Vps39 (VPS39 subunit of HOPS complex) - Rat Genome Database

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Gene: Vps39 (VPS39 subunit of HOPS complex) Rattus norvegicus
Analyze
Symbol: Vps39
Name: VPS39 subunit of HOPS complex
RGD ID: 1304858
Description: Predicted to be involved in endocytic recycling; lysosomal transport; and vesicle fusion. Predicted to be located in late endosome membrane and lysosomal membrane. Predicted to be part of AP-3 adaptor complex and lysosomal HOPS complex. Predicted to be active in cytoplasm and membrane. Orthologous to human VPS39 (VPS39 subunit of HOPS complex); INTERACTS WITH 3-chloropropane-1,2-diol; 4,4'-sulfonyldiphenol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362199; vacuolar protein sorting 39; vacuolar protein sorting 39 (yeast); vacuolar protein sorting 39 homolog; vacuolar protein sorting 39 homolog (S. cerevisiae); Vam6; VPS39 HOPS complex subunit
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
GRCr83127,721,076 - 127,758,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3127,721,076 - 127,758,768 (-)EnsemblGRCr8
mRatBN7.23107,266,846 - 107,304,884 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3107,267,310 - 107,304,975 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3110,942,113 - 110,979,866 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03119,537,671 - 119,575,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03117,198,055 - 117,235,810 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03112,087,213 - 112,125,307 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3112,087,677 - 112,125,318 (-)Ensemblrn6Rnor6.0
Rnor_5.03118,634,996 - 118,673,028 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43106,803,136 - 106,842,405 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3106,175,713 - 106,213,173 (-)NCBICelera
RGSC_v3.13106,699,565 - 106,738,812 (-)NCBI
Cytogenetic Map3q35NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Mammalian late vacuole protein sorting orthologues participate in early endosomal fusion and interact with the cytoskeleton. Richardson SC, etal., Mol Biol Cell 2004 Mar;15(3):1197-210. Epub 2003 Dec 10.
Additional References at PubMed
PMID:12477932   PMID:17897319   PMID:19109425   PMID:21411634   PMID:23167963   PMID:23901104   PMID:24554770   PMID:25266290   PMID:25783203  


Genomics

Comparative Map Data
Vps39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83127,721,076 - 127,758,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3127,721,076 - 127,758,768 (-)EnsemblGRCr8
mRatBN7.23107,266,846 - 107,304,884 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3107,267,310 - 107,304,975 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3110,942,113 - 110,979,866 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03119,537,671 - 119,575,426 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03117,198,055 - 117,235,810 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03112,087,213 - 112,125,307 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3112,087,677 - 112,125,318 (-)Ensemblrn6Rnor6.0
Rnor_5.03118,634,996 - 118,673,028 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43106,803,136 - 106,842,405 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3106,175,713 - 106,213,173 (-)NCBICelera
RGSC_v3.13106,699,565 - 106,738,812 (-)NCBI
Cytogenetic Map3q35NCBI
VPS39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381542,158,701 - 42,208,304 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1542,158,701 - 42,208,326 (-)Ensemblhg38GRCh38
GRCh371542,450,899 - 42,500,502 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361540,238,191 - 40,287,794 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341540,238,191 - 40,287,794NCBI
Celera1519,218,602 - 19,268,201 (-)NCBICelera
Cytogenetic Map15q15.1NCBI
HuRef1519,299,375 - 19,348,651 (-)NCBIHuRef
CHM1_11542,569,358 - 42,618,969 (-)NCBICHM1_1
T2T-CHM13v2.01539,964,724 - 40,014,333 (-)NCBIT2T-CHM13v2.0
Vps39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392120,146,942 - 120,183,618 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2120,146,942 - 120,183,618 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm382120,316,461 - 120,353,142 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2120,316,461 - 120,353,137 (-)Ensemblmm10GRCm38
MGSCv372120,142,197 - 120,178,869 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362120,008,978 - 120,044,551 (-)NCBIMGSCv36mm8
Celera2121,470,840 - 121,507,455 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.31NCBI
Vps39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554168,893,249 - 8,936,351 (-)Ensembl
ChiLan1.0NW_0049554168,893,249 - 8,936,351 (-)NCBIChiLan1.0ChiLan1.0
VPS39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21631,402,580 - 31,452,291 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11535,555,736 - 35,605,474 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01521,113,047 - 21,162,738 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11539,273,546 - 39,323,196 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1539,273,546 - 39,323,196 (-)EnsemblpanPan2panpan1.1
VPS39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1309,166,510 - 9,213,806 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl309,166,656 - 9,213,629 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha309,224,925 - 9,271,967 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0309,301,394 - 9,348,552 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl309,301,405 - 9,348,551 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1309,221,763 - 9,268,866 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0309,326,778 - 9,373,930 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0309,461,083 - 9,508,187 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vps39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864087,609,300 - 87,664,890 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364715,457,035 - 5,512,625 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364715,457,363 - 5,512,966 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1129,144,344 - 129,198,761 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11129,144,338 - 129,198,760 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21144,088,787 - 144,140,115 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS39
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12640,787,204 - 40,834,065 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2640,801,245 - 40,834,113 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666048100,169,128 - 100,216,225 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps39
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248049,284,104 - 9,337,892 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248049,286,614 - 9,337,149 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Vps39
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1598,450,919 - 98,488,966 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vps39
239 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:486
Count of miRNA genes:249
Interacting mature miRNAs:308
Transcripts:ENSRNOT00000011155
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
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)396509147141509147Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3122654702136118980Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3116582412136118980Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)385062224136118980Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)385062224136118980Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)3104545086149545086Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)381425008141509147Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)393829559138829559Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3101255536134750886Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)396509147141509147Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)390755164141509147Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)3125814931139636791Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat

Markers in Region
RH127512  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23107,267,656 - 107,267,976 (+)MAPPERmRatBN7.2
Rnor_6.03112,088,024 - 112,088,343NCBIRnor6.0
Rnor_5.03118,635,343 - 118,635,662UniSTSRnor5.0
RGSC_v3.43106,803,483 - 106,803,802UniSTSRGSC3.4
Celera3106,176,060 - 106,176,379UniSTS
RH 3.4 Map3935.6UniSTS
Cytogenetic Map3q35UniSTS
D15S802  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr83127,722,734 - 127,723,665 (+)Marker Load Pipeline
mRatBN7.23107,268,968 - 107,269,899 (+)MAPPERmRatBN7.2
Rnor_6.03112,089,336 - 112,090,266NCBIRnor6.0
Rnor_5.03118,636,655 - 118,637,585UniSTSRnor5.0
RGSC_v3.43106,804,795 - 106,805,725UniSTSRGSC3.4
Celera3106,177,372 - 106,178,302UniSTS
Cytogenetic Map3q35UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000011155   ⟹   ENSRNOP00000011155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3127,721,076 - 127,758,768 (-)Ensembl
mRatBN7.2 Ensembl3107,267,310 - 107,304,975 (-)Ensembl
Rnor_6.0 Ensembl3112,087,677 - 112,125,290 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085132   ⟹   ENSRNOP00000075259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3127,721,076 - 127,758,768 (-)Ensembl
mRatBN7.2 Ensembl3107,267,310 - 107,304,975 (-)Ensembl
Rnor_6.0 Ensembl3112,087,796 - 112,125,318 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102893   ⟹   ENSRNOP00000079382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3107,267,310 - 107,299,904 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105454   ⟹   ENSRNOP00000095308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3127,728,722 - 127,758,621 (-)Ensembl
mRatBN7.2 Ensembl3107,267,312 - 107,304,857 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000119603   ⟹   ENSRNOP00000086938
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3127,721,076 - 127,758,642 (-)Ensembl
mRatBN7.2 Ensembl3107,267,310 - 107,304,878 (-)Ensembl
RefSeq Acc Id: NM_001012186   ⟹   NP_001012186
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,721,076 - 127,758,642 (-)NCBI
mRatBN7.23107,267,310 - 107,304,878 (-)NCBI
Rnor_6.03112,087,677 - 112,125,290 (-)NCBI
Rnor_5.03118,634,996 - 118,673,028 (-)NCBI
RGSC_v3.43106,803,136 - 106,842,405 (-)RGD
Celera3106,175,713 - 106,213,173 (-)RGD
Sequence:
RefSeq Acc Id: XM_006234782   ⟹   XP_006234844
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,721,223 - 127,758,658 (-)NCBI
mRatBN7.23107,266,846 - 107,304,884 (-)NCBI
Rnor_6.03112,087,213 - 112,125,307 (-)NCBI
Rnor_5.03118,634,996 - 118,673,028 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105457   ⟹   XP_038961385
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83127,721,223 - 127,758,645 (-)NCBI
mRatBN7.23107,266,846 - 107,304,884 (-)NCBI
RefSeq Acc Id: NP_001012186   ⟸   NM_001012186
- UniProtKB: E9PT04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234844   ⟸   XM_006234782
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KA50 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075259   ⟸   ENSRNOT00000085132
Ensembl Acc Id: ENSRNOP00000011155   ⟸   ENSRNOT00000011155
RefSeq Acc Id: XP_038961385   ⟸   XM_039105457
- Peptide Label: isoform X2
- UniProtKB: E9PT04 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000095308   ⟸   ENSRNOT00000105454
Ensembl Acc Id: ENSRNOP00000079382   ⟸   ENSRNOT00000102893
Ensembl Acc Id: ENSRNOP00000086938   ⟸   ENSRNOT00000119603
Protein Domains
CNH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KA50-F1-model_v2 AlphaFold A0A0G2KA50 1-886 view protein structure

Transcriptome

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

Promoters
RGD ID:13692340
Promoter ID:EPDNEW_R2864
Type:multiple initiation site
Name:Vps39_1
Description:VPS39 HOPS complex subunit
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_6.03112,125,290 - 112,125,350EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304858 AgrOrtholog
BioCyc Gene G2FUF-48178 BioCyc
Ensembl Genes ENSRNOG00000008316 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011155 ENTREZGENE
  ENSRNOT00000011155.7 UniProtKB/TrEMBL
  ENSRNOT00000085132 ENTREZGENE
  ENSRNOT00000085132.3 UniProtKB/TrEMBL
  ENSRNOT00000105454.2 UniProtKB/TrEMBL
  ENSRNOT00000119603.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112790 IMAGE-MGC_LOAD
InterPro Citron UniProtKB/TrEMBL
  Clathrin_H-chain/VPS_repeat UniProtKB/TrEMBL
  VAM6/VPS39 UniProtKB/TrEMBL
  VPS39/TGF_beta_rcpt-assoc_1 UniProtKB/TrEMBL
  VPS39/TGF_beta_rcpt-assoc_2 UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:93907 IMAGE-MGC_LOAD
NCBI Gene 362199 ENTREZGENE
PANTHER PTHR12894 UniProtKB/TrEMBL
  VAM6_VPS39-LIKE PROTEIN UniProtKB/TrEMBL
Pfam CNH UniProtKB/TrEMBL
  Vps39_1 UniProtKB/TrEMBL
  Vps39_2 UniProtKB/TrEMBL
PhenoGen Vps39 PhenoGen
PROSITE CHCR UniProtKB/TrEMBL
  CNH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008316 RatGTEx
SMART CNH UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/TrEMBL
UniProt A0A0G2KA50 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A3C4_RAT UniProtKB/TrEMBL
  A0A8I6AL66_RAT UniProtKB/TrEMBL
  E9PT04 ENTREZGENE, UniProtKB/TrEMBL
  Q5PQS9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Vps39  VPS39 subunit of HOPS complex  Vps39  VPS39 HOPS complex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Vps39  VPS39 HOPS complex subunit  Vps39  vacuolar protein sorting 39 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Vps39  vacuolar protein sorting 39 homolog (S. cerevisiae)  Vps39  vacuolar protein sorting 39 (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Vps39  vacuolar protein sorting 39 (yeast)  Vps39_predicted  vacuolar protein sorting 39 (yeast) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Vps39_predicted  vacuolar protein sorting 39 (yeast) (predicted)      Symbol and Name status set to approved 70820 APPROVED