Rab3d (RAB3D, member RAS oncogene family) - Rat Genome Database

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Gene: Rab3d (RAB3D, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab3d
Name: RAB3D, member RAS oncogene family
RGD ID: 620924
Description: Predicted to enable GTP-dependent protein binding activity; GTPase activity; and myosin V binding activity. Predicted to be involved in several processes, including bone resorption; protein localization to plasma membrane; and secretion by cell. Predicted to act upstream of or within peptidyl-cysteine methylation. Located in transport vesicle. Orthologous to human RAB3D (RAB3D, member RAS oncogene family); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GTP-binding protein Rab-3D; MGC93243
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
mRatBN7.2820,438,622 - 20,449,269 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,439,294 - 20,449,185 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,470,805 - 24,480,001 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0822,766,348 - 22,775,546 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0820,669,763 - 20,678,801 (-)NCBIRnor_WKY
Rnor_6.0822,920,238 - 22,929,368 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,918,699 - 22,929,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,975,020 - 22,984,130 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4821,012,295 - 21,021,327 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1821,012,298 - 21,021,327 (-)NCBI
Celera821,831,432 - 21,840,414 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-chloropropane-1,2-diol  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
chloroprene  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
coumarin  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dichlorine  (EXP)
dioxygen  (ISO)
doxorubicin  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
furan  (EXP)
gentamycin  (EXP)
hydralazine  (ISO)
ivermectin  (ISO)
lithocholic acid  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nickel sulfate  (ISO)
orphenadrine  (EXP)
ozone  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SCH 23390  (EXP)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
trichloroethene  (ISO)
trichostatin A  (EXP,ISO)
triphenyl phosphate  (EXP)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Interaction cloning of Rabin3, a novel protein that associates with the Ras-like GTPase Rab3A. Brondyk WH, etal., Mol Cell Biol 1995 Mar;15(3):1137-43.
2. rab15, a novel low molecular weight GTP-binding protein specifically expressed in rat brain. Elferink LA, etal., J Biol Chem 1992 Mar 25;267(9):5768-75.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Intracellular accumulation of pIgA-R and regulators of transcytotic trafficking in cholestatic rat hepatocytes. Larkin JM, etal., Hepatology 2003 Nov;38(5):1199-209.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. RT-PCR cloning of Rab3 isoforms expressed in peritoneal mast cells. Oberhauser AF, etal., FEBS Lett 1994 Feb 14;339(1-2):171-4.
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Involvement of the ras-like GTPase rab3d in RBL-2H3 mast cell exocytosis following stimulation via high affinity IgE receptors (Fc epsilonRI). Roa M, etal., J Immunol 1997 Sep 15;159(6):2815-23.
12. Localization of the small monomeric GTPases Rab3D and Rab3A in the AtT-20 rat pituitary cell line. Tabellini G, etal., Eur J Histochem 2001;45(4):347-56.
Additional References at PubMed
PMID:9716267   PMID:11121396   PMID:12167638   PMID:12192047   PMID:12477932   PMID:14566969   PMID:15489334   PMID:17395899   PMID:18614015   PMID:19056867   PMID:21080055   PMID:21262767  
PMID:22367855   PMID:22899725   PMID:23533145   PMID:24006491   PMID:24625528   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Rab3d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2820,438,622 - 20,449,269 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,439,294 - 20,449,185 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx824,470,805 - 24,480,001 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0822,766,348 - 22,775,546 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0820,669,763 - 20,678,801 (-)NCBIRnor_WKY
Rnor_6.0822,920,238 - 22,929,368 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,918,699 - 22,929,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,975,020 - 22,984,130 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4821,012,295 - 21,021,327 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1821,012,298 - 21,021,327 (-)NCBI
Celera821,831,432 - 21,840,414 (-)NCBICelera
Cytogenetic Map8q13NCBI
RAB3D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381911,322,068 - 11,339,657 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1911,322,068 - 11,346,270 (-)EnsemblGRCh38hg38GRCh38
GRCh371911,432,744 - 11,450,333 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361911,296,093 - 11,311,321 (-)NCBINCBI36Build 36hg18NCBI36
Build 341911,296,093 - 11,311,321NCBI
Celera1911,327,595 - 11,345,218 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1911,008,726 - 11,026,403 (-)NCBIHuRef
CHM1_11911,433,747 - 11,451,370 (-)NCBICHM1_1
T2T-CHM13v2.01911,449,052 - 11,466,642 (-)NCBIT2T-CHM13v2.0
Rab3d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,818,787 - 21,829,623 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl921,818,787 - 21,829,488 (-)EnsemblGRCm39 Ensembl
GRCm38921,907,491 - 21,918,199 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,907,491 - 21,918,192 (-)EnsemblGRCm38mm10GRCm38
MGSCv37921,711,954 - 21,722,565 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36921,657,912 - 21,668,523 (-)NCBIMGSCv36mm8
Celera919,176,743 - 19,187,354 (-)NCBICelera
Cytogenetic Map9A3NCBI
Rab3d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554952,251,818 - 2,259,233 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554952,254,336 - 2,259,211 (-)NCBIChiLan1.0ChiLan1.0
RAB3D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11911,579,669 - 11,597,158 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,579,669 - 11,597,158 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01910,869,402 - 10,887,005 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RAB3D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,974,592 - 49,985,362 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2049,974,590 - 49,983,062 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2049,848,103 - 49,858,871 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02050,495,316 - 50,506,087 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2050,495,296 - 50,505,295 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12049,705,599 - 49,716,368 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,131,973 - 50,142,965 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02050,374,931 - 50,385,923 (+)NCBIUU_Cfam_GSD_1.0
Rab3d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,914,661 - 208,925,144 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366591,429,562 - 1,438,876 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB3D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl270,026,181 - 70,035,680 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1270,023,470 - 70,035,679 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,378,188 - 70,398,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAB3D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1610,250,538 - 10,273,340 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl610,250,360 - 10,273,295 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660749,620,582 - 9,636,711 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rab3d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248283,144,914 - 3,149,359 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248283,142,955 - 3,149,549 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
RH127735  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,440,210 - 20,440,413 (+)MAPPERmRatBN7.2
Rnor_6.0822,920,296 - 22,920,498NCBIRnor6.0
Rnor_5.0822,975,078 - 22,975,280UniSTSRnor5.0
RGSC_v3.4821,012,353 - 21,012,555UniSTSRGSC3.4
Celera821,831,490 - 21,831,692UniSTS
RH 3.4 Map8180.8UniSTS
Cytogenetic Map8q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:586
Count of miRNA genes:259
Interacting mature miRNAs:318
Transcripts:ENSRNOT00000015609
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 20 16 7 16 48 20 25 11
Low 17 37 25 12 25 8 11 26 15 16 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015609   ⟹   ENSRNOP00000015609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl820,439,294 - 20,449,185 (-)Ensembl
Rnor_6.0 Ensembl822,918,699 - 22,929,294 (-)Ensembl
RefSeq Acc Id: NM_080580   ⟹   NP_542147
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,440,153 - 20,449,185 (-)NCBI
Rnor_6.0822,920,238 - 22,929,270 (-)NCBI
Rnor_5.0822,975,020 - 22,984,130 (-)NCBI
RGSC_v3.4821,012,295 - 21,021,327 (-)RGD
Celera821,831,432 - 21,840,414 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242593   ⟹   XP_006242655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,438,622 - 20,449,269 (-)NCBI
Rnor_6.0822,920,238 - 22,929,166 (-)NCBI
Rnor_5.0822,975,020 - 22,984,130 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242594   ⟹   XP_006242656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,438,622 - 20,449,268 (-)NCBI
Rnor_6.0822,920,238 - 22,929,368 (-)NCBI
Rnor_5.0822,975,020 - 22,984,130 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595422   ⟹   XP_017450911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2820,438,622 - 20,449,268 (-)NCBI
Rnor_6.0822,920,238 - 22,929,153 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_542147   ⟸   NM_080580
- UniProtKB: P35291 (UniProtKB/Swiss-Prot),   Q63942 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242656   ⟸   XM_006242594
- Peptide Label: isoform X2
- UniProtKB: P35291 (UniProtKB/Swiss-Prot),   Q63942 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242655   ⟸   XM_006242593
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450911   ⟸   XM_017595422
- Peptide Label: isoform X2
- UniProtKB: P35291 (UniProtKB/Swiss-Prot),   Q63942 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000015609   ⟸   ENSRNOT00000015609

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63942-F1-model_v2 AlphaFold Q63942 1-219 view protein structure

Transcriptome

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

Promoters
RGD ID:13695792
Promoter ID:EPDNEW_R6316
Type:initiation region
Name:Rab3d_1
Description:RAB3D, member RAS oncogene family
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_6.0822,929,271 - 22,929,331EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
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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)
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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)
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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
DA/OlaHsd (2019)
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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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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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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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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/Stm (2019)
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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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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
FXLE16/Stm (2020)
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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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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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620924 AgrOrtholog
BioCyc Gene G2FUF-31404 BioCyc
Ensembl Genes ENSRNOG00000011582 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000015609 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000015609 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7110109 IMAGE-MGC_LOAD
InterPro P-loop_NTPase UniProtKB/Swiss-Prot
  Rab3 UniProtKB/Swiss-Prot
  Small_GTP-bd_dom UniProtKB/Swiss-Prot
  Small_GTPase UniProtKB/Swiss-Prot
KEGG Report rno:140665 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93243 IMAGE-MGC_LOAD
NCBI Gene 140665 ENTREZGENE
Pfam Ras UniProtKB/Swiss-Prot
PhenoGen Rab3d PhenoGen
PROSITE RAB UniProtKB/Swiss-Prot
SMART RHO UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
TIGRFAMs small_GTP UniProtKB/Swiss-Prot
UniProt P35291 ENTREZGENE
  Q63942 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P35291 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Rab3d  RAB3D, member RAS oncogene family      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Rab3d  RAB3D, member RAS oncogene family      Symbol and Name status set to provisional 70820 PROVISIONAL