VPS16 (VPS16 core subunit of CORVET and HOPS complexes) - Rat Genome Database

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Gene: VPS16 (VPS16 core subunit of CORVET and HOPS complexes) Canis lupus familiaris
Analyze
Symbol: VPS16
Name: VPS16 core subunit of CORVET and HOPS complexes
RGD ID: 12162819
Description: ENCODES a protein that exhibits actin filament binding (ortholog); INVOLVED IN symbiont entry into host cell (ortholog); ASSOCIATED WITH dystonia 30 (ortholog); genetic disease (ortholog); Huntington's disease-like 1 (ortholog); FOUND IN actin filament (ortholog); AP-3 adaptor complex (ortholog); axon (ortholog); INTERACTS WITH mocetinostat
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting 16 homolog A; vacuolar protein sorting-associated protein 16 homolog; VPS16, CORVET/HOPS core subunit; VPS16A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12418,401,440 - 18,424,605 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2418,399,572 - 18,424,510 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2418,230,648 - 18,253,873 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02418,822,276 - 18,845,277 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2418,820,406 - 18,845,244 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12418,415,491 - 18,438,476 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02418,526,233 - 18,549,247 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02418,854,786 - 18,877,793 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
mocetinostat  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
VPS16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12418,401,440 - 18,424,605 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2418,399,572 - 18,424,510 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2418,230,648 - 18,253,873 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02418,822,276 - 18,845,277 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2418,820,406 - 18,845,244 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12418,415,491 - 18,438,476 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02418,526,233 - 18,549,247 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02418,854,786 - 18,877,793 (-)NCBIUU_Cfam_GSD_1.0
VPS16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38202,840,745 - 2,866,732 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl202,840,703 - 2,866,732 (+)EnsemblGRCh38hg38GRCh38
GRCh37202,821,391 - 2,847,378 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36202,769,373 - 2,795,380 (+)NCBINCBI36Build 36hg18NCBI36
Build 34202,792,592 - 2,795,380NCBI
Celera202,882,628 - 2,909,733 (+)NCBICelera
Cytogenetic Map20p13NCBI
HuRef202,769,563 - 2,796,285 (+)NCBIHuRef
CHM1_1202,821,383 - 2,847,380 (+)NCBICHM1_1
T2T-CHM13v2.0202,871,419 - 2,897,578 (+)NCBIT2T-CHM13v2.0
Vps16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392130,265,744 - 130,286,189 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2130,266,259 - 130,286,189 (+)EnsemblGRCm39 Ensembl
GRCm382130,424,320 - 130,444,269 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2130,424,339 - 130,444,269 (+)EnsemblGRCm38mm10GRCm38
MGSCv372130,250,056 - 130,270,005 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362130,115,830 - 130,135,175 (+)NCBIMGSCv36mm8
Celera2131,648,775 - 131,668,719 (+)NCBICelera
Cytogenetic Map2F1NCBI
cM Map263.22NCBI
Vps16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83138,075,649 - 138,097,154 (+)NCBIGRCr8
mRatBN7.23117,622,534 - 117,644,041 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3117,622,542 - 117,646,441 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3121,519,900 - 121,541,340 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03130,115,373 - 130,136,866 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03127,776,026 - 127,797,466 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03122,947,887 - 122,969,543 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3122,947,913 - 122,969,541 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03129,448,219 - 129,469,258 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43118,037,765 - 118,058,841 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13117,943,337 - 117,964,412 (+)NCBI
Celera3116,436,997 - 116,458,059 (+)NCBICelera
Cytogenetic Map3q36NCBI
Vps16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541513,791,611 - 13,813,500 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541513,791,611 - 13,813,500 (+)NCBIChiLan1.0ChiLan1.0
VPS16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2213,812,589 - 3,837,504 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1203,809,414 - 3,834,329 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0202,931,553 - 2,956,604 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1202,695,335 - 2,720,032 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl202,695,335 - 2,720,030 (+)Ensemblpanpan1.1panPan2
Vps16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640167,446,685 - 167,469,186 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648515,879,327 - 15,900,544 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648515,879,324 - 15,900,544 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1732,803,412 - 32,825,933 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11732,803,596 - 32,825,974 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21737,174,405 - 37,196,780 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VPS16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1233,527,526 - 33,554,742 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl233,527,554 - 33,557,145 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607110,955,876 - 10,988,194 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247413,959,363 - 3,991,191 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247413,959,561 - 3,991,191 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VPS16
200 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 18 2 6 2 6 12 1 10 6
Low 5 4 4 4 6 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003639850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014107172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022408918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038433300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038433301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038508503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038508504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038571774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038571775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038636019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038636020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000010595   ⟹   ENSCAFP00000009824
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2418,399,572 - 18,424,510 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000074165   ⟹   ENSCAFP00000047505
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2418,401,483 - 18,424,510 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845028052   ⟹   ENSCAFP00845022071
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2418,820,406 - 18,845,166 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845028069   ⟹   ENSCAFP00845022084
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2418,822,294 - 18,845,244 (-)Ensembl
RefSeq Acc Id: XM_003639850   ⟹   XP_003639898
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12418,401,440 - 18,424,605 (-)NCBI
Dog10K_Boxer_Tasha2418,230,648 - 18,253,873 (-)NCBI
Sequence:
RefSeq Acc Id: XM_022408918   ⟹   XP_022264626
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12418,401,440 - 18,407,625 (-)NCBI
Dog10K_Boxer_Tasha2418,230,648 - 18,236,824 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038433300   ⟹   XP_038289228
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02418,822,276 - 18,845,277 (-)NCBI
RefSeq Acc Id: XM_038433301   ⟹   XP_038289229
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02418,822,276 - 18,828,452 (-)NCBI
RefSeq Acc Id: XM_038508503   ⟹   XP_038364431
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12418,415,491 - 18,438,476 (-)NCBI
RefSeq Acc Id: XM_038508504   ⟹   XP_038364432
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12418,415,491 - 18,421,667 (-)NCBI
RefSeq Acc Id: XM_038571774   ⟹   XP_038427702
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02418,854,786 - 18,877,793 (-)NCBI
RefSeq Acc Id: XM_038571775   ⟹   XP_038427703
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02418,854,786 - 18,860,963 (-)NCBI
RefSeq Acc Id: XM_038636019   ⟹   XP_038491947
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02418,526,233 - 18,549,247 (-)NCBI
RefSeq Acc Id: XM_038636020   ⟹   XP_038491948
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02418,526,233 - 18,532,410 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_003639898   ⟸   XM_003639850
- Peptide Label: isoform X1
- UniProtKB: A0A8P0SBY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022264626   ⟸   XM_022408918
- Peptide Label: isoform X2
- UniProtKB: A0A8P0SBY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000047505   ⟸   ENSCAFT00000074165
RefSeq Acc Id: ENSCAFP00000009824   ⟸   ENSCAFT00000010595
RefSeq Acc Id: XP_038364431   ⟸   XM_038508503
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038364432   ⟸   XM_038508504
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038491947   ⟸   XM_038636019
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038491948   ⟸   XM_038636020
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038289228   ⟸   XM_038433300
- Peptide Label: isoform X1
- UniProtKB: A0A8C0JR36 (UniProtKB/TrEMBL),   A0A8C0M5A1 (UniProtKB/TrEMBL),   A0A8P0SBY1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038289229   ⟸   XM_038433301
- Peptide Label: isoform X2
- UniProtKB: A0A8P0SBY1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038427702   ⟸   XM_038571774
- Peptide Label: isoform X1
- UniProtKB: A0A8C0JR36 (UniProtKB/TrEMBL),   A0A8C0M5A1 (UniProtKB/TrEMBL),   A0A8P0SBY1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038427703   ⟸   XM_038571775
- Peptide Label: isoform X2
- UniProtKB: A0A8P0SBY1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845022084   ⟸   ENSCAFT00845028069
RefSeq Acc Id: ENSCAFP00845022071   ⟸   ENSCAFT00845028052
Protein Domains
Vps16 C-terminal   Vps16 N-terminal

Promoters
RGD ID:13687541
Promoter ID:EPDNEW_C5608
Type:initiation region
Name:VPS16_1
Description:VPS16, CORVET/HOPS core subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12418,424,530 - 18,424,590EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000006534 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030003854 UniProtKB/TrEMBL
  ENSCAFG00040017127 UniProtKB/TrEMBL
  ENSCAFG00845015734 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000010595.5 UniProtKB/TrEMBL
  ENSCAFT00000074165.2 UniProtKB/TrEMBL
  ENSCAFT00030007484.1 UniProtKB/TrEMBL
  ENSCAFT00030007654.1 UniProtKB/TrEMBL
  ENSCAFT00040032416.1 UniProtKB/TrEMBL
  ENSCAFT00845028052 ENTREZGENE
  ENSCAFT00845028052.1 UniProtKB/TrEMBL
  ENSCAFT00845028069.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.780 UniProtKB/TrEMBL
InterPro VPS16 UniProtKB/TrEMBL
  Vps16_C UniProtKB/TrEMBL
  Vps16_C_sf UniProtKB/TrEMBL
  Vps16_N UniProtKB/TrEMBL
NCBI Gene VPS16 ENTREZGENE
PANTHER PTHR12811 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG UniProtKB/TrEMBL
Pfam Vps16_C UniProtKB/TrEMBL
  Vps16_N UniProtKB/TrEMBL
PIRSF VPS16 UniProtKB/TrEMBL
UniProt A0A8C0JR36 ENTREZGENE
  A0A8C0M5A1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0SWV0_CANLF UniProtKB/TrEMBL
  A0A8I3NNJ0_CANLF UniProtKB/TrEMBL
  A0A8I3P100_CANLF UniProtKB/TrEMBL
  A0A8P0NXL1_CANLF UniProtKB/TrEMBL
  A0A8P0SBY1 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:48278 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-30 VPS16  VPS16 core subunit of CORVET and HOPS complexes    VPS16, CORVET/HOPS core subunit  Symbol and/or name change 5135510 APPROVED