Human Gene VPS39 (uc001zpc.3) Description and Page Index
  Description: Homo sapiens vacuolar protein sorting 39 homolog (S. cerevisiae) (VPS39), mRNA.
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].
Transcript (Including UTRs)
   Position: hg19 chr15:42,450,899-42,500,502 Size: 49,604 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr15:42,452,952-42,500,351 Size: 47,400 Coding Exon Count: 25 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:42,450,899-42,500,502)mRNA (may differ from genome)Protein (875 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VPS39
CDC HuGE Published Literature: VPS39

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -69.10151-0.458 Picture PostScript Text
3' UTR -767.292053-0.374 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
  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 Q96JC1-2
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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
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  BC015817 - Homo sapiens vacuolar protein sorting 39 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3938667), partial cds.
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.
KJ902329 - Synthetic construct Homo sapiens clone ccsbBroadEn_11723 VPS39 gene, encodes complete protein.
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.
AK074193 - Homo sapiens cDNA FLJ23613 fis, clone ADKA03214.
AK025334 - Homo sapiens cDNA: FLJ21681 fis, clone COL09261.
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.
JD019113 - Sequence 137 from Patent EP1572962.
JD033489 - Sequence 14513 from Patent EP1572962.
CU686671 - Synthetic construct Homo sapiens gateway clone IMAGE:100022983 5' read VPS39 mRNA.
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: KIAA0770, NM_015289, NP_056104, Q96JC1-2, TLP, VAM6
UCSC ID: uc001zpc.3
RefSeq Accession: NM_015289
Protein: Q96JC1-2, splice isoform of Q96JC1 CCDS: CCDS10083.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015289.2
exon count: 25CDS single in 3' UTR: no RNA size: 4851
ORF size: 2628CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5429.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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