Rab3b (RAB3B, member RAS oncogene family)

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Gene: Rab3b (RAB3B, member RAS oncogene family) Rattus norvegicus

Analyze

Symbol:

Rab3b

Name:

RAB3B, member RAS oncogene family

RGD ID:

620922

Description:

Predicted to have several functions, including GDP binding activity; GTP-dependent protein binding activity; and myosin V binding activity. Predicted to be involved in several processes, including peptidyl-cysteine methylation; positive regulation of dopamine uptake involved in synaptic transmission; and regulation of vesicle-mediated transport. Localizes to anchored component of synaptic vesicle membrane and cytosol. Predicted to colocalize with secretory granule. Orthologous to human RAB3B (RAB3B, member RAS oncogene family); INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 3',5'-cyclic AMP; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

ras-related protein Rab-3B

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RAB3B (RAB3B, member RAS oncogene family)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Rab3b (RAB3B, member RAS oncogene family)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Rab3b (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RAB3B (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RAB3B (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rab3b (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RAB3B (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	RAB3B (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rab3b (RAB3B, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RAB3B (RAB3B, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Rab3b (RAB3B, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Danio rerio (zebrafish):	rab3b (RAB3B, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	SEC4	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	rab-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Rab3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	123,629,562 - 123,697,410 (+)	NCBI
Rnor_6.0 Ensembl	5	128,501,847 - 128,568,188 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	128,501,789 - 128,568,170 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	132,343,152 - 132,408,838 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	130,185,155 - 130,284,038 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	130,229,349 - 130,288,894 (+)	NCBI
Celera	5	122,364,678 - 122,431,394 (+)	NCBI		Celera
Cytogenetic Map	5	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane (EXP)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-hydroxypropanoic acid (ISO)

3',5'-cyclic AMP (EXP)

3,3',5-triiodo-L-thyronine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (ISO)

butanal (ISO)

Butylbenzyl phthalate (EXP)

C60 fullerene (EXP)

carbon nanotube (ISO)

cisplatin (EXP,ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (EXP)

dexamethasone (ISO)

dibutyl phthalate (EXP)

dichlorine (EXP)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

disodium selenite (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

ethanol (ISO)

fenamidone (ISO)

flavonoids (EXP)

folic acid (ISO)

geldanamycin (ISO)

gentamycin (EXP)

hydroquinone (ISO)

indometacin (ISO)

L-ascorbic acid (EXP,ISO)

lead(0) (ISO)

lead(2+) (ISO)

methylmercury chloride (ISO)

nickel atom (ISO)

ozone (EXP)

pentanal (ISO)

phenylephrine (EXP)

pirinixic acid (ISO)

progesterone (ISO)

propanal (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

SB 431542 (ISO)

Se-methyl-L-selenocysteine (ISO)

Se-methylselenocysteine (ISO)

silicon dioxide (ISO)

sodium fluoride (ISO)

tetrachloromethane (EXP)

thimerosal (ISO)

torcetrapib (ISO)

triadimefon (ISO)

tributylstannane (EXP)

trichostatin A (EXP,ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

zidovudine (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antigen processing and presentation (ISO)

peptidyl-cysteine methylation (ISO)

positive regulation of dopamine uptake involved in synaptic transmission (ISO)

protein localization to plasma membrane (IBA)

protein secretion (IBA)

regulation of exocytosis (IBA,ISO,TAS)

regulation of synaptic vesicle cycle (ISO)

regulation of vesicle size (ISO)

vesicle docking involved in exocytosis (IBA)

Cellular Component

anchored component of synaptic vesicle membrane (EXP,IDA,ISO)

cytoplasm (ISO)

cytosol (IDA)

dopaminergic synapse (ISO)

endosome (IBA)

Golgi apparatus (IEA)

perinuclear region of cytoplasm (ISO)

plasma membrane (IBA)

secretory granule (ISO)

synaptic vesicle (IBA,ISO)

vesicle (ISO)

Molecular Function

GDP binding (ISO)

GTP binding (NAS)

GTP-dependent protein binding (ISO)

GTPase activity (ISO)

myosin V binding (ISO)

protein binding (ISO)

References

References - curated


1.	Cormont M, etal., J Biol Chem. 1993 Sep 15;268(26):19491-7.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	Klengel R, etal., Biochem Biophys Res Commun 1997 Jul 30;236(3):719-22.
5.	MGD data from the GO Consortium
6.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	Pavlos NJ, etal., J Neurosci. 2010 Oct 6;30(40):13441-53. doi: 10.1523/JNEUROSCI.0907-10.2010.
8.	RGD automated data pipeline
9.	RGD automated import pipeline for gene-chemical interactions
10.	Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.

Additional References at PubMed

PMID:7508866	PMID:7532276	PMID:8889548	PMID:9252191	PMID:10748113	PMID:11121396	PMID:12167638	PMID:12192047	PMID:12477932	PMID:16043482	PMID:16822953	PMID:19056867
PMID:19717423	PMID:20007772	PMID:20807725	PMID:21262767	PMID:22321395	PMID:23533145	PMID:24006491	PMID:24891604	PMID:29476059

Genomics

Comparative Map Data

Rab3b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	123,629,562 - 123,697,410 (+)	NCBI
Rnor_6.0 Ensembl	5	128,501,847 - 128,568,188 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	128,501,789 - 128,568,170 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	132,343,152 - 132,408,838 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	130,185,155 - 130,284,038 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	130,229,349 - 130,288,894 (+)	NCBI
Celera	5	122,364,678 - 122,431,394 (+)	NCBI		Celera
Cytogenetic Map	5	q34	NCBI

RAB3B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	51,907,956 - 51,990,700 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	51,907,956 - 51,990,700 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	52,373,628 - 52,456,372 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	52,157,420 - 52,228,936 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	52,096,857 - 52,168,369	NCBI
Celera	1	50,660,966 - 50,743,913 (-)	NCBI
Cytogenetic Map	1	p32.3	NCBI
HuRef	1	50,490,781 - 50,573,849 (-)	NCBI		HuRef
CHM1_1	1	52,491,166 - 52,573,953 (-)	NCBI		CHM1_1

Rab3b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	108,736,267 - 108,800,521 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	108,736,260 - 108,800,521 (+)	Ensembl
GRCm38	4	108,879,070 - 108,943,324 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	108,879,063 - 108,943,324 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	108,551,675 - 108,615,929 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	108,377,002 - 108,441,256 (+)	NCBI			mm8
Celera	4	107,216,795 - 107,279,795 (+)	NCBI		Celera
Cytogenetic Map	4	C7	NCBI

Rab3b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955464	7,117,883 - 7,177,534 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955464	7,117,908 - 7,177,138 (+)	NCBI	ChiLan1.0	ChiLan1.0

RAB3B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	1	52,655,120 - 52,737,856 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	52,666,713 - 52,723,975 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	51,170,956 - 51,242,828 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

RAB3B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	15	9,319,057 - 9,372,518 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	15	9,305,495 - 9,378,003 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Rab3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936522	8,924,724 - 8,985,309 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RAB3B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	160,202,562 - 160,255,632 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	160,194,488 - 160,255,635 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	147,898,185 - 147,958,774 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RAB3B
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	80,963,320 - 81,036,058 (+)	NCBI
ChlSab1.1 Ensembl	20	80,963,398 - 81,035,657 (+)	Ensembl

Rab3b
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624859	1,184,733 - 1,250,402 (+)	NCBI

Position Markers

RH128978

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	128,567,944 - 128,568,128	NCBI	Rnor6.0
Rnor_5.0	5	132,408,612 - 132,408,796	UniSTS	Rnor5.0
RGSC_v3.4	5	130,283,815 - 130,283,999	UniSTS	RGSC3.4
Celera	5	122,431,171 - 122,431,355	UniSTS
RH 3.4 Map	5	812.5	UniSTS
Cytogenetic Map	5	q35	UniSTS

RH136876

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	128,567,878 - 128,568,027	NCBI	Rnor6.0
Rnor_5.0	5	132,408,546 - 132,408,695	UniSTS	Rnor5.0
RGSC_v3.4	5	130,283,749 - 130,283,898	UniSTS	RGSC3.4
Celera	5	122,431,105 - 122,431,254	UniSTS
RH 3.4 Map	5	812.7	UniSTS
Cytogenetic Map	5	q35	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	136640934	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31926122	136640934	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35788756	147487820	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40777918	154732375	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	44404276	134502294	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	51418671	147487820	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	56991667	137729065	Rat
1358895	Bp254	Blood pressure QTL 254	3.6	0.0003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	60072951	133313852	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	61086525	149030144	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
2306971	Anxrr21	Anxiety related response QTL 21	9.47		fear/anxiety-related behavior trait (VT:1000241)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	5	65696672	129038896	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	71552569	157225114	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
1298086	Bp156	Blood pressure QTL 156			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	89502294	134502294	Rat
7411582	Foco3	Food consumption QTL 3	7.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	91585539	136585539	Rat
7411601	Foco12	Food consumption QTL 12	19.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	91585539	136585539	Rat
7411564	Bw135	Body weight QTL 135		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	91585539	136585539	Rat
6903316	Bw113	Body weight QTL 113	2	0.0103	body mass (VT:0001259)	body weight (CMO:0000012)	5	91884213	136884213	Rat
1358889	Bp261	Blood pressure QTL 261	2.86		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	93037304	133313852	Rat
1358909	Kidm25	Kidney mass QTL 25	1.87		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	93037304	133313852	Rat
631527	Tls1	T-lymphoma susceptibility QTL 1	0	0.001	thymus integrity trait (VT:0010555)	post-insult time to onset of T-cell lymphoma (CMO:0001907)	5	93273130	138273130	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	97921932	149030144	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	100723739	153577831	Rat
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	101265591	141912026	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	102945579	154732228	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	107119214	152119214	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	111278451	156278451	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	112279412	157279412	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	112279412	157279412	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	112279412	157279412	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	112279412	157279412	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	112279412	157279412	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	116767924	161767924	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	116767924	161767924	Rat
7794739	Bp372	Blood pressure QTL 372		0.0058	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	122679716	130167412	Rat
1582230	Bw78	Body weight QTL 78	3.2	0.0016	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	123852489	133313852	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	125455818	149568944	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	125455818	157225114	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	278
Count of miRNA genes:	179
Interacting mature miRNAs:	200
Transcripts:	ENSRNOT00000010645
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		37							64			4
Low	3	6	17	6	7	6			10	25	28	7
Below cutoff			16	12	11	12	8	11		10	12		8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031091	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238531	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039110839	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC060562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BF524240	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BI293875	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB711467	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U68184	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Y14019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000010645 ⟹ ENSRNOP00000010645

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	128,501,847 - 128,568,188 (+)	Ensembl

RefSeq Acc Id:

NM_031091 ⟹ NP_112353

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	123,630,402 - 123,697,407 (+)	NCBI
Rnor_6.0	5	128,501,833 - 128,568,167 (+)	NCBI
Rnor_5.0	5	132,343,152 - 132,408,838 (+)	NCBI
RGSC_v3.4	5	130,185,155 - 130,284,038 (+)	RGD
Celera	5	122,364,678 - 122,431,394 (+)	RGD

Sequence:

show sequence

TCAACCCTCCGTAGCCGAGGTGGGAACCAGACCCGCCCCGCCTGCCTCTCGTCCACTACTGCCA
GGTGCAACAGTCCGGCTGCAGTGTGCCGCGAGCCAGCTCTTATCCGAGATGGCCTCAGTAACTG
ATGGTAACACTGGAATCAGAGATGCCTCTGACCAGAACTTTGACTACATGTTCAAACTGCTCAT
CATTGGCAACAGCAGCGTCGGGAAGACCTCCTTCCTTTTCCGCTATGCTGATGACACCTTCACC
CCTGCCTTTGTCAGCACTGTGGGTATCGACTTCAAAGTGAAGACAGTTTACCGTCATGAGAAGC
GTGTGAAGCTGCAGATATGGGACACGGCAGGGCAAGAGCGGTACCGGACCATCACCACAGCCTA
CTACCGCGGGGCCATGGGCTTCATTCTCATGTATGACATCACCAACGAGGAGTCCTTCAACGCT
GTCCAGGACTGGGCTACTCAGATCAAGACCTACTCCTGGGACAACGCACAGGTCATTCTCGTGG
GGAATAAATGTGATATGGAAGAGGAAAGGGTGATCCCGACTGAGAAGGGCCGGCTCCTAGCAGA
GCAACTTGGGTTTGACTTCTTTGAAGCCAGTGCCAAGGAGAACATCAGTGTGAGGCAGGCCTTC
GAGCGTCTGGTGGACGCCATCTGCGATAAGATGTCTGACTCAATGGACACAGACCCCTCCGTGC
TGGGCGCCTCCAAGACCACACGGCTCTCGGACACCCCGCCGCTGCTCCAGCAGAACTGCTCTTG
CTAGGCAAGGCCCGCCCTGCTGTTCCCCCCATGTCATGCCCACTTCTCCTCTGCTTCTCTCTGT
TACTGTCTGCTCCCCGAACCCCAAGCCAGCTGAGTTCTTTGCCAGCCCCTGTGGTTCTCTGCAG
ACGGCCCCAGCTACAGATACTAACTGCAGGTTACTGTGTGGGTGAAGACTCCTCTTACAACAGA
AAACTCCCTCTTAGGAAGGAGGTTCAACATAGAGACTTGGAAAGAACCTTTTCTGCCCTTAAAA
TAAAATTCCCTTCATTTACCAAGATACAACTCCCACACGCACTCCTTAGGGGTTGACCAGTGTG
TAAAGTGAGGCCCACCTGCACAGCTGATACTATTAAAGAAAATGTCTCAAAGCAAAAAAAAAAA
AAAAAAA

hide sequence

RefSeq Acc Id:

XM_006238531 ⟹ XP_006238593

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	123,630,351 - 123,697,410 (+)	NCBI
Rnor_6.0	5	128,501,789 - 128,568,170 (+)	NCBI
Rnor_5.0	5	132,343,152 - 132,408,838 (+)	NCBI

Sequence:

show sequence

GGGCCTGGACCCAGCGGGAACCCAACCCATCTTCTGCCAGAGCCTCAACCCTCCGTAGCCGAGG
TGGGAACCAGACCCGCCCCGCCTGCCTCTCGTCCACTACTGCCAGGTGCAACAGTCCGGCTGCA
GTGTGCCGCGAGCCAGCTCTTATCCGAGATGGCCTCAGTAACTGATGGTAACACTGGAATCAGA
GATGCCTCTGACCAGAACTTTGACTACATGTTCAAACTGCTCATCATTGGCAACAGCAGCGTCG
GGAAGACCTCCTTCCTTTTCCGCTATGCTGATGACACCTTCACCCCTGCCTTTGTCAGCACTGT
GGGTATCGACTTCAAAGTGAAGACAGTTTACCGTCATGAGAAGCGTGTGAAGCTGCAGATATGG
GACACGGCAGGGCAAGAGCGGTACCGGACCATCACCACAGCCTACTACCGCGGGGCCATGGGCT
TCATTCTCATGTATGACATCACCAACGAGGAGTCCTTCAACGCTGTCCAGGACTGGGCTACTCA
GATCAAGACCTACTCCTGGGACAACGCACAGGTCATTCTCGTGGGGAATAAATGTGATATGGAA
GAGGAAAGGGTTATCCCGACTGAGAAGGGCCGGCTCCTAGCAGAGCAACTTGGTATGCACACGG
CACATACGTACACATGGTTTGACTTCTTTGAAGCCAGTGCCAAGGAGAACATCAGTGTGAGGCA
GGCCTTCGAGCGTCTGGTGGACGCCATCTGCGATAAGATGTCTGACTCAATGGACACAGACCCC
TCCGTGCTGGGCGCCTCCAAGACCACACGGCTCTCGGACACCCCGCCGCTGCTCCAGCAGAACT
GCTCTTGCTAGGCAAGGCCCGCCCTGCTGTTCCCCCCATGTCATGCCCACTTCTCCTCTGCTTC
TCTCTGTTACTGTCCGCTCCCCGAACCCCAAGCCAGCTGAGTTCTTTGCCAGCCCCTGTGGTTC
TCTGCAGACGGCCCCAGCTACAGATACTAACTGCAGGTTACTGTGTGGGTGAAGACTCCTCTTA
CAACAGAAAACTCCCTCTTAGGAAGGAGGTTCAACATAGAGACTTGGAAAGAACCTTTTCTGCC
CTTAAAATAAAATTCCCTTCATTTACCAAGATACAACTCCCACACGCACTCCTTAGGGGTTGAC
CAGTGTGTAAAGTGAGGCCCACCTGCACAGCTGATACTATTAAAGAAAATGTCTCAAAGCATAA

hide sequence

RefSeq Acc Id:

XM_039110839 ⟹ XP_038966767

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	123,629,562 - 123,635,880 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_112353	(Get FASTA)	NCBI Sequence Viewer
	XP_006238593	(Get FASTA)	NCBI Sequence Viewer
	XP_038966767	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD53965	(Get FASTA)	NCBI Sequence Viewer
	AAH60562	(Get FASTA)	NCBI Sequence Viewer
	CAA74341	(Get FASTA)	NCBI Sequence Viewer
	EDL90382	(Get FASTA)	NCBI Sequence Viewer
	EDL90383	(Get FASTA)	NCBI Sequence Viewer
	Q63941	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_112353 ⟸ NM_031091

- UniProtKB:

Q63941 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MASVTDGNTGIRDASDQNFDYMFKLLIIGNSSVGKTSFLFRYADDTFTPAFVSTVGIDFKVKTV
YRHEKRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNA
QVILVGNKCDMEEERVIPTEKGRLLAEQLGFDFFEASAKENISVRQAFERLVDAICDKMSDSMD
TDPSVLGASKTTRLSDTPPLLQQNCSC

hide sequence

RefSeq Acc Id:	XP_006238593 ⟸ XM_006238531
- Peptide Label:	isoform X1
- UniProtKB:	Q6P9W6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MASVTDGNTGIRDASDQNFDYMFKLLIIGNSSVGKTSFLFRYADDTFTPAFVSTVGIDFKVKTV YRHEKRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNA QVILVGNKCDMEEERVIPTEKGRLLAEQLGMHTAHTYTWFDFFEASAKENISVRQAFERLVDAI CDKMSDSMDTDPSVLGASKTTRLSDTPPLLQQNCSC hide sequence

RefSeq Acc Id:

ENSRNOP00000010645 ⟸ ENSRNOT00000010645

RefSeq Acc Id:	XP_038966767 ⟸ XM_039110839
- Peptide Label:	isoform X2

Transcriptome

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

Promoters

RGD ID:

13693906

Promoter ID:

EPDNEW_R4430

Type:

initiation region

Name:

Rab3b_1

Description:

RAB3B, 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	128,501,835 - 128,501,895	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/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)

ACI/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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

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)

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

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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CSV

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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

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/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

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620922	AgrOrtholog
Ensembl Genes	ENSRNOG00000008001	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000010645	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000010645	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:6918181	IMAGE-MGC_LOAD
InterPro	P-loop_NTPase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Rab3	UniProtKB/Swiss-Prot
	Small_GTP-bd_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Small_GTPase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:81755	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72799	IMAGE-MGC_LOAD
NCBI Gene	81755	ENTREZGENE
Pfam	Ras	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Rab3b	PhenoGen
PROSITE	RAB	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF52540	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	small_GTP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	Q63941	ENTREZGENE
	Q6P9W6	ENTREZGENE, UniProtKB/TrEMBL
	Q9QYT8_RAT	UniProtKB/TrEMBL
	RAB3B_RAT	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Rab3b	RAB3B, member RAS oncogene family		Rab3B protein	Name updated	1299863	APPROVED
2002-08-07	Rab3b	Rab3B protein			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_regulation	mRNA expression is induced by dexamethasone in pancreatic acinar cells	729749

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)