Human Gene VPS39 (ENST00000318006.10) from GENCODE V44
  Description: Homo sapiens VPS39 subunit of HOPS complex (VPS39), transcript variant 2, mRNA. (from RefSeq NM_015289)
RefSeq Summary (NM_015289): This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014].
Gencode Transcript: ENST00000318006.10
Gencode Gene: ENSG00000166887.16
Transcript (Including UTRs)
   Position: hg38 chr15:42,158,701-42,208,304 Size: 49,604 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg38 chr15:42,160,754-42,208,153 Size: 47,400 Coding Exon Count: 25 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:42,158,701-42,208,304)mRNA (may differ from genome)Protein (875 aa)
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BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPS39_HUMAN
DESCRIPTION: RecName: Full=Vam6/Vps39-like protein; AltName: Full=TRAP1-like protein;; Short=hVam6p;
FUNCTION: May play a role in clustering and fusion of late endosomes and lysosomes. Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.
SUBUNIT: Homooligomer. Interacts with TGFBR2 and, less efficiently, with TGFBR1; interaction with TGFBR2 is independent of the receptor kinase activity and of the presence of TGF-beta. Also interacts with ACVR2B, but not with BMPR2. Interacts with SMAD4, preferentially following TGF-beta treatment. Does not interact with SAMD2 or SMAD3.
SUBCELLULAR LOCATION: Cytoplasm. Lysosome membrane; Peripheral membrane protein. Late endosome membrane; Peripheral membrane protein. Note=Colocalizes with TGFBR1 and TGFBR2 in cytoplasmic vesicular structures and most prominently in cortical vesicles.
TISSUE SPECIFICITY: Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen.
SIMILARITY: Belongs to the VAM6/VPS39 family.
SIMILARITY: Contains 1 CNH domain.
SEQUENCE CAUTION: Sequence=BAA34490.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VPS39
Diseases sorted by gene-association score: arthrogryposis, renal dysfunction, and cholestasis 1 (7)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.77 RPKM in Spleen
Total median expression: 1113.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.70151-0.448 Picture PostScript Text
3' UTR -739.102053-0.360 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001180 - Citron
IPR019452 - VPS39/TGF_beta_rcpt-assoc_1
IPR019453 - VPS39/TGF_beta_rcpt-assoc_2

Pfam Domains:
PF00780 - CNH domain
PF10366 - Vacuolar sorting protein 39 domain 1
PF10367 - Vacuolar sorting protein 39 domain 2

ModBase Predicted Comparative 3D Structure on Q96JC1
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
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Gene Details    Gene Details
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MGIRGDEnsemblEnsemblWormBaseSGD
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006886 intracellular protein transport
GO:0006914 autophagy
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034058 endosomal vesicle fusion
GO:1902774 late endosome to lysosome transport
GO:1990126 retrograde transport, endosome to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0016020 membrane
GO:0030123 AP-3 adaptor complex
GO:0030897 HOPS complex
GO:0031902 late endosome membrane


-  Descriptions from all associated GenBank mRNAs
  AB018313 - Homo sapiens KIAA0770 mRNA for KIAA0770 protein.
AF281052 - Homo sapiens VPS39 mRNA, complete cds.
BX537404 - Homo sapiens mRNA; cDNA DKFZp686A2451 (from clone DKFZp686A2451); complete cds.
BC068559 - Homo sapiens vacuolar protein sorting 39 homolog (S. cerevisiae), mRNA (cDNA clone MGC:87483 IMAGE:5295166), complete cds.
AM392538 - Synthetic construct Homo sapiens clone IMAGE:100001914 for hypothetical protein (VPS39 gene).
AM393769 - Synthetic construct Homo sapiens clone IMAGE:100002309 for hypothetical protein (VPS39 gene).
AF280814 - Homo sapiens Vam6/Vps39-like protein mRNA, complete cds.
KJ893359 - Synthetic construct Homo sapiens clone ccsbBroadEn_02753 VPS39 gene, encodes complete protein.
AB383984 - Synthetic construct DNA, clone: pF1KSDA0770, Homo sapiens VPS39 gene for vacuolar protein sorting 39 homolog, complete cds, without stop codon, in Flexi system.
CU686671 - Synthetic construct Homo sapiens gateway clone IMAGE:100022983 5' read VPS39 mRNA.
AK074193 - Homo sapiens cDNA FLJ23613 fis, clone ADKA03214.
AK025334 - Homo sapiens cDNA: FLJ21681 fis, clone COL09261.
BC015817 - Homo sapiens vacuolar protein sorting 39 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3938667), partial cds.
AK124255 - Homo sapiens cDNA FLJ42261 fis, clone TKIDN2012034.
AL117456 - Homo sapiens mRNA; cDNA DKFZp586K2217 (from clone DKFZp586K2217).
AK128403 - Homo sapiens cDNA FLJ46546 fis, clone THYMU3038214, highly similar to Vam6/Vps39-like protein.
JD465839 - Sequence 446863 from Patent EP1572962.
JD098078 - Sequence 79102 from Patent EP1572962.
JD464233 - Sequence 445257 from Patent EP1572962.
JD354586 - Sequence 335610 from Patent EP1572962.
JD052024 - Sequence 33048 from Patent EP1572962.
JD322580 - Sequence 303604 from Patent EP1572962.
JD437088 - Sequence 418112 from Patent EP1572962.
JD068262 - Sequence 49286 from Patent EP1572962.
JD081554 - Sequence 62578 from Patent EP1572962.
JD281531 - Sequence 262555 from Patent EP1572962.
JD276210 - Sequence 257234 from Patent EP1572962.
JD396883 - Sequence 377907 from Patent EP1572962.
JD133708 - Sequence 114732 from Patent EP1572962.
JD467454 - Sequence 448478 from Patent EP1572962.
JD324006 - Sequence 305030 from Patent EP1572962.
JD413794 - Sequence 394818 from Patent EP1572962.
JD080142 - Sequence 61166 from Patent EP1572962.
JD522136 - Sequence 503160 from Patent EP1572962.
JD535825 - Sequence 516849 from Patent EP1572962.
JD158284 - Sequence 139308 from Patent EP1572962.
JD446645 - Sequence 427669 from Patent EP1572962.
JD107955 - Sequence 88979 from Patent EP1572962.
JD369034 - Sequence 350058 from Patent EP1572962.
JD454696 - Sequence 435720 from Patent EP1572962.
JD098189 - Sequence 79213 from Patent EP1572962.
JD134053 - Sequence 115077 from Patent EP1572962.
JD108938 - Sequence 89962 from Patent EP1572962.
JD348734 - Sequence 329758 from Patent EP1572962.
JD432911 - Sequence 413935 from Patent EP1572962.
JD425691 - Sequence 406715 from Patent EP1572962.
JD282362 - Sequence 263386 from Patent EP1572962.
JD159959 - Sequence 140983 from Patent EP1572962.
JD437851 - Sequence 418875 from Patent EP1572962.
JD265379 - Sequence 246403 from Patent EP1572962.
JD075797 - Sequence 56821 from Patent EP1572962.
JD044921 - Sequence 25945 from Patent EP1572962.
JD204972 - Sequence 185996 from Patent EP1572962.
JD141535 - Sequence 122559 from Patent EP1572962.
JD152055 - Sequence 133079 from Patent EP1572962.
DQ601430 - Homo sapiens piRNA piR-39496, complete sequence.
JD389026 - Sequence 370050 from Patent EP1572962.
JD330558 - Sequence 311582 from Patent EP1572962.
JD528927 - Sequence 509951 from Patent EP1572962.
JD375064 - Sequence 356088 from Patent EP1572962.
JD277711 - Sequence 258735 from Patent EP1572962.
JD498394 - Sequence 479418 from Patent EP1572962.
JD064701 - Sequence 45725 from Patent EP1572962.
JD137339 - Sequence 118363 from Patent EP1572962.
JD543582 - Sequence 524606 from Patent EP1572962.
JD207259 - Sequence 188283 from Patent EP1572962.
JD135122 - Sequence 116146 from Patent EP1572962.
JD456920 - Sequence 437944 from Patent EP1572962.
JD383220 - Sequence 364244 from Patent EP1572962.
KJ902329 - Synthetic construct Homo sapiens clone ccsbBroadEn_11723 VPS39 gene, encodes complete protein.
JD019113 - Sequence 137 from Patent EP1572962.
JD033489 - Sequence 14513 from Patent EP1572962.
LF205851 - JP 2014500723-A/13354: Polycomb-Associated Non-Coding RNAs.
MA441428 - JP 2018138019-A/13354: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000318006.1, ENST00000318006.2, ENST00000318006.3, ENST00000318006.4, ENST00000318006.5, ENST00000318006.6, ENST00000318006.7, ENST00000318006.8, ENST00000318006.9, KIAA0770, NM_015289, O94869, Q71SQ6, Q7Z3V3, Q96B93, Q96JC1, Q96RM0, TLP, uc001zpc.1, uc001zpc.2, uc001zpc.3, uc001zpc.4, uc001zpc.5, VAM6, VPS39_HUMAN
UCSC ID: ENST00000318006.10
RefSeq Accession: NM_015289
Protein: Q96JC1 (aka VPS39_HUMAN or VP39_HUMAN)
CCDS: CCDS10083.1, CCDS73710.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.