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 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) Chlorocebus sabaeus
Analyze
Symbol: VPS13A
Name: vacuolar protein sorting 13 homolog A
RGD ID: 18731522
Description: INVOLVED IN adult locomotory behavior (ortholog); autophagy (ortholog); brain-derived neurotrophic factor receptor signaling pathway (ortholog); ASSOCIATED WITH choreaacanthocytosis (ortholog); choreatic disease (ortholog); genetic disease (ortholog); FOUND IN endoplasmic reticulum (ortholog); mitochondrion (ortholog); neuron projection (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting-associated protein 13A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603876,526,493 - 76,716,430 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603876,526,493 - 76,716,430 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37979,792,450 - 80,036,453 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36978,982,181 - 79,222,219 (+)NCBINCBI36Build 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 Ensembl
GRCm381916,615,366 - 16,781,071 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1916,615,366 - 16,780,933 (-)EnsemblGRCm38mm10GRCm38
MGSCv371916,691,164 - 16,855,417 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361916,683,693 - 16,847,946 (-)NCBIMGSCv36mm8
Celera1917,275,535 - 17,440,000 (-)NCBICelera
Cytogenetic Map19A- BNCBI
cM Map1911.71NCBI
Vps13a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81223,328,784 - 223,555,500 (-)NCBIGRCr8
mRatBN7.21213,901,999 - 214,128,638 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1213,901,999 - 214,128,555 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1222,230,525 - 222,462,915 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01229,165,841 - 229,392,426 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01221,985,083 - 222,217,463 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01235,352,513 - 235,813,597 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1235,653,121 - 235,813,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01242,670,357 - 243,128,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41219,987,826 - 220,221,494 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11220,153,337 - 220,385,366 (-)NCBI
Celera1211,235,485 - 211,455,239 (-)NCBICelera
Cytogenetic Map1q43NCBI
Vps13a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555122,039,115 - 2,267,099 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha181,654,790 - 81,889,759 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0181,603,680 - 81,839,234 (-)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11230,069,339 - 230,331,343 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21256,783,098 - 256,879,557 (+)NCBISscrofa10.2Sscrofa10.2susScr3
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248114,639,926 - 4,902,749 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VPS13A
5259 total Variants

Expression

RNA-SEQ Expression

ectoderm
endocrine system
hemolymphoid system
mesenchyme
mesoderm
nervous system
reproductive system
76 36 20 36 36 60 20

Sequence


Ensembl Acc Id: ENSCSAT00000005821   ⟹   ENSCSAP00000004034
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl1288,167,258 - 88,379,614 (+)Ensembl
RefSeq Acc Id: XM_037998526   ⟹   XP_037854454
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603876,526,493 - 76,716,430 (+)NCBI
RefSeq Acc Id: XM_037998527   ⟹   XP_037854455
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603876,526,493 - 76,682,398 (+)NCBI
RefSeq Acc Id: XM_037998528   ⟹   XP_037854456
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603876,526,493 - 76,682,398 (+)NCBI
RefSeq Acc Id: XM_037998529   ⟹   XP_037854457
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603876,582,966 - 76,716,430 (+)NCBI
RefSeq Acc Id: XR_005240458
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603876,526,493 - 76,716,430 (+)NCBI
Protein Sequences
Protein RefSeqs XP_037854454 (Get FASTA)   NCBI Sequence Viewer  
  XP_037854455 (Get FASTA)   NCBI Sequence Viewer  
  XP_037854456 (Get FASTA)   NCBI Sequence Viewer  
  XP_037854457 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000004034.1
Ensembl Acc Id: ENSCSAP00000004034   ⟸   ENSCSAT00000005821
RefSeq Acc Id: XP_037854454   ⟸   XM_037998526
- Peptide Label: isoform X1
- UniProtKB: A0A0D9R5Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037854456   ⟸   XM_037998528
- Peptide Label: isoform X3
- UniProtKB: A0A0D9R5Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037854455   ⟸   XM_037998527
- Peptide Label: isoform X2
- UniProtKB: A0A0D9R5Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037854457   ⟸   XM_037998529
- Peptide Label: isoform X4


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000007781 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000005821.1 UniProtKB/TrEMBL
InterPro Autophagy-rel_C UniProtKB/TrEMBL
  SHR-BD UniProtKB/TrEMBL
  VPS13 UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_mid_rpt UniProtKB/TrEMBL
  VPS13_N2 UniProtKB/TrEMBL
NCBI Gene VPS13A ENTREZGENE
PANTHER PTHR16166 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 13A UniProtKB/TrEMBL
Pfam ATG_C UniProtKB/TrEMBL
  SHR-BD UniProtKB/TrEMBL
  VPS13 UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_C UniProtKB/TrEMBL
  VPS13_mid_rpt UniProtKB/TrEMBL
UniProt A0A0D9R5Z5 ENTREZGENE, UniProtKB/TrEMBL