VPS35 (VPS35 retromer complex component) - Rat Genome Database

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Gene: VPS35 (VPS35 retromer complex component) Canis lupus familiaris
Analyze
Symbol: VPS35
Name: VPS35 retromer complex component
RGD ID: 12429909
Description: ENCODES a protein that exhibits D1 dopamine receptor binding (inferred); INVOLVED IN lysosome organization (ortholog); modulation of chemical synaptic transmission (ortholog); negative regulation of gene expression (ortholog); PARTICIPATES IN altered retromer-mediated pathway; Parkinson's disease pathway; retromer-mediated pathway; ASSOCIATED WITH genetic disease (ortholog); glycogen storage disease IXB (ortholog); late onset Parkinson's disease (ortholog); FOUND IN cytoplasm (ortholog); dopaminergic synapse (ortholog); glutamatergic synapse (ortholog); INTERACTS WITH mocetinostat
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vacuolar protein sorting 35 homolog; vacuolar protein sorting-associated protein 35; VPS35, retromer complex component
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1158,428,073 - 8,454,601 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl158,428,172 - 8,454,049 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,581,899 - 8,608,418 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0158,544,407 - 8,570,955 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl158,544,515 - 8,571,199 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1158,373,461 - 8,399,977 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0158,454,130 - 8,480,928 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0158,469,932 - 8,496,696 (+)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

Biological Process
endocytic recycling  (IEA)
lysosome organization  (ISO)
mitochondrial fragmentation involved in apoptotic process  (IEA)
mitochondrion to lysosome vesicle-mediated transport  (IEA)
modulation of chemical synaptic transmission  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of inflammatory response  (IEA)
negative regulation of late endosome to lysosome transport  (IEA)
negative regulation of lysosomal protein catabolic process  (ISO)
negative regulation of protein homooligomerization  (ISO)
negative regulation of protein localization  (ISO)
neurotransmitter receptor transport, endosome to plasma membrane  (IEA)
neurotransmitter receptor transport, endosome to postsynaptic membrane  (ISO)
positive regulation of canonical Wnt signaling pathway  (ISO)
positive regulation of dopamine biosynthetic process  (ISO)
positive regulation of dopamine receptor signaling pathway  (IEA)
positive regulation of gene expression  (IEA)
positive regulation of locomotion involved in locomotory behavior  (ISO)
positive regulation of mitochondrial fission  (IEA)
positive regulation of protein catabolic process  (IEA)
positive regulation of protein localization to cell periphery  (IEA)
positive regulation of Wnt protein secretion  (ISO)
protein destabilization  (ISO)
protein localization to endosome  (IEA)
protein localization to organelle  (ISO)
protein transport  (IEA)
regulation of dendritic spine maintenance  (IEA)
regulation of mitochondrion organization  (IEA)
regulation of postsynapse assembly  (ISO)
regulation of protein metabolic process  (IEA)
regulation of protein stability  (IEA)
regulation of synapse maturation  (ISO)
regulation of terminal button organization  (IEA)
retrograde transport, endosome to Golgi  (IEA)
transcytosis  (IEA)
vesicle-mediated transport in synapse  (ISO)
voluntary musculoskeletal movement  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
VPS35
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1158,428,073 - 8,454,601 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl158,428,172 - 8,454,049 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,581,899 - 8,608,418 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0158,544,407 - 8,570,955 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl158,544,515 - 8,571,199 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1158,373,461 - 8,399,977 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0158,454,130 - 8,480,928 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0158,469,932 - 8,496,696 (+)NCBIUU_Cfam_GSD_1.0
VPS35
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381646,656,132 - 46,689,178 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1646,656,132 - 46,689,518 (-)EnsemblGRCh38hg38GRCh38
GRCh371646,690,044 - 46,723,090 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361645,251,090 - 45,280,645 (-)NCBINCBI36Build 36hg18NCBI36
Build 341645,251,091 - 45,280,593NCBI
Celera1631,201,751 - 31,231,306 (-)NCBICelera
Cytogenetic Map16q11.2NCBI
HuRef1632,582,305 - 32,611,908 (-)NCBIHuRef
CHM1_11648,100,524 - 48,130,101 (-)NCBICHM1_1
T2T-CHM13v2.01652,452,996 - 52,486,052 (-)NCBIT2T-CHM13v2.0
Vps35
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,987,014 - 86,026,146 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl885,987,021 - 86,026,431 (-)EnsemblGRCm39 Ensembl
GRCm38885,260,385 - 85,299,517 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl885,260,392 - 85,299,802 (-)EnsemblGRCm38mm10GRCm38
MGSCv37887,784,291 - 87,823,396 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36888,150,497 - 88,189,603 (-)NCBIMGSCv36mm8
Celera889,541,447 - 89,580,450 (-)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.61NCBI
Vps35
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81937,938,989 - 37,974,887 (+)NCBIGRCr8
mRatBN7.21921,765,771 - 21,801,620 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1921,765,749 - 21,801,618 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1923,455,852 - 23,491,776 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01928,650,370 - 28,686,295 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01931,613,200 - 31,649,098 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01927,464,937 - 27,500,636 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1927,464,937 - 27,500,636 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01938,430,733 - 38,466,263 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41923,124,790 - 23,161,655 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1921,625,446 - 21,661,413 (+)NCBICelera
Cytogenetic Map19q11NCBI
Vps35
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955448204,991 - 240,160 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955448207,582 - 240,264 (-)NCBIChiLan1.0ChiLan1.0
VPS35
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21856,118,897 - 56,148,460 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11662,024,010 - 62,053,586 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01626,924,901 - 26,954,443 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11645,815,716 - 45,846,672 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1645,817,371 - 45,846,531 (-)Ensemblpanpan1.1panPan2
Vps35
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934959,511,247 - 59,538,597 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647550,321 - 78,097 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647550,476 - 77,797 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS35
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl637,944,127 - 37,986,171 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1637,944,099 - 37,977,091 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
VPS35
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1532,509,037 - 32,539,371 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl532,508,580 - 32,539,343 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604744,064,261 - 44,095,348 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps35
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624914160,483 - 188,490 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624914160,483 - 188,534 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VPS35
340 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence


Ensembl Acc Id: ENSCAFT00000005941   ⟹   ENSCAFP00000005503
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl158,428,172 - 8,454,049 (+)Ensembl
Ensembl Acc Id: ENSCAFT00000070851   ⟹   ENSCAFP00000064146
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl158,428,172 - 8,453,989 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845030802   ⟹   ENSCAFP00845024149
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl158,544,515 - 8,571,199 (+)Ensembl
RefSeq Acc Id: XM_005628985   ⟹   XP_005629042
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1158,429,722 - 8,454,601 (+)NCBI
Dog10K_Boxer_Tasha158,583,556 - 8,608,418 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038495624   ⟹   XP_038351552
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1158,373,461 - 8,399,977 (+)NCBI
RefSeq Acc Id: XM_038495625   ⟹   XP_038351553
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1158,375,118 - 8,399,977 (+)NCBI
RefSeq Acc Id: XM_038557980   ⟹   XP_038413908
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0158,469,932 - 8,496,696 (+)NCBI
RefSeq Acc Id: XM_038557981   ⟹   XP_038413909
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0158,471,588 - 8,496,696 (+)NCBI
RefSeq Acc Id: XM_038621851   ⟹   XP_038477779
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0158,454,130 - 8,480,928 (+)NCBI
RefSeq Acc Id: XM_038621852   ⟹   XP_038477780
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0158,455,786 - 8,480,928 (+)NCBI
RefSeq Acc Id: XM_038687613   ⟹   XP_038543541
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0158,544,407 - 8,570,955 (+)NCBI
RefSeq Acc Id: XM_038687614   ⟹   XP_038543542
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0158,546,064 - 8,570,955 (+)NCBI
RefSeq Acc Id: XM_532570   ⟹   XP_532570
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1158,428,073 - 8,454,601 (+)NCBI
Dog10K_Boxer_Tasha158,581,899 - 8,608,418 (+)NCBI
Sequence:
RefSeq Acc Id: XP_532570   ⟸   XM_532570
- Peptide Label: isoform X1
- UniProtKB: A0A8C0KCU5 (UniProtKB/TrEMBL),   A0A8C0NC57 (UniProtKB/TrEMBL),   A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005629042   ⟸   XM_005628985
- Peptide Label: isoform X2
- UniProtKB: A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000005503   ⟸   ENSCAFT00000005941
Ensembl Acc Id: ENSCAFP00000064146   ⟸   ENSCAFT00000070851
RefSeq Acc Id: XP_038351552   ⟸   XM_038495624
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038351553   ⟸   XM_038495625
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038477779   ⟸   XM_038621851
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038477780   ⟸   XM_038621852
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038543541   ⟸   XM_038687613
- Peptide Label: isoform X1
- UniProtKB: A0A8C0KCU5 (UniProtKB/TrEMBL),   A0A8C0NC57 (UniProtKB/TrEMBL),   A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038543542   ⟸   XM_038687614
- Peptide Label: isoform X2
- UniProtKB: A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038413908   ⟸   XM_038557980
- Peptide Label: isoform X1
- UniProtKB: A0A8C0KCU5 (UniProtKB/TrEMBL),   A0A8C0NC57 (UniProtKB/TrEMBL),   A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038413909   ⟸   XM_038557981
- Peptide Label: isoform X2
- UniProtKB: A0A8I3NTA9 (UniProtKB/TrEMBL),   A0A8P0S9E6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845024149   ⟸   ENSCAFT00845030802

Promoters
RGD ID:13685876
Promoter ID:EPDNEW_C3944
Type:initiation region
Name:VPS35_1
Description:VPS35, retromer complex component
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
CanFam3.1158,428,191 - 8,428,251EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000003688 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030014041 UniProtKB/TrEMBL
  ENSCAFG00040009703 UniProtKB/TrEMBL
  ENSCAFG00845017379 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000005941.5 UniProtKB/TrEMBL
  ENSCAFT00030026016.1 UniProtKB/TrEMBL
  ENSCAFT00040018017.1 UniProtKB/TrEMBL
  ENSCAFT00845030802 ENTREZGENE
  ENSCAFT00845030802.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.660 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  Vps35 UniProtKB/TrEMBL
  Vps35_C UniProtKB/TrEMBL
NCBI Gene VPS35 ENTREZGENE
PANTHER PTHR11099 UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35 UniProtKB/TrEMBL
Pfam Vps35 UniProtKB/TrEMBL
PIRSF Retromer_Vps35 UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt A0A8C0KCU5 ENTREZGENE
  A0A8C0NC57 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NTA9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0S9E6 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:48285 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-30 VPS35  VPS35 retromer complex component    VPS35, retromer complex component  Symbol and/or name change 5135510 APPROVED