Vps13a (vacuolar protein sorting 13 homolog A) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Vps13a (vacuolar protein sorting 13 homolog A) Rattus norvegicus
Analyze
Symbol: Vps13a
Name: vacuolar protein sorting 13 homolog A
RGD ID: 1311340
Description: Predicted to be involved in several processes, including lysosomal protein catabolic process; protein retention in Golgi apparatus; and protein targeting to vacuole. Predicted to act upstream of or within several processes, including brain-derived neurotrophic factor receptor signaling pathway; long-term synaptic depression; and myeloid cell differentiation. Predicted to be located in several cellular components, including bounding membrane of organelle; neuronal dense core vesicle lumen; and sperm midpiece. Predicted to be active in several cellular components, including endoplasmic reticulum; mitochondrion; and neuronal cell body. Human ortholog(s) of this gene implicated in choreaacanthocytosis and choreatic disease. Orthologous to human VPS13A (vacuolar protein sorting 13 homolog A); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: chorein; intermembrane lipid transfer protein VPS13A; LOC309243; LOC361737; RGD1311340; similar to chorein isoform B; vacuolar protein sorting 13 homolog A (S. cerevisiae); vacuolar protein sorting 13A; vacuolar protein sorting 13A (yeast); vacuolar protein sorting-associated protein 13A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81223,328,784 - 223,555,500 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1223,328,784 - 223,555,331 (-)EnsemblGRCr8
mRatBN7.21213,901,999 - 214,128,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1213,901,999 - 214,128,555 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1222,230,525 - 222,462,915 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01229,165,841 - 229,392,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01221,985,083 - 222,217,463 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01235,352,513 - 235,813,597 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1235,653,121 - 235,813,030 (-)Ensemblrn6Rnor6.0
Rnor_5.01242,670,357 - 243,128,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41219,987,826 - 220,221,494 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1211,235,485 - 211,455,239 (-)NCBICelera
RGSC_v3.11220,153,337 - 220,385,366 (-)NCBI
Cytogenetic Map1q43NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amitrole  (EXP)
aristolochic acid A  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
clorgyline  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
Dibutyl phosphate  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
indometacin  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
testosterone  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. A conserved sorting-associated protein is mutant in chorea-acanthocytosis. Rampoldi L, etal., Nat Genet. 2001 Jun;28(2):119-20.
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15686477   PMID:22366033   PMID:25996471   PMID:29928881   PMID:30709847   PMID:30741634   PMID:34800366  


Genomics

Comparative Map Data
Vps13a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81223,328,784 - 223,555,500 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1223,328,784 - 223,555,331 (-)EnsemblGRCr8
mRatBN7.21213,901,999 - 214,128,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1213,901,999 - 214,128,555 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1222,230,525 - 222,462,915 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01229,165,841 - 229,392,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01221,985,083 - 222,217,463 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01235,352,513 - 235,813,597 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1235,653,121 - 235,813,030 (-)Ensemblrn6Rnor6.0
Rnor_5.01242,670,357 - 243,128,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41219,987,826 - 220,221,494 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1211,235,485 - 211,455,239 (-)NCBICelera
RGSC_v3.11220,153,337 - 220,385,366 (-)NCBI
Cytogenetic Map1q43NCBI
VPS13A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38977,177,534 - 77,421,537 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl977,177,445 - 77,421,537 (+)Ensemblhg38GRCh38
GRCh37979,792,450 - 80,036,453 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36978,982,181 - 79,222,219 (+)NCBIBuild 36Build 36hg18NCBI36
Celera950,369,484 - 50,609,533 (+)NCBICelera
Cytogenetic Map9q21.2NCBI
HuRef949,623,817 - 49,863,840 (+)NCBIHuRef
CHM1_1979,938,844 - 80,179,199 (+)NCBICHM1_1
T2T-CHM13v2.0989,334,100 - 89,578,104 (+)NCBIT2T-CHM13v2.0
Vps13a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391916,592,730 - 16,758,433 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1916,592,730 - 16,758,297 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381916,615,366 - 16,781,071 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1916,615,366 - 16,780,933 (-)Ensemblmm10GRCm38
MGSCv371916,691,164 - 16,855,417 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361916,683,693 - 16,847,946 (-)NCBIMGSCv36mm8
Celera1917,275,535 - 17,440,000 (-)NCBICelera
Cytogenetic Map19A- BNCBI
cM Map1911.71NCBI
Vps13a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555122,039,115 - 2,267,099 (-)Ensembl
ChiLan1.0NW_0049555122,037,803 - 2,267,197 (-)NCBIChiLan1.0ChiLan1.0
VPS13A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21176,337,834 - 76,581,678 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1976,343,550 - 76,587,617 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0947,424,921 - 47,668,150 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1976,032,292 - 76,275,155 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl976,032,286 - 76,269,636 (+)EnsemblpanPan2panpan1.1
VPS13A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1181,191,125 - 81,426,337 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl181,192,349 - 81,426,322 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha181,654,790 - 81,889,759 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0181,603,680 - 81,839,234 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl181,604,885 - 81,839,239 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1181,389,076 - 81,624,112 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0181,110,788 - 81,346,344 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0181,839,940 - 82,075,231 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vps13a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947128,315,230 - 128,566,983 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650312,606,014 - 12,858,005 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493650312,606,019 - 12,857,807 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS13A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1230,069,368 - 230,331,200 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11230,069,339 - 230,331,343 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21256,783,098 - 256,879,557 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS13A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11288,140,842 - 88,380,966 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1288,167,258 - 88,379,614 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603876,526,493 - 76,716,430 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps13a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248114,640,090 - 4,901,510 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248114,639,926 - 4,902,749 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps13a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1216,655,182 - 16,865,619 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps13a
1362 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:73
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000014800
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8693637Alc29Alcohol consumption QTL 292.70.258drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367243666627Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1207243873252243873Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1186658830266453731Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1210980612255980612Rat
2293673Bss27Bone structure and strength QTL 2718.630.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)1181059071226059071Rat
2293677Bss41Bone structure and strength QTL 419.380.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1181059071226059071Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1182039247227039247Rat
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1183564652228564652Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1205233991267096252Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1218829748263829748Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1186658830266453731Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1176288899270518180Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1193964073238964073Rat
8693661Alc34Alcohol consumption QTL 342.20.611drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367238041033Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
2293689Bss47Bone structure and strength QTL 477.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)1181059071226059071Rat
152025235Bw194Body weight QTL 1944.86body mass (VT:0001259)1132966869252856240Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1210980612255980612Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1139442053223964440Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
2293693Bss22Bone structure and strength QTL 2233.520.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1181059071226059071Rat
2300161Bmd43Bone mineral density QTL 438.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1181059071226059071Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1194575422239575422Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1193400541238400541Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1200449456256003563Rat
631214Bw61Body weight QTL613.40.0001intramuscular adipose amount (VT:0010044)intramuscular fat area (CMO:0001162)1182535316227535316Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1146080545243492863Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1207163993269633915Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1210980612255980612Rat
2300174Bmd42Bone mineral density QTL 428.40.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)1181059071226059071Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1153679879232414077Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1223134011262090599Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1160574007235238518Rat
2293654Bss30Bone structure and strength QTL 3032.650.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1181059071226059071Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1210980612255980612Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1207243873252243873Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
2300187Bmd41Bone mineral density QTL 418.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1181059071226059071Rat
2314011Gluco56Glucose level QTL 56blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1209203273254203273Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1202543537247543537Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
1358292Cm37Cardiac mass QTL 376.28e-07heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1205674651250674651Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1207243873252243873Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1208479811269633915Rat
634312Bp143Blood pressure QTL 14330.0002arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1203300512229359342Rat
1358294Bw37Body weight QTL 3750.000011body mass (VT:0001259)body weight (CMO:0000012)1180739993225739993Rat
724559Pancm1Pancreatic morphology QTL 17.1islet of Langerhans morphology trait (VT:0005215)pancreatic islet damage composite score (CMO:0001156)1191190115223964326Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1172718770228180370Rat
10059600Bp378Blood pressure QTL 3783.080.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1212738576257738576Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1194786607262083703Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1188241285250779312Rat
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1208798288253798288Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1139442053223964440Rat
1331790Bp201Blood pressure QTL 2013.127arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1221820316234540296Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1192995199237995199Rat
61403Niddm4Non-insulin dependent diabetes mellitus QTL 4blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1201464383246464383Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1186298393231298393Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1203675682248675682Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1205674651250674651Rat
1600380Niddm70Non-insulin dependent diabetes mellitus QTL 703.10.0008blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1185979875230979875Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
1582206Kidm33Kidney mass QTL 336.9kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1197807365233480676Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1210980612255980612Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1210980612255980612Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1193400541238400541Rat
634338Hcar4Hepatocarcinoma resistance QTL 44.6liver integrity trait (VT:0010547)liver tumorous lesion number to liver area ratio (CMO:0001210)1202851915223964440Rat
6903303Scl34Serum cholesterol QTL 342.50.0033blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)1173363824227535316Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1207099883252099883Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1210980612255980612Rat
8693618Alc25Alcohol consumption QTL 2530.28drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367238041033Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1191260175236260175Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1111949780228180370Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1185857683270518180Rat
2325727Pia41Pristane induced arthritis QTL 41joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1188241285233241285Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1210980612255980612Rat

Markers in Region
D1Got207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21214,072,102 - 214,072,315 (+)MAPPERmRatBN7.2
Rnor_6.01235,758,150 - 235,758,362NCBIRnor6.0
Rnor_5.01243,071,107 - 243,071,319UniSTSRnor5.0
RGSC_v3.41220,161,832 - 220,162,045RGDRGSC3.4
RGSC_v3.41220,161,833 - 220,162,045UniSTSRGSC3.4
Celera1211,405,264 - 211,405,466UniSTS
RGSC_v3.11220,325,855 - 220,326,068RGD
RH 2.0 Map11174.7RGD
Cytogenetic Map1q43UniSTS
D1Got218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21214,072,046 - 214,072,306 (+)MAPPERmRatBN7.2
Rnor_6.01235,758,094 - 235,758,353NCBIRnor6.0
Rnor_5.01243,071,051 - 243,071,310UniSTSRnor5.0
RGSC_v3.41220,161,776 - 220,162,036RGDRGSC3.4
RGSC_v3.41220,161,777 - 220,162,036UniSTSRGSC3.4
Celera1211,405,208 - 211,405,457UniSTS
RGSC_v3.11220,325,799 - 220,326,059RGD
RH 2.0 Map11174.9RGD
Cytogenetic Map1q43UniSTS
D1Got216  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21215,510,738 - 215,510,986 (-)MAPPERmRatBN7.2
Rnor_6.01235,520,066 - 235,520,313NCBIRnor6.0
Rnor_5.01242,834,382 - 242,834,629UniSTSRnor5.0
RGSC_v3.41221,680,328 - 221,680,576RGDRGSC3.4
RGSC_v3.41221,680,329 - 221,680,576UniSTSRGSC3.4
Celera1212,820,570 - 212,820,817UniSTS
RGSC_v3.11221,844,352 - 221,844,599RGD
RH 3.4 Map9758.1RGD
RH 3.4 Map9758.1UniSTS
Cytogenetic Map1q43UniSTS
RH127917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21213,923,813 - 213,924,002 (+)MAPPERmRatBN7.2
Rnor_6.01235,372,683 - 235,372,871NCBIRnor6.0
Rnor_5.01242,690,527 - 242,690,715UniSTSRnor5.0
RGSC_v3.41220,009,645 - 220,009,833UniSTSRGSC3.4
Celera1211,257,292 - 211,257,480UniSTS
RH 3.4 Map11619.92UniSTS
Cytogenetic Map1q43UniSTS
RH128324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21213,902,062 - 213,902,251 (+)MAPPERmRatBN7.2
Rnor_6.01235,352,577 - 235,352,765NCBIRnor6.0
Rnor_5.01242,670,421 - 242,670,609UniSTSRnor5.0
RGSC_v3.41219,987,890 - 219,988,078UniSTSRGSC3.4
Celera1211,235,549 - 211,235,737UniSTS
Cytogenetic Map1q43UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000014800   ⟹   ENSRNOP00000014800
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,390,117 - 223,555,180 (-)Ensembl
mRatBN7.2 Ensembl1213,963,334 - 214,128,404 (-)Ensembl
Rnor_6.0 Ensembl1235,653,121 - 235,813,030 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098661   ⟹   ENSRNOP00000077688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,328,784 - 223,555,331 (-)Ensembl
mRatBN7.2 Ensembl1213,902,861 - 214,128,555 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102736   ⟹   ENSRNOP00000085879
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,328,784 - 223,555,331 (-)Ensembl
mRatBN7.2 Ensembl1213,901,999 - 214,128,555 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000112707   ⟹   ENSRNOP00000082655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,352,776 - 223,555,331 (-)Ensembl
mRatBN7.2 Ensembl1213,925,991 - 214,128,555 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000142855   ⟹   ENSRNOP00000099419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,358,994 - 223,555,331 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000144564   ⟹   ENSRNOP00000107187
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,358,441 - 223,555,331 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000148487   ⟹   ENSRNOP00000106743
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,345,634 - 223,555,331 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000168353   ⟹   ENSRNOP00000103448
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1223,349,852 - 223,555,331 (-)Ensembl
RefSeq Acc Id: NM_001100975   ⟹   NP_001094445
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,328,784 - 223,555,331 (-)NCBI
mRatBN7.21213,901,999 - 214,128,555 (-)NCBI
Rnor_6.01235,352,513 - 235,813,181 (-)NCBI
Rnor_5.01242,670,357 - 243,128,666 (-)NCBI
RGSC_v3.41219,987,826 - 220,221,494 (-)RGD
Celera1211,235,485 - 211,455,239 (-)RGD
Sequence:
RefSeq Acc Id: XM_039079911   ⟹   XP_038935839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,350,340 - 223,555,500 (-)NCBI
mRatBN7.21213,923,553 - 214,128,633 (-)NCBI
RefSeq Acc Id: XM_039079914   ⟹   XP_038935842
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,350,340 - 223,555,500 (-)NCBI
mRatBN7.21213,923,553 - 214,128,633 (-)NCBI
RefSeq Acc Id: XM_039079915   ⟹   XP_038935843
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,329,112 - 223,490,671 (-)NCBI
mRatBN7.21213,902,312 - 214,063,893 (-)NCBI
RefSeq Acc Id: XM_039079920   ⟹   XP_038935848
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,397,871 - 223,555,500 (-)NCBI
mRatBN7.21213,971,088 - 214,128,638 (-)NCBI
RefSeq Acc Id: XM_063264468   ⟹   XP_063120538
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81223,358,994 - 223,555,500 (-)NCBI
RefSeq Acc Id: NP_001094445   ⟸   NM_001100975
- UniProtKB: A0A8I6A4A2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014800   ⟸   ENSRNOT00000014800
RefSeq Acc Id: XP_038935843   ⟸   XM_039079915
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038935839   ⟸   XM_039079911
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935842   ⟸   XM_039079914
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZJJ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935848   ⟸   XM_039079920
- Peptide Label: isoform X5
- UniProtKB: D4A899 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000082655   ⟸   ENSRNOT00000112707
Ensembl Acc Id: ENSRNOP00000077688   ⟸   ENSRNOT00000098661
Ensembl Acc Id: ENSRNOP00000085879   ⟸   ENSRNOT00000102736
RefSeq Acc Id: XP_063120538   ⟸   XM_063264468
- Peptide Label: isoform X3
- UniProtKB: D4A899 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099419   ⟸   ENSRNOT00000142855
Ensembl Acc Id: ENSRNOP00000103448   ⟸   ENSRNOT00000168353
Ensembl Acc Id: ENSRNOP00000107187   ⟸   ENSRNOT00000144564
Ensembl Acc Id: ENSRNOP00000106743   ⟸   ENSRNOT00000148487
Protein Domains
Chorein N-terminal   Intermembrane lipid transfer protein VPS13-like C-   Vacuolar protein sorting-associated protein 13 VPS13   VPS13-like middle region

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A899-F1-model_v2 AlphaFold D4A899 1-2335 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311340 AgrOrtholog
BioCyc Gene G2FUF-56217 BioCyc
Ensembl Genes ENSRNOG00000025539 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014800 ENTREZGENE
  ENSRNOT00000014800.9 UniProtKB/TrEMBL
  ENSRNOT00000098661.2 UniProtKB/TrEMBL
  ENSRNOT00000102736 ENTREZGENE
  ENSRNOT00000102736.2 UniProtKB/TrEMBL
  ENSRNOT00000112707.2 UniProtKB/TrEMBL
  ENSRNOT00000142855 ENTREZGENE
  ENSRNOT00000142855.1 UniProtKB/TrEMBL
  ENSRNOT00000144564.1 UniProtKB/TrEMBL
  ENSRNOT00000148487.1 UniProtKB/TrEMBL
  ENSRNOT00000168353 ENTREZGENE
  ENSRNOT00000168353.1 UniProtKB/TrEMBL
InterPro SHR-BD UniProtKB/TrEMBL
  VPS13 UniProtKB/TrEMBL
  VPS13-like_C UniProtKB/TrEMBL
  VPS13-like_M UniProtKB/TrEMBL
  VPS13_N UniProtKB/TrEMBL
KEGG Report rno:309243 UniProtKB/TrEMBL
NCBI Gene 309243 ENTREZGENE
PANTHER PTHR16166 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 13A UniProtKB/TrEMBL
Pfam Chorein_N UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_M UniProtKB/TrEMBL
  VPS13_VAB UniProtKB/TrEMBL
PhenoGen Vps13a PhenoGen
RatGTEx ENSRNOG00000025539 RatGTEx
UniProt A0A8I5ZJJ9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZVN0_RAT UniProtKB/TrEMBL
  A0A8I6A4A2 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L4R1_RAT UniProtKB/TrEMBL
  A0ABK0LDG7_RAT UniProtKB/TrEMBL
  A0ABK0LY18_RAT UniProtKB/TrEMBL
  A0ABK0M1B5_RAT UniProtKB/TrEMBL
  D4A899 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-19 Vps13a  vacuolar protein sorting 13 homolog A  Vps13a  vacuolar protein sorting 13A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 Vps13a  vacuolar protein sorting 13A  Vps13a  vacuolar protein sorting 13 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-06-15 Vps13a  vacuolar protein sorting 13 homolog A (S. cerevisiae)  Vps13a_predicted  vacuolar protein sorting 13A (yeast) (predicted)  Data merged from RGD:1304705 1643240 APPROVED
2008-09-25 Vps13a  vacuolar protein sorting 13 homolog A (S. cerevisiae)  Vps13a  vacuolar protein sorting 13A (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-27 Vps13a  vacuolar protein sorting 13A (yeast)  RGD1311340_predicted  similar to chorein isoform B; chorein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1311340_predicted  similar to chorein isoform B; chorein (predicted)  LOC309243_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC309243_predicted  similar to chorein isoform B; chorein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Vps13a_predicted  vacuolar protein sorting 13A (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED