Vps53 (VPS53 subunit of GARP complex)

Gene: Vps53 (VPS53 subunit of GARP complex) Rattus norvegicus

Analyze

Symbol:

Vps53

Name:

VPS53 subunit of GARP complex

RGD ID:

1311391

Description:

Predicted to be involved in cytosolic transport; endocytic recycling; and protein targeting to lysosome. Predicted to act upstream of or within lysosomal transport. Predicted to be located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Predicted to be part of EARP complex and GARP complex. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2E. Orthologous to human VPS53 (VPS53 subunit of GARP complex); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC287535; RGD1311391; similar to hypothetical protein FLJ10979; vacuolar protein sorting 53 (yeast) ; vacuolar protein sorting 53 homolog; vacuolar protein sorting 53 homolog (S. cerevisiae); vacuolar protein sorting-associated protein 53 homolog; VPS53 GARP complex subunit

RGD Orthologs

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):	VPS53 (VPS53 subunit of GARP complex)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Vps53 (VPS53 GARP complex subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vps53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VPS53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VPS53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vps53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VPS53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VPS53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vps53 (VPS53 subunit of GARP complex)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Vps53 (VPS53 GARP complex subunit)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	VPS53 (VPS53 subunit of GARP complex)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	vps53 (VPS53 subunit of GARP complex)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	VPS53	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Vps53	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	vps-53	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	vps53	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	61,418,076 - 61,536,912 (-)	NCBI		GRCr8
mRatBN7.2	10	60,919,820 - 61,038,674 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,676 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	65,561,939 - 65,680,825 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	65,067,390 - 65,186,273 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	60,537,918 - 60,656,979 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	64,218,596 - 64,341,064 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	64,222,276 - 64,341,109 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	63,672,733 - 63,793,858 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	63,410,886 - 63,535,682 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	63,424,683 - 63,543,200 (-)	NCBI
Celera	10	59,935,404 - 60,054,107 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

microcephaly (ISO)

Neurodevelopmental Disorders (ISO)

pontocerebellar hypoplasia (ISO)

pontocerebellar hypoplasia type 1B (ISO)

pontocerebellar hypoplasia type 2E (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

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

2,4,6-tribromophenol (ISO)

2,6-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

aristolochic acid A (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

caffeine (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

decabromodiphenyl ether (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

fenthion (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

FR900359 (ISO)

fulvestrant (ISO)

L-methionine (ISO)

metformin (ISO)

methidathion (ISO)

methotrexate (ISO)

paracetamol (EXP)

pentanal (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

propanal (ISO)

rac-lactic acid (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sulindac (EXP)

sunitinib (ISO)

thimerosal (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichostatin A (ISO)

Triptolide (EXP)

valproic acid (ISO)

vinclozolin (EXP)

vincristine (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

endocytic recycling (ISO)

lysosomal transport (ISO)

protein targeting to lysosome (ISO)

retrograde transport, endosome to Golgi (IBA,ISO)

vesicle-mediated cholesterol transport (ISO)

Cellular Component

cytosol (IEA,ISO)

EARP complex (ISO)

endosome membrane (IEA)

GARP complex (IBA,ISO)

Golgi apparatus (ISO)

intracellular membrane-bounded organelle (ISO)

membrane (ISO)

perinuclear region of cytoplasm (ISO)

recycling endosome (ISO)

trans-Golgi network (IEA)

Molecular Function

protein binding (IPI,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles.	Topalidou I, etal., PLoS Genet. 2016 May 18;12(5):e1006074. doi: 10.1371/journal.pgen.1006074. eCollection 2016 May.

Additional References at PubMed

PMID:12477932	PMID:15878329	PMID:19620288	PMID:25799061	PMID:27440922

Genomics

Comparative Map Data

Vps53
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	61,418,076 - 61,536,912 (-)	NCBI		GRCr8
mRatBN7.2	10	60,919,820 - 61,038,674 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,676 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	65,561,939 - 65,680,825 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	65,067,390 - 65,186,273 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	60,537,918 - 60,656,979 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	64,218,596 - 64,341,064 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	64,222,276 - 64,341,109 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	63,672,733 - 63,793,858 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	63,410,886 - 63,535,682 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	63,424,683 - 63,543,200 (-)	NCBI
Celera	10	59,935,404 - 60,054,107 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

VPS53
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	508,668 - 714,839 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	508,503 - 721,717 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	411,908 - 618,079 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	382,698 - 564,758 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	17	423,924 - 629,862 (-)	NCBI		Celera
Cytogenetic Map	17	p13.3	NCBI
HuRef	17	325,008 - 528,642 (-)	NCBI		HuRef
CHM1_1	17	418,907 - 623,396 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	391,960 - 599,311 (-)	NCBI		T2T-CHM13v2.0

Vps53
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	75,937,052 - 76,070,464 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	75,937,052 - 76,070,473 (-)	Ensembl		GRCm39 Ensembl
GRCm38	11	76,046,226 - 76,179,638 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	76,046,226 - 76,179,647 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	75,859,728 - 75,993,132 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	75,862,421 - 75,995,825 (-)	NCBI		MGSCv36	mm8
Celera	11	83,555,285 - 83,692,488 (-)	NCBI		Celera
Cytogenetic Map	11	B5	NCBI
cM Map	11	45.92	NCBI

Vps53
(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_004955481	2,130,888 - 2,264,924 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955481	2,130,669 - 2,265,065 (-)	NCBI	ChiLan1.0	ChiLan1.0

VPS53
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	19	8,042,929 - 8,261,718 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	17	9,602,776 - 9,812,194 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	400,048 - 576,119 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	416,136 - 604,705 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	414,782 - 604,705 (-)	Ensembl	panpan1.1		panPan2

VPS53
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	45,074,066 - 45,239,569 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	45,074,100 - 45,214,066 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	44,224,566 - 44,391,993 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	45,892,548 - 46,060,240 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	45,892,566 - 46,035,516 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	44,670,971 - 44,838,890 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	44,964,695 - 45,132,085 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	45,043,233 - 45,211,135 (+)	NCBI		UU_Cfam_GSD_1.0

Vps53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	44,189,381 - 44,329,957 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936538	7,067,327 - 7,205,768 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936538	7,067,332 - 7,207,852 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VPS53
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	47,143,098 - 47,291,161 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	47,141,749 - 47,291,169 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	49,308,850 - 49,456,068 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

VPS53
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	302,771 - 464,572 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	303,414 - 464,574 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666059	21,622,848 - 21,752,483 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vps53
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624786	3,614,811 - 3,778,069 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624786	3,614,775 - 3,779,644 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Vps53
772 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	40
Count of miRNA genes:	38
Interacting mature miRNAs:	40
Transcripts:	ENSRNOT00000010010
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.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	1	80676123	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	743364	63851208	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5801990	62146030	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6154182	73453136	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6357896	96121100	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9658275	104670812	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14487011	89062041	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14487011	104060283	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14487011	107057807	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	18167841	63167841	Rat
2313055	Bw96	Body weight QTL 96	3.6	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	10	19606483	64606483	Rat
2313087	Bmd80	Bone mineral density QTL 80	3.2	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	10	19606483	64606483	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	19816042	99406971	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21329805	61345413	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22427500	90627625	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	23444813	104060283	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	26521957	61345413	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	26521957	98003205	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	26521957	98952741	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	26944628	71944628	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	27606468	72606468	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	28453136	73453136	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	29299504	64155584	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	29299504	107211142	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	30632053	75632053	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31224026	75632053	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	31297439	76297439	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	33973921	78973921	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	35392267	64155584	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	35392457	63642539	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	37565079	82565079	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	37565079	82565079	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	40035094	102359817	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	40035094	104060283	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	41142633	86142633	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	41333258	86333258	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	41944526	78307017	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	42045676	104670812	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	42323132	87323132	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	42323132	87323132	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	42323132	87323132	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	42876766	79813922	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	44441699	89441699	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	44441699	89441699	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	44441699	89441699	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	45029650	95600334	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	47369470	92369470	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	10	49444551	81709989	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	49444551	81709989	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	49444551	81709989	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	49444551	81709989	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	50574707	95574707	Rat
70364	Bp72	Blood pressure QTL 72			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	51121100	96121100	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	51770177	107211142	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	51770177	107211142	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	51772940	96772940	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	51774612	95600334	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	51786282	91669536	Rat
2306787	Ean3	Experimental allergic neuritis QTL 3	3.1		nervous system integrity trait (VT:0010566)	body weight loss (CMO:0001399)	10	53797385	66979128	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	53797385	107211142	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	53797494	98952626	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	54809292	99809292	Rat
2312662	Slep8	Serum leptin concentration QTL 8		0.05	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	10	57134272	102134272	Rat
2312668	Scl65	Serum cholesterol level QTL 65		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	57134272	102134272	Rat
2312672	Insul15	Insulin level QTL 15		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	10	57134272	102134272	Rat
1549831	Bss6	Bone structure and strength QTL 6	4		lumbar vertebra strength trait (VT:0010574)	vertebra ultimate force (CMO:0001678)	10	57576521	102576521	Rat
2293698	Bss43	Bone structure and strength QTL 43	5.33	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	10	59209888	104209888	Rat

Markers in Region

D10Got79

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	60,988,321 - 60,988,448 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	64,290,723 - 64,290,849	NCBI	Rnor6.0
Rnor_5.0	10	63,722,456 - 63,722,582	UniSTS	Rnor5.0
RGSC_v3.4	10	63,481,417 - 63,481,544	RGD	RGSC3.4
RGSC_v3.4	10	63,481,418 - 63,481,544	UniSTS	RGSC3.4
RGSC_v3.1	10	63,495,040 - 63,495,167	RGD
Celera	10	60,003,799 - 60,003,925	UniSTS
RH 2.0 Map	10	637.9	RGD
Cytogenetic Map	10	q24	UniSTS

D10Got83

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	60,943,408 - 60,943,565 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	64,245,818 - 64,245,974	NCBI	Rnor6.0
Celera	10	59,958,961 - 59,959,105	UniSTS
RH 2.0 Map	10	642.8	RGD
Cytogenetic Map	10	q24	UniSTS

RH143717

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	60,987,569 - 60,987,676 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	64,289,971 - 64,290,077	NCBI	Rnor6.0
Rnor_5.0	10	63,723,228 - 63,723,334	UniSTS	Rnor5.0
RGSC_v3.4	10	63,480,666 - 63,480,772	UniSTS	RGSC3.4
Celera	10	60,003,047 - 60,003,153	UniSTS
Cytogenetic Map	10	q24	UniSTS

BF388451

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	60,993,383 - 60,993,627 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	64,295,785 - 64,296,028	NCBI	Rnor6.0
Rnor_5.0	10	63,717,277 - 63,717,520	UniSTS	Rnor5.0
RGSC_v3.4	10	63,486,329 - 63,486,572	UniSTS	RGSC3.4
Celera	10	60,008,861 - 60,009,104	UniSTS
Cytogenetic Map	10	q24	UniSTS

BF390779

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	60,982,373 - 60,982,528 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	64,284,775 - 64,284,929	NCBI	Rnor6.0
Rnor_5.0	10	63,728,392 - 63,728,546	UniSTS	Rnor5.0
RGSC_v3.4	10	63,475,462 - 63,475,616	UniSTS	RGSC3.4
Celera	10	59,997,851 - 59,998,005	UniSTS
Cytogenetic Map	10	q24	UniSTS

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	32	35	22	19	22		2	74	31	41	11
Low		11	22	19		19	8	9		4			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001105813	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039085521	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC112732	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC168148	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000010	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000010010 ⟹ ENSRNOP00000010010

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,674 (-)	Ensembl
Rnor_6.0 Ensembl	10	64,222,276 - 64,341,109 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082825 ⟹ ENSRNOP00000074043

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,873 - 61,038,676 (-)	Ensembl
Rnor_6.0 Ensembl	10	64,222,285 - 64,341,066 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000096693 ⟹ ENSRNOP00000096444

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,327 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000099955 ⟹ ENSRNOP00000081957

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,456 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000112514 ⟹ ENSRNOP00000089534

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,820 - 61,038,674 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000116582 ⟹ ENSRNOP00000096750

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	60,919,820 - 61,034,347 (-)	Ensembl

RefSeq Acc Id:

NM_001105813 ⟹ NP_001099283

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	10	61,418,076 - 61,536,912 (-)	NCBI
mRatBN7.2	10	60,919,820 - 61,038,674 (-)	NCBI
Rnor_6.0	10	64,222,232 - 64,341,064 (-)	NCBI
Rnor_5.0	10	63,672,733 - 63,793,858 (+)	NCBI
RGSC_v3.4	10	63,410,886 - 63,535,682 (-)	RGD
Celera	10	59,935,404 - 60,054,107 (-)	RGD

Sequence:

show sequence

CGGAAGTGCCGGGCTAGACGAGCGAGTAGCGGCTTTCTCGAGCCCTGTACCTGGAGGATTGCAA
TTCTGGGGTCCTGGTGATAGACAGATCACGACAGGGTTGGAGAGGGCGTCGGGGGCTGAGCGGC
GGGATGATGGAGGAGGAGGAACTGGAGTTTGTGGAGGAGCTGGAGGCTGTGCTGCAGCTCACGC
CAGAGGTGCAACTAGCCATCGAGCAGGTATTCCCAAGCCAGGATCCTCTTGATCAAGCTGACTT
CAATGCCGTTGAGTACATCAATACTCTGTTCCCAACAGAGCAATCTCTGGCAAACATTGACGAT
GTTGTGAACAAGATTAGACTGAAAATAAGGAGACTGGATGATAATATCCGCACTGTCGTAAGAG
GTCAGACAAATGTGGGACAGGATGGAAGGCAAGCACTTGAAGAAGCCCAGAAAGCCATTCAGCA
ACTCTTTGGCAAAATCAAGGATATTAAAGACAAAGCAGAAAAGTCAGAACAAATGGTGAAAGAG
ATCACCCGAGATATTAAGCAGTTAGATCACGCCAAGCGCCACCTGACCACCTCGATCACAACAC
TGAACCACCTGCACATGCTGGCAGGCGGGGTGGACTCCTTGGAAGCCATGACCAGACGCAGACA
GTATGGAGAAGTTGCTAATCTCCTTCAGGGTGTAATGAATGTTCTGGAGCACTTTCACAAGTAC
ATGGGAATCCCACAGATCCGACAGCTTTCTGAACGGGTGAAGGCTGCACAGACAGAGCTAGGAC
AGCAAATCCTGGCTGATTTTGAAGAAGCATTTCCTTCACAGGGTACCAAGAGGCCAGGAGGACC
CAGCAATGTCCTGAGAGATGCGTGCCTGGTGGCTAATATTTTGGACCCCAGAATCAAACAAGAA
ATCATCAAAAAGTTTATTAAACAGCATCTATCAGAGTATCTAGTACTTTTTCAAGAAAATCAAG
ATGTCGCCTGGCTGGACAAAATTGACAGACGTTATGCCTGGGTAAAACGCCAGCTTGTGGACTA
TGAAGAGAAGTATGGTCGGATGTTTCCTCGTGAGTGGTGCATGACAGAGAGAATCTCAGTAGAA
TTTTGCCATGTGACGAGGACAGAACTTTCCAAAATCATGCGAGCCAGAGCTAAGGAAATTGAGG
TGAAGTTGCTTCTTTTTGCCATTCAGAGAACAACTAACTTTGAGGGGTTTCTCGCAAAACGCTT
CTCCGGTTGCACCTTGACAGATGGAACCCTGAAAAAGCTGGAGTCCCCACCGCCATCTACCAAT
CCCTTCCTGGAAGATGAGACAGCAGCAGAGACGGAGGAGCTGGCTCTGGAGAAGGGAGAGTTAG
AGCAACCAAAGAAGCCCAAAGCCCCAGATAATCCATTTCATGGCATTGTTTCCAAGTGTTTCGA
GCCTCATCTCTACGTGTACATTGAGTCCCAGGACAAAAACCTCAGTGAGCTGATAGACCGGTTT
GTGGCAGATTTCAAAGCCCAGGGCCCACCCAAGCCCAACACTGATGAAGGGGGTGCTGTACTCC
CCAGCTGTGCTGACCTCTTTGTCTACTATAAGAAGTGCATGGTACAGTGCTCACAGCTCAGCAC
AGGCGAGCCCATGATTGCCCTGACCACCATCTTCCAGAAGTACCTCCGAGAATACGCCTGGAAA
ATCCTCTCTGGCAACCTGCCTAAAACCAGCAGCAGCAGTGGGGGGCTGACCATCAGCAGCCTCC
TCAAAGAGAAAGAGGGCTCAGAAGTGGCCAGATTCACTCTGGAGGAGCTGTGTCTCATCTGCAG
CATCCTGAGCACAGCCGAGTACTGTCTGGCTACCACTCAGCAGCTAGAAGAAAAACTCAAAGAA
AAAGTTGATGTGAGTCTGACTGAGCGAATTAACCTCACAGGAGAAATGGACACATTCAGCACTG
TCATCTCCAGCAGCATTCAGCTGTTGGTTCAAGATCTAGATGCAGCCTGTGACCCTGCCCTGAT
TGCCATGAGCAAGATGCCGTGGCAGAACGTGGAGCATGTTGGTGACCAGAGCCCTTATGTCACC
TCTGTTATTCTTCACATAAAGCAGAATGTCCCCATCATCCGTGACAACCTGGCTTCCACACGGA
AATACTTCACACAGTTCTGCATTAAATTTGCAAATTCGTTCATTCCCAAATTCATCACCCACCT
CTTCAAGTGTAAGCCGATCAGCATGGTGGGAGCAGAGCAGCTTCTGCTGGACACCCACTCCCTG
AAGATGGTCCTGCTCGATCTCCCGTCCATTGGCTCACAGGTGGTGAGGAAGGCCCCTGCCAGTT
ACACTAAGATTGTCGTGAAAGGCATGACCCGGGCTGAAATGATCCTCAAGGTGGTGATGGCCCC
TCATGAACCATTGGTAGTATTTGTTGACAACTACATCAAACTCCTTACAGACTGCAACACAGAA
ACCTTCCAGAAAATACTGGATATGAAGGGGCTGAAGAGGAGTGAGCAGAGCAGCATGCTGGAAC
TTTTGCGGCAGAGGCTCCCTGCCCCACCCTCAGGGACAGAAAGTTCTAGCACACTGTCCCTGAT
GGCCCCAACACCAGAGCAGGAATCATCACGCATCCGAAAACTTGAAAAACTGATTAAAAAGAGA
CTGTAAGGAACATGCCGACATTGCCAGGGTCCCTGAGCAACTGATTTCTGGAAACCCTCGCCCT
TATGACTCCAGGTCCTAAGTCCTGAAGGCTCTGAGGACATTACGGTTATTAAAGTATCTCTCCC
AGAACATGTCTTACTTTCTATCTCAGTCAGGGACGTTCAGTGAAGTCTGGCTT

hide sequence

RefSeq Acc Id:

XM_039085521 ⟹ XP_038941449

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	10	61,418,125 - 61,507,108 (-)	NCBI
mRatBN7.2	10	60,919,869 - 61,004,995 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001099283	(Get FASTA)	NCBI Sequence Viewer
	XP_038941449	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68148	(Get FASTA)	NCBI Sequence Viewer
	EDM05249	(Get FASTA)	NCBI Sequence Viewer
	EDM05250	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000010010
	ENSRNOP00000010010.2
	ENSRNOP00000074043.1
	ENSRNOP00000081957.1
	ENSRNOP00000089534.1
	ENSRNOP00000096444.1
	ENSRNOP00000096750.1

RefSeq Acc Id:

NP_001099283 ⟸ NM_001105813

- UniProtKB:

D3ZPE5 (UniProtKB/TrEMBL), A6HGU5 (UniProtKB/TrEMBL), B4F763 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDQADFNAVEYINTLFPTEQSLANIDDV
VNKIRLKIRRLDDNIRTVVRGQTNVGQDGRQALEEAQKAIQQLFGKIKDIKDKAEKSEQMVKEI
TRDIKQLDHAKRHLTTSITTLNHLHMLAGGVDSLEAMTRRRQYGEVANLLQGVMNVLEHFHKYM
GIPQIRQLSERVKAAQTELGQQILADFEEAFPSQGTKRPGGPSNVLRDACLVANILDPRIKQEI
IKKFIKQHLSEYLVLFQENQDVAWLDKIDRRYAWVKRQLVDYEEKYGRMFPREWCMTERISVEF
CHVTRTELSKIMRARAKEIEVKLLLFAIQRTTNFEGFLAKRFSGCTLTDGTLKKLESPPPSTNP
FLEDETAAETEELALEKGELEQPKKPKAPDNPFHGIVSKCFEPHLYVYIESQDKNLSELIDRFV
ADFKAQGPPKPNTDEGGAVLPSCADLFVYYKKCMVQCSQLSTGEPMIALTTIFQKYLREYAWKI
LSGNLPKTSSSSGGLTISSLLKEKEGSEVARFTLEELCLICSILSTAEYCLATTQQLEEKLKEK
VDVSLTERINLTGEMDTFSTVISSSIQLLVQDLDAACDPALIAMSKMPWQNVEHVGDQSPYVTS
VILHIKQNVPIIRDNLASTRKYFTQFCIKFANSFIPKFITHLFKCKPISMVGAEQLLLDTHSLK
MVLLDLPSIGSQVVRKAPASYTKIVVKGMTRAEMILKVVMAPHEPLVVFVDNYIKLLTDCNTET
FQKILDMKGLKRSEQSSMLELLRQRLPAPPSGTESSSTLSLMAPTPEQESSRIRKLEKLIKKRL

hide sequence

RefSeq Acc Id:

ENSRNOP00000074043 ⟸ ENSRNOT00000082825

RefSeq Acc Id:

ENSRNOP00000010010 ⟸ ENSRNOT00000010010

RefSeq Acc Id:	XP_038941449 ⟸ XM_039085521
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5ZUQ6 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000096444 ⟸ ENSRNOT00000096693

RefSeq Acc Id:

ENSRNOP00000081957 ⟸ ENSRNOT00000099955

RefSeq Acc Id:

ENSRNOP00000096750 ⟸ ENSRNOT00000116582

RefSeq Acc Id:

ENSRNOP00000089534 ⟸ ENSRNOT00000112514

Protein Domains

Vps53 C-terminal Vps53 N-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZPE5-F1-model_v2	AlphaFold	D3ZPE5	1-832	view protein structure

Transcriptome

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

Promoters

RGD ID:

13697450

Promoter ID:

EPDNEW_R7973

Type:

initiation region

Name:

Vps53_1

Description:

VPS53 GARP complex subunit

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	10	64,341,063 - 64,341,123	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311391	AgrOrtholog
BioCyc Gene	G2FUF-24170	BioCyc
Ensembl Genes	ENSRNOG00000006895	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000010010	ENTREZGENE
	ENSRNOT00000010010.5	UniProtKB/TrEMBL
	ENSRNOT00000082825.2	UniProtKB/TrEMBL
	ENSRNOT00000096693.1	UniProtKB/TrEMBL
	ENSRNOT00000099955.1	UniProtKB/TrEMBL
	ENSRNOT00000112514.1	UniProtKB/TrEMBL
	ENSRNOT00000116582.1	UniProtKB/TrEMBL
Gene3D-CATH	1.10.357.110	UniProtKB/TrEMBL
	Methyl-accepting chemotaxis protein	UniProtKB/TrEMBL
InterPro	Vps53	UniProtKB/TrEMBL
	Vps53_C	UniProtKB/TrEMBL
	Vps53_C_sf	UniProtKB/TrEMBL
	Vps53_N	UniProtKB/TrEMBL
KEGG Report	rno:287535	UniProtKB/TrEMBL
NCBI Gene	287535	ENTREZGENE
PANTHER	PTHR12820	UniProtKB/TrEMBL
	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 53 HOMOLOG	UniProtKB/TrEMBL
Pfam	VPS53_C	UniProtKB/TrEMBL
	Vps53_N	UniProtKB/TrEMBL
PhenoGen	Vps53	PhenoGen
RatGTEx	ENSRNOG00000006895	RatGTEx
UniProt	A0A8I5ZUQ6	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AQS5_RAT	UniProtKB/TrEMBL
	A0A8I6B4Q5_RAT	UniProtKB/TrEMBL
	A0A8I6GI69_RAT	UniProtKB/TrEMBL
	A6HGU5	ENTREZGENE, UniProtKB/TrEMBL
	B4F763	ENTREZGENE, UniProtKB/TrEMBL
	D3ZPE5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-04-02	Vps53	VPS53 subunit of GARP complex	Vps53	VPS53 GARP complex subunit	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-11-25	Vps53	VPS53 GARP complex subunit	Vps53	vacuolar protein sorting 53 homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-25	Vps53	vacuolar protein sorting 53 homolog (S. cerevisiae)	Vps53	vacuolar protein sorting 53 (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Vps53	vacuolar protein sorting 53 (yeast)	Vps53_predicted	vacuolar protein sorting 53 (yeast) (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-30	Vps53_predicted	vacuolar protein sorting 53 (yeast) (predicted)	RGD1311391_predicted	similar to hypothetical protein FLJ10979 (predicted)	Symbol and Name updated	1299863	APPROVED
2005-01-20	RGD1311391_predicted	similar to hypothetical protein FLJ10979 (predicted)	LOC287535_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC287535_predicted	similar to hypothetical protein FLJ10979 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM