Human Gene VPS25 (uc002ibi.3) Description and Page Index
  Description: Homo sapiens vacuolar protein sorting 25 homolog (S. cerevisiae) (VPS25), mRNA.
RefSeq Summary (NM_032353): This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A pseudogene of this gene is present on chromosome 1. [provided by RefSeq, Jul 2013]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC006282.2, SRR5189658.41531.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000253794.7/ ENSP00000253794.1 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:40,925,454-40,931,617 Size: 6,164 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr17:40,925,494-40,931,087 Size: 5,594 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:40,925,454-40,931,617)mRNA (may differ from genome)Protein (176 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: VPS25_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein-sorting-associated protein 25; Short=hVps25; AltName: Full=Dermal papilla-derived protein 9; AltName: Full=ELL-associated protein of 20 kDa; AltName: Full=ESCRT-II complex subunit VPS25;
FUNCTION: Component of the ESCRT-II complex (endosomal sorting complex required for transport II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation, possibly via its interaction with ELL. The ESCRT-II complex may be involved in facilitating the budding of certain RNA viruses.
SUBUNIT: Component of a complex at least composed of ELL, SNF8/EAP30, VPS25/EAP20 and VPS36/EAP45 (By similarity). Component of the endosomal sorting complex required for transport II (ESCRT- II), composed of SNF8, VPS36 and 2 copies of VPS25. Interacts with CFTR; the interaction requires misfolded CFTR. Interacts (via C- terminal half) with the ESCRT-III subunit CHMP6 (via N-terminal half).
SUBCELLULAR LOCATION: Cytoplasm. Endosome membrane. Nucleus, nucleoplasm. Note=Distributes diffusely throughout the cytoplasm and nucleoplasm, but exhibits a punctate distribution on coexpression with CHMP6.
TISSUE SPECIFICITY: Expressed at the mRNA level in kidney, liver, pancreas, and placenta. Lower levels of expression are found in heart, skeletal muscle, brain and lung.
SIMILARITY: Belongs to the VPS25 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VPS25
CDC HuGE Published Literature: VPS25

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 43.91 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 972.67 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 -13.2040-0.330 Picture PostScript Text
3' UTR -204.04530-0.385 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
IPR008570 - ESCRT-II_cplx_vps25-sub
IPR014040 - ESCRT-II_cplx_Vps25-sub_C
IPR014041 - ESCRT-II_cplx_Vps25-sub_N

Pfam Domains:
PF05871 - ESCRT-II complex subunit

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2ZME
- X-ray MuPIT

3CUQ
- X-ray MuPIT

3HTU
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9BRG1
FrontTopSide
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 orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
   Gene DetailsGene DetailsGene Details
   Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0047485 protein N-terminus binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007175 negative regulation of epidermal growth factor-activated receptor activity
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0016236 macroautophagy
GO:0036258 multivesicular body assembly
GO:0043328 protein targeting to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0071985 multivesicular body sorting pathway

Cellular Component:
GO:0000814 ESCRT II complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC006282 - Homo sapiens vacuolar protein sorting 25 homolog (S. cerevisiae), mRNA (cDNA clone MGC:10540 IMAGE:4025884), complete cds.
AK312092 - Homo sapiens cDNA, FLJ92373.
CU675329 - Synthetic construct Homo sapiens gateway clone IMAGE:100020161 5' read VPS25 mRNA.
AB014763 - Homo sapiens mRNA for DERP9 (dermal papilla derived protein 9), complete cds.
HQ448303 - Synthetic construct Homo sapiens clone IMAGE:100071718; CCSB004839_03 vacuolar protein sorting 25 homolog (S. cerevisiae) (VPS25) gene, encodes complete protein.
KJ894979 - Synthetic construct Homo sapiens clone ccsbBroadEn_04373 VPS25 gene, encodes complete protein.
JD108373 - Sequence 89397 from Patent EP1572962.
JD203946 - Sequence 184970 from Patent EP1572962.
JD221191 - Sequence 202215 from Patent EP1572962.
JD507247 - Sequence 488271 from Patent EP1572962.
JD316437 - Sequence 297461 from Patent EP1572962.
JD552839 - Sequence 533863 from Patent EP1572962.
JD112586 - Sequence 93610 from Patent EP1572962.
JD050279 - Sequence 31303 from Patent EP1572962.
JD451322 - Sequence 432346 from Patent EP1572962.
JD551989 - Sequence 533013 from Patent EP1572962.
JD424358 - Sequence 405382 from Patent EP1572962.
JD310253 - Sequence 291277 from Patent EP1572962.
JD400907 - Sequence 381931 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

Reactome (by CSHL, EBI, and GO)

Protein Q9BRG1 (Reactome details) participates in the following event(s):

R-HSA-917696 Cargo Sequestration
R-HSA-917700 MVB Vesicle Formation
R-HSA-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B2R581, DERP9, EAP20, NM_032353, NP_115729, Q9BRG1, VPS25_HUMAN
UCSC ID: uc002ibi.3
RefSeq Accession: NM_032353
Protein: Q9BRG1 (aka VPS25_HUMAN)
CCDS: CCDS11438.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032353.2
exon count: 6CDS single in 3' UTR: no RNA size: 1122
ORF size: 531CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1262.00frame shift in genome: no % Coverage: 98.13
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.