Vps36 (vacuolar protein sorting 36 homolog) - Rat Genome Database

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Gene: Vps36 (vacuolar protein sorting 36 homolog) Rattus norvegicus
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Symbol: Vps36
Name: vacuolar protein sorting 36 homolog
RGD ID: 1309754
Description: Predicted to enable ubiquitin binding activity. Predicted to be involved in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway. Predicted to be located in cytosol; late endosome; and lysosome. Predicted to be part of ESCRT II complex. Predicted to be active in late endosome membrane. Orthologous to human VPS36 (vacuolar protein sorting 36 homolog); PARTICIPATES IN endocytosis pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ELL-associated protein of 45 kDa; ESCRT-II complex subunit VPS36; LOC290851; RGD1309754; similar to RIKEN cDNA 2210415M20; vacuolar protein sorting 36; vacuolar protein sorting 36 (yeast); vacuolar protein sorting 36 homolog (S. cerevisiae); vacuolar protein-sorting-associated protein 36
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
GRCr81676,512,851 - 76,537,235 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1676,512,860 - 76,537,246 (-)EnsemblGRCr8
mRatBN7.21669,810,404 - 69,834,789 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1669,808,193 - 69,834,810 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,084,083 - 75,108,470 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,522,770 - 78,547,313 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01673,772,051 - 73,796,601 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01674,719,642 - 74,743,921 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,719,553 - 74,743,927 (-)Ensemblrn6Rnor6.0
Rnor_5.01674,355,181 - 74,378,989 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41674,462,427 - 74,486,889 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1667,699,712 - 67,723,982 (-)NCBICelera
RGSC_v3.11674,462,685 - 74,487,153 (-)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
cytosol  (ISO)
endosome  (IEA,ISO,ISS)
ESCRT II complex  (IBA,IEA,ISO)
late endosome  (IEA,ISO)
late endosome membrane  (IBA,IEA,ISO)
lysosome  (IEA,ISO)
membrane  (IEA)
nucleus  (IEA)
plasma membrane  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11278625   PMID:12477932   PMID:15057822   PMID:15755741   PMID:16973552   PMID:17010938   PMID:19056867   PMID:20682791   PMID:22871113   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Vps36
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81676,512,851 - 76,537,235 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1676,512,860 - 76,537,246 (-)EnsemblGRCr8
mRatBN7.21669,810,404 - 69,834,789 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1669,808,193 - 69,834,810 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,084,083 - 75,108,470 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,522,770 - 78,547,313 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01673,772,051 - 73,796,601 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01674,719,642 - 74,743,921 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,719,553 - 74,743,927 (-)Ensemblrn6Rnor6.0
Rnor_5.01674,355,181 - 74,378,989 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41674,462,427 - 74,486,889 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1667,699,712 - 67,723,982 (-)NCBICelera
RGSC_v3.11674,462,685 - 74,487,153 (-)NCBI
Cytogenetic Map16q12.5NCBI
VPS36
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381352,412,606 - 52,450,634 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1352,412,602 - 52,450,684 (-)Ensemblhg38GRCh38
GRCh371352,986,741 - 53,024,769 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361351,884,738 - 51,922,764 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341351,887,319 - 51,922,735NCBI
Celera1333,972,434 - 34,010,460 (+)NCBICelera
Cytogenetic Map13q14.3NCBI
HuRef1333,725,057 - 33,763,914 (-)NCBIHuRef
CHM1_11352,954,794 - 52,992,839 (-)NCBICHM1_1
T2T-CHM13v2.01351,627,427 - 51,665,457 (-)NCBIT2T-CHM13v2.0
Vps36
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39822,682,849 - 22,710,969 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl822,682,825 - 22,710,859 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38822,192,833 - 22,220,953 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl822,192,809 - 22,220,843 (+)Ensemblmm10GRCm38
MGSCv37823,303,332 - 23,329,069 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36823,658,405 - 23,684,142 (+)NCBIMGSCv36mm8
Celera823,685,519 - 23,711,451 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map811.14NCBI
Vps36
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554315,443,050 - 5,463,366 (+)Ensembl
ChiLan1.0NW_0049554315,443,050 - 5,466,577 (+)NCBIChiLan1.0ChiLan1.0
VPS36
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21453,701,390 - 53,739,422 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11352,345,676 - 52,383,673 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01333,398,165 - 33,436,615 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11352,336,484 - 52,372,851 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,336,484 - 52,372,851 (-)EnsemblpanPan2panpan1.1
VPS36
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.125150,984 - 191,531 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl25150,150 - 191,544 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha25270,159 - 314,363 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.025253,768 - 297,980 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl25252,947 - 297,978 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.125134,622 - 178,867 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.025149,317 - 193,530 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.025217,148 - 261,346 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vps36
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945161,414,915 - 161,437,361 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365654,898,965 - 4,918,414 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365654,898,969 - 4,921,411 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS36
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1115,701,373 - 15,735,474 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11115,701,370 - 15,735,469 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21115,968,921 - 16,003,061 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS36
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,112,245 - 30,147,976 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl330,112,322 - 30,145,275 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605713,667,873 - 13,701,090 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps36
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247481,881,411 - 1,908,505 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247481,880,542 - 1,908,541 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps36
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11364,224,134 - 64,248,775 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps36
134 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:11
Count of miRNA genes:10
Interacting mature miRNAs:11
Transcripts:ENSRNOT00000016995
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)163188527176885271Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)167523528581732231Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat

Markers in Region
RH130023  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21669,810,086 - 69,810,270 (+)MAPPERmRatBN7.2
Rnor_6.01674,719,325 - 74,719,508NCBIRnor6.0
Rnor_5.01674,354,864 - 74,355,047UniSTSRnor5.0
RGSC_v3.41674,462,110 - 74,462,293UniSTSRGSC3.4
Celera1667,699,395 - 67,699,578UniSTS
RH 3.4 Map16663.21UniSTS
Cytogenetic Map16q12.5UniSTS


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: ENSRNOT00000016995   ⟹   ENSRNOP00000016995
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1676,512,860 - 76,537,246 (-)Ensembl
mRatBN7.2 Ensembl1669,808,193 - 69,834,795 (-)Ensembl
Rnor_6.0 Ensembl1674,719,553 - 74,743,927 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094456   ⟹   ENSRNOP00000077525
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1669,808,193 - 69,834,810 (-)Ensembl
RefSeq Acc Id: NM_001106092   ⟹   NP_001099562
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81676,512,851 - 76,537,235 (-)NCBI
mRatBN7.21669,810,404 - 69,834,789 (-)NCBI
Rnor_6.01674,719,642 - 74,743,921 (-)NCBI
Rnor_5.01674,355,181 - 74,378,989 (-)NCBI
RGSC_v3.41674,462,427 - 74,486,889 (-)RGD
Celera1667,699,712 - 67,723,982 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099562 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60860 (Get FASTA)   NCBI Sequence Viewer  
  EDM08991 (Get FASTA)   NCBI Sequence Viewer  
  EDM08992 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016995
GenBank Protein P0C0A2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001099562   ⟸   NM_001106092
- UniProtKB: P0C0A2 (UniProtKB/Swiss-Prot),   B1H248 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000016995   ⟸   ENSRNOT00000016995
Ensembl Acc Id: ENSRNOP00000077525   ⟸   ENSRNOT00000094456
Protein Domains
GLUE C-terminal   GLUE N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C0A2-F1-model_v2 AlphaFold P0C0A2 1-386 view protein structure

Transcriptome

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

Promoters
RGD ID:13700192
Promoter ID:EPDNEW_R10716
Type:multiple initiation site
Name:Vps36_1
Description:vacuolar protein sorting 36 homolog
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_6.01674,743,923 - 74,743,983EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309754 AgrOrtholog
BioCyc Gene G2FUF-10863 BioCyc
Ensembl Genes ENSRNOG00000012654 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000016995 ENTREZGENE
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot
  2.30.29.30 UniProtKB/Swiss-Prot
  6.10.140.260 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7321877 IMAGE-MGC_LOAD
InterPro GLUE_dom UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  Snf8/Vps36 UniProtKB/Swiss-Prot
  Vps36 UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
  WH_DNA-bd_sf UniProtKB/Swiss-Prot
MGC_CLONE MGC:188216 IMAGE-MGC_LOAD
NCBI Gene 290851 ENTREZGENE
PANTHER PTHR13128 UniProtKB/Swiss-Prot
  VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 36 UniProtKB/Swiss-Prot
Pfam EAP30 UniProtKB/Swiss-Prot
  Vps36_ESCRT-II UniProtKB/Swiss-Prot
PhenoGen Vps36 PhenoGen
PROSITE GLUE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000012654 RatGTEx
Superfamily-SCOP PH domain-like UniProtKB/Swiss-Prot
  SSF46785 UniProtKB/Swiss-Prot
UniProt B1H248 ENTREZGENE, UniProtKB/TrEMBL
  P0C0A2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-19 Vps36  vacuolar protein sorting 36 homolog  Vps36  vacuolar protein sorting 36  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 Vps36  vacuolar protein sorting 36  Vps36  vacuolar protein sorting 36 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps36  vacuolar protein sorting 36 homolog (S. cerevisiae)  Vps36  vacuolar protein sorting 36 (yeast)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Vps36  vacuolar protein sorting 36 (yeast)   Vps36_predicted  vacuolar protein sorting 36 (yeast) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Vps36_predicted  vacuolar protein sorting 36 (yeast) (predicted)  RGD1309754_predicted  similar to RIKEN cDNA 2210415M20 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309754_predicted  similar to RIKEN cDNA 2210415M20 (predicted)  LOC290851_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290851_predicted  similar to RIKEN cDNA 2210415M20 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL