ensembl
GRCm38639,603,231 - 39,725,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl639,603,237 - 39,725,463 (-)EnsemblGRCm38mm10GRCm38
MGSCv37639,553,236 - 39,675,462 (-)NCBIGRCm37mm9NCBIm37
MGSCv36639,557,807 - 39,675,462 (-)NCBImm8
Celera639,588,093 - 39,710,723 (-)NCBICelera
Cytogenetic Map6B1NCBI
cM Map618.43NCBI
Braf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554942,567,238 - 2,712,708 (+)NCBIChiLan1.0ChiLan1.0
BRAF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17145,124,291 - 145,327,115 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7145,138,510 - 145,327,115 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07132,651,908 - 132,855,422 (-)NCBIMhudiblu_PPA_v0panPan3
BRAF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1168,222,909 - 8,318,179 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl168,222,907 - 8,317,906 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha168,989,501 - 9,160,850 (+)NCBI
ROS_Cfam_1.0168,065,738 - 8,237,942 (+)NCBI
UMICH_Zoey_3.1168,017,140 - 8,188,930 (+)NCBI
UNSW_CanFamBas_1.0167,861,588 - 8,033,660 (+)NCBI
UU_Cfam_GSD_1.0167,929,505 - 8,101,841 (+)NCBI
Braf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511814,385,958 - 14,495,443 (+)NCBI
SpeTri2.0NW_0049365924,728,371 - 4,833,830 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRAF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl188,957,959 - 9,132,553 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1188,957,963 - 9,132,558 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2189,522,257 - 9,636,501 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BRAF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121109,495,525 - 109,690,261 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660726,137,051 - 6,336,885 (-)NCBIVero_WHO_p1.0
Braf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476520,766,368 - 20,951,560 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AW529263  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2468,494,111 - 68,494,314 (+)MAPPERmRatBN7.2
Rnor_6.0467,504,571 - 67,504,773NCBIRnor6.0
Rnor_5.0467,311,711 - 67,311,913UniSTSRnor5.0
RGSC_v3.4467,227,180 - 67,227,382UniSTSRGSC3.4
Celera463,498,578 - 63,498,780UniSTS
RH 3.4 Map4407.4UniSTS
Cytogenetic Map4q21-q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)457114432102114432Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
2312569Pur19Proteinuria QTL 193.40.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)46588210796130297Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)46699318572752834Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)46699318572752834Rat
2317577Eae24Experimental allergic encephalomyelitis QTL 24nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)46699318572752834Rat
2306547Iddm38Insulin dependent diabetes mellitus QTL 38blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)46738666970362197Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:36
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000014604
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 12 7 4 4 4 74 20 36 11
Low 3 31 50 37 15 37 8 11 15 5 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001070228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602780 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_231692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF352172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014604   ⟹   ENSRNOP00000014604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl468,388,299 - 68,474,089 (-)Ensembl
Rnor_6.0 Ensembl467,396,192 - 67,520,356 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100954   ⟹   ENSRNOP00000091382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl468,384,649 - 68,510,463 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111433   ⟹   ENSRNOP00000096915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl468,384,649 - 68,510,463 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113323   ⟹   ENSRNOP00000092085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl468,384,649 - 68,510,463 (-)Ensembl
RefSeq Acc Id: XM_006236357   ⟹   XP_006236419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,378,673 - 68,510,646 (-)NCBI
Rnor_6.0467,389,331 - 67,520,549 (-)NCBI
Rnor_5.0467,196,477 - 67,327,649 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236359   ⟹   XP_006236421
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,378,673 - 68,510,642 (-)NCBI
Rnor_6.0467,389,331 - 67,520,549 (-)NCBI
Rnor_5.0467,196,477 - 67,327,649 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108630   ⟹   XP_038964558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,650 (-)NCBI
RefSeq Acc Id: XM_039108631   ⟹   XP_038964559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,649 (-)NCBI
RefSeq Acc Id: XM_039108632   ⟹   XP_038964560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,378,673 - 68,510,649 (-)NCBI
RefSeq Acc Id: XM_039108633   ⟹   XP_038964561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,650 (-)NCBI
RefSeq Acc Id: XM_039108634   ⟹   XP_038964562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,648 (-)NCBI
RefSeq Acc Id: XM_039108635   ⟹   XP_038964563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,652 (-)NCBI
RefSeq Acc Id: XM_039108636   ⟹   XP_038964564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,648 (-)NCBI
RefSeq Acc Id: XM_039108637   ⟹   XP_038964565
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,646 (-)NCBI
RefSeq Acc Id: XM_039108638   ⟹   XP_038964566
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,375,484 - 68,510,644 (-)NCBI
RefSeq Acc Id: XM_039108639   ⟹   XP_038964567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,378,673 - 68,510,645 (-)NCBI
RefSeq Acc Id: XM_231692   ⟹   XP_231692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2468,378,673 - 68,510,649 (-)NCBI
Rnor_6.0467,389,331 - 67,520,549 (-)NCBI
Rnor_5.0467,196,477 - 67,327,649 (-)NCBI
RGSC_v3.4467,117,759 - 67,243,058 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_231692   ⟸   XM_231692
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006236419   ⟸   XM_006236357
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006236421   ⟸   XM_006236359
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: ENSRNOP00000014604   ⟸   ENSRNOT00000014604
RefSeq Acc Id: XP_038964563   ⟸   XM_039108635
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038964561   ⟸   XM_039108633
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038964558   ⟸   XM_039108630
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964559   ⟸   XM_039108631
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964562   ⟸   XM_039108634
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038964564   ⟸   XM_039108636
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038964565   ⟸   XM_039108637
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038964566   ⟸   XM_039108638
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038964560   ⟸   XM_039108632
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038964567   ⟸   XM_039108639
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000092085   ⟸   ENSRNOT00000113323
RefSeq Acc Id: ENSRNOP00000096915   ⟸   ENSRNOT00000111433
RefSeq Acc Id: ENSRNOP00000091382   ⟸   ENSRNOT00000100954
Protein Domains
Phorbol-ester/DAG-type   Protein kinase   RBD

Transcriptome

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


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)
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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)
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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
F344/DuCrl (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
F344/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
F344/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
F344/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
F344/NRrrc (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
F344/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
FHH/EurMcwi (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/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
FXLE18/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
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
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)
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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 (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)
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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
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)
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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/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