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

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Gene: Vps39 (VPS39 subunit of HOPS complex) Heterocephalus glaber
Analyze
Symbol: Vps39
Name: VPS39 subunit of HOPS complex
RGD ID: 18908473
Description: INVOLVED IN autophagosome-lysosome fusion (ortholog); endocytic recycling (ortholog); endosome to lysosome transport (ortholog); ASSOCIATED WITH Bloom syndrome (ortholog); Breast Neoplasms (ortholog); cerebellar ataxia (ortholog); FOUND IN AP-3 adaptor complex (ortholog); HOPS complex (ortholog); late endosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: vam6/Vps39-like protein; VPS39, HOPS complex subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248049,284,104 - 9,337,892 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248049,286,614 - 9,337,149 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248049,286,614 - 9,337,149 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
VPS39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381542,158,701 - 42,208,304 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1542,158,701 - 42,208,307 (-)EnsemblGRCh38hg38GRCh38
GRCh371542,450,899 - 42,500,502 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361540,238,191 - 40,287,794 (-)NCBINCBI36Build 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 Ensembl
GRCm382120,316,461 - 120,353,142 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2120,316,461 - 120,353,137 (-)EnsemblGRCm38mm10GRCm38
MGSCv372120,142,197 - 120,178,869 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362120,008,978 - 120,044,551 (-)NCBIMGSCv36mm8
Celera2121,470,840 - 121,507,455 (-)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.31NCBI
Vps39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83127,721,076 - 127,758,658 (-)NCBIGRCr8
mRatBN7.23107,266,846 - 107,304,884 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3107,267,310 - 107,304,975 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3110,942,113 - 110,979,866 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03119,537,671 - 119,575,426 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03117,198,055 - 117,235,810 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03112,087,213 - 112,125,307 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3112,087,677 - 112,125,318 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03118,634,996 - 118,673,028 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43106,803,136 - 106,842,405 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13106,699,565 - 106,738,812 (-)NCBI
Celera3106,175,713 - 106,213,173 (-)NCBICelera
Cytogenetic Map3q35NCBI
Vps39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554168,893,249 - 8,936,351 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha309,224,925 - 9,271,967 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0309,301,394 - 9,348,552 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048100,169,128 - 100,216,225 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000012125   ⟹   ENSHGLP00000011993
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248049,284,104 - 9,337,892 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000012126   ⟹   ENSHGLP00000011994
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046248049,288,442 - 9,336,993 (-)Ensembl
RefSeq Acc Id: XM_004861639   ⟹   XP_004861696
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248049,286,614 - 9,337,149 (-)NCBI
RefSeq Acc Id: XM_021241657   ⟹   XP_021097316
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046248049,286,614 - 9,337,149 (-)NCBI
Protein Sequences
Protein RefSeqs XP_004861696 (Get FASTA)   NCBI Sequence Viewer  
  XP_021097316 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000011993
  ENSHGLP00000011994
  ENSHGLP00100057130
GenBank Protein JAO00976 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_004861696   ⟸   XM_004861639
- Peptide Label: isoform X2
- UniProtKB: A0A0P6J9K6 (UniProtKB/TrEMBL),   G5BM25 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_021097316   ⟸   XM_021241657
- Peptide Label: isoform X1
- UniProtKB: G5BM25 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000011994   ⟸   ENSHGLT00000012126
RefSeq Acc Id: ENSHGLP00000011993   ⟸   ENSHGLT00000012125


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000008591 Ensembl, ENTREZGENE
  ENSHGLG00100005880 UniProtKB/TrEMBL
Ensembl Transcript ENSHGLT00000012125 ENTREZGENE
  ENSHGLT00000012126 ENTREZGENE
  ENSHGLT00100067189 UniProtKB/TrEMBL
InterPro Clathrin_H-chain/VPS_repeat UniProtKB/TrEMBL
  CNH_dom UniProtKB/TrEMBL
  Vam6/VPS39/TRAP1 UniProtKB/TrEMBL
  VPS39/TGF_beta_rcpt-assoc_1 UniProtKB/TrEMBL
  VPS39/TGF_beta_rcpt-assoc_2 UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report hgl:101706571 UniProtKB/TrEMBL
NCBI Gene Vps39 ENTREZGENE
PANTHER PTHR12894 UniProtKB/TrEMBL
  VAM6_VPS39-LIKE PROTEIN UniProtKB/TrEMBL
Pfam CNH UniProtKB/TrEMBL
  Vps39_1 UniProtKB/TrEMBL
  Vps39_2 UniProtKB/TrEMBL
PROSITE CHCR UniProtKB/TrEMBL
  CNH UniProtKB/TrEMBL
SMART CNH UniProtKB/TrEMBL
Superfamily-SCOP SSF50978 UniProtKB/TrEMBL
UniProt A0A0P6J9K6 ENTREZGENE, UniProtKB/TrEMBL
  G5BM25 ENTREZGENE, UniProtKB/TrEMBL