Vps53 (VPS53 subunit of GARP complex) - Rat Genome Database

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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. Located in recycling endosome and trans-Golgi network. 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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81061,418,076 - 61,536,912 (-)NCBIGRCr8
mRatBN7.21060,919,820 - 61,038,674 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1060,919,820 - 61,038,676 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1065,561,939 - 65,680,825 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,067,390 - 65,186,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01060,537,918 - 60,656,979 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01064,218,596 - 64,341,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1064,222,276 - 64,341,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01063,672,733 - 63,793,858 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41063,410,886 - 63,535,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11063,424,683 - 63,543,200 (-)NCBI
Celera1059,935,404 - 60,054,107 (-)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. EARP is a multisubunit tethering complex involved in endocytic recycling. Schindler C, etal., Nat Cell Biol. 2015 May;17(5):639-50. doi: 10.1038/ncb3129. Epub 2015 Mar 23.
6. 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:27440922  


Genomics

Comparative Map Data
Vps53
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81061,418,076 - 61,536,912 (-)NCBIGRCr8
mRatBN7.21060,919,820 - 61,038,674 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1060,919,820 - 61,038,676 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1065,561,939 - 65,680,825 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,067,390 - 65,186,273 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01060,537,918 - 60,656,979 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01064,218,596 - 64,341,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1064,222,276 - 64,341,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01063,672,733 - 63,793,858 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41063,410,886 - 63,535,682 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11063,424,683 - 63,543,200 (-)NCBI
Celera1059,935,404 - 60,054,107 (-)NCBICelera
Cytogenetic Map10q24NCBI
VPS53
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3817508,668 - 714,839 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl17508,503 - 721,717 (-)EnsemblGRCh38hg38GRCh38
GRCh3717411,908 - 618,079 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3617382,698 - 564,758 (-)NCBINCBI36Build 36hg18NCBI36
Celera17423,924 - 629,862 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef17325,008 - 528,642 (-)NCBIHuRef
CHM1_117418,907 - 623,396 (-)NCBICHM1_1
T2T-CHM13v2.017391,960 - 599,311 (-)NCBIT2T-CHM13v2.0
Vps53
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391175,937,052 - 76,070,464 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1175,937,052 - 76,070,473 (-)EnsemblGRCm39 Ensembl
GRCm381176,046,226 - 76,179,638 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,046,226 - 76,179,647 (-)EnsemblGRCm38mm10GRCm38
MGSCv371175,859,728 - 75,993,132 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361175,862,421 - 75,995,825 (-)NCBIMGSCv36mm8
Celera1183,555,285 - 83,692,488 (-)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.92NCBI
Vps53
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554812,130,888 - 2,264,924 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554812,130,669 - 2,265,065 (-)NCBIChiLan1.0ChiLan1.0
VPS53
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,042,929 - 8,261,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1179,602,776 - 9,812,194 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v017400,048 - 576,119 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.117416,136 - 604,705 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl17414,782 - 604,705 (-)Ensemblpanpan1.1panPan2
VPS53
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1945,074,066 - 45,239,569 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl945,074,100 - 45,214,066 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha944,224,566 - 44,391,993 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,892,548 - 46,060,240 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,892,566 - 46,035,516 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1944,670,971 - 44,838,890 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,964,695 - 45,132,085 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0945,043,233 - 45,211,135 (+)NCBIUU_Cfam_GSD_1.0
Vps53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560244,189,381 - 44,329,957 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365387,067,327 - 7,205,768 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365387,067,332 - 7,207,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS53
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1247,143,098 - 47,291,161 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11247,141,749 - 47,291,169 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21249,308,850 - 49,456,068 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS53
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.116302,771 - 464,572 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl16303,414 - 464,574 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605921,622,848 - 21,752,483 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps53
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247863,614,811 - 3,778,069 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247863,614,775 - 3,779,644 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vps53
773 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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103571058068663659Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
152025227Bw195Body weight QTL 1955.73body mass (VT:0001259)104698969968663659Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
152025224Bw193Body weight QTL 1936.47body mass (VT:0001259)105166340575085664Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)104944455181709989Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat

Markers in Region
D10Got79  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,988,321 - 60,988,448 (+)MAPPERmRatBN7.2
Rnor_6.01064,290,723 - 64,290,849NCBIRnor6.0
Rnor_5.01063,722,456 - 63,722,582UniSTSRnor5.0
RGSC_v3.41063,481,417 - 63,481,544RGDRGSC3.4
RGSC_v3.41063,481,418 - 63,481,544UniSTSRGSC3.4
RGSC_v3.11063,495,040 - 63,495,167RGD
Celera1060,003,799 - 60,003,925UniSTS
RH 2.0 Map10637.9RGD
Cytogenetic Map10q24UniSTS
D10Got83  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,943,408 - 60,943,565 (+)MAPPERmRatBN7.2
Rnor_6.01064,245,818 - 64,245,974NCBIRnor6.0
Celera1059,958,961 - 59,959,105UniSTS
RH 2.0 Map10642.8RGD
Cytogenetic Map10q24UniSTS
RH143717  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,987,569 - 60,987,676 (+)MAPPERmRatBN7.2
Rnor_6.01064,289,971 - 64,290,077NCBIRnor6.0
Rnor_5.01063,723,228 - 63,723,334UniSTSRnor5.0
RGSC_v3.41063,480,666 - 63,480,772UniSTSRGSC3.4
Celera1060,003,047 - 60,003,153UniSTS
Cytogenetic Map10q24UniSTS
BF388451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,993,383 - 60,993,627 (+)MAPPERmRatBN7.2
Rnor_6.01064,295,785 - 64,296,028NCBIRnor6.0
Rnor_5.01063,717,277 - 63,717,520UniSTSRnor5.0
RGSC_v3.41063,486,329 - 63,486,572UniSTSRGSC3.4
Celera1060,008,861 - 60,009,104UniSTS
Cytogenetic Map10q24UniSTS
BF390779  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,982,373 - 60,982,528 (+)MAPPERmRatBN7.2
Rnor_6.01064,284,775 - 64,284,929NCBIRnor6.0
Rnor_5.01063,728,392 - 63,728,546UniSTSRnor5.0
RGSC_v3.41063,475,462 - 63,475,616UniSTSRGSC3.4
Celera1059,997,851 - 59,998,005UniSTS
Cytogenetic Map10q24UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000010010   ⟹   ENSRNOP00000010010
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,820 - 61,038,674 (-)Ensembl
Rnor_6.0 Ensembl1064,222,276 - 64,341,109 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082825   ⟹   ENSRNOP00000074043
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,873 - 61,038,676 (-)Ensembl
Rnor_6.0 Ensembl1064,222,285 - 64,341,066 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096693   ⟹   ENSRNOP00000096444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,820 - 61,038,327 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000099955   ⟹   ENSRNOP00000081957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,820 - 61,038,456 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000112514   ⟹   ENSRNOP00000089534
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,820 - 61,038,674 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116582   ⟹   ENSRNOP00000096750
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1060,919,820 - 61,034,347 (-)Ensembl
RefSeq Acc Id: NM_001105813   ⟹   NP_001099283
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81061,418,076 - 61,536,912 (-)NCBI
mRatBN7.21060,919,820 - 61,038,674 (-)NCBI
Rnor_6.01064,222,232 - 64,341,064 (-)NCBI
Rnor_5.01063,672,733 - 63,793,858 (+)NCBI
RGSC_v3.41063,410,886 - 63,535,682 (-)RGD
Celera1059,935,404 - 60,054,107 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085521   ⟹   XP_038941449
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81061,418,125 - 61,507,108 (-)NCBI
mRatBN7.21060,919,869 - 61,004,995 (-)NCBI
RefSeq Acc Id: NP_001099283   ⟸   NM_001105813
- UniProtKB: D3ZPE5 (UniProtKB/TrEMBL),   A6HGU5 (UniProtKB/TrEMBL),   B4F763 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074043   ⟸   ENSRNOT00000082825
Ensembl Acc Id: ENSRNOP00000010010   ⟸   ENSRNOT00000010010
RefSeq Acc Id: XP_038941449   ⟸   XM_039085521
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZUQ6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000096444   ⟸   ENSRNOT00000096693
Ensembl Acc Id: ENSRNOP00000081957   ⟸   ENSRNOT00000099955
Ensembl Acc Id: ENSRNOP00000096750   ⟸   ENSRNOT00000116582
Ensembl 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 AssemblyChrPosition (strand)Source
Rnor_6.01064,341,063 - 64,341,123EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311391 AgrOrtholog
BioCyc Gene G2FUF-24170 BioCyc
Ensembl Genes ENSRNOG00000006895 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript 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