Human Gene VPS41 (uc003tgy.3)
  Description: Homo sapiens vacuolar protein sorting 41 homolog (S. cerevisiae) (VPS41), transcript variant 1, mRNA.
RefSeq Summary (NM_014396): Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr7:38,763,543-38,948,800 Size: 185,258 Total Exon Count: 29 Strand: -
Coding Region
   Position: hg19 chr7:38,765,846-38,948,774 Size: 182,929 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:38,763,543-38,948,800)mRNA (may differ from genome)Protein (854 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPS41_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 41 homolog; AltName: Full=S53;
FUNCTION: Required for vacuolar assembly and vacuolar traffic.
INTERACTION: Q9H9C1:SPE39; NbExp=4; IntAct=EBI-2130459, EBI-749080;
SIMILARITY: Belongs to the VPS41 family.
SIMILARITY: Contains 1 clathrin repeat.
SIMILARITY: Contains 1 RING-type zinc finger.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): VPS41
CDC HuGE Published Literature: VPS41
Positive Disease Associations: C-Reactive Protein , Carotid Artery Diseases , CD40 Ligand , Cholesterol, HDL , Cognitive performance , Parkinson Disease , Psychomotor Performance , Socioeconomic Factors , Tunica Media
Related Studies:
  1. C-Reactive Protein
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. C-Reactive Protein
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  3. Carotid Artery Diseases
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: VPS41
Diseases sorted by gene-association score: early-onset familial alzheimer disease (2)

-  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: 14.32 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 399.17 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 -5.4026-0.208 Picture PostScript Text
3' UTR -658.262303-0.286 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
IPR000547 - Clathrin_H-chain/VPS_repeat
IPR011990 - TPR-like_helical
IPR016902 - VPS41
IPR015943 - WD40/YVTN_repeat-like_dom
IPR017986 - WD40_repeat_dom
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00637 - Region in Clathrin and VPS

SCOP Domains:
48371 - ARM repeat
101898 - NHL repeat
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50978 - WD40 repeat-like
69322 - Tricorn protease domain 2
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on P49754
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 Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0042802 identical protein binding
GO:0043621 protein self-association
GO:0046872 metal ion binding
GO:0051020 GTPase binding

Biological Process:
GO:0006623 protein targeting to vacuole
GO:0006886 intracellular protein transport
GO:0006914 autophagy
GO:0008150 biological_process
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034058 endosomal vesicle fusion
GO:0035542 regulation of SNARE complex assembly
GO:0042144 vacuole fusion, non-autophagic
GO:0045055 regulated exocytosis
GO:0046907 intracellular transport
GO:0048193 Golgi vesicle transport
GO:1902774 late endosome to lysosome transport

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005794 Golgi apparatus
GO:0005798 Golgi-associated vesicle
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0015630 microtubule cytoskeleton
GO:0016020 membrane
GO:0030123 AP-3 adaptor complex
GO:0030136 clathrin-coated vesicle
GO:0030897 HOPS complex
GO:0031410 cytoplasmic vesicle
GO:0031902 late endosome membrane
GO:0033263 CORVET complex
GO:0071439 clathrin complex


-  Descriptions from all associated GenBank mRNAs
  BX648347 - Homo sapiens mRNA; cDNA DKFZp686I08170 (from clone DKFZp686I08170).
LF209695 - JP 2014500723-A/17198: Polycomb-Associated Non-Coding RNAs.
LP895582 - Sequence 446 from Patent EP3253886.
U87309 - Human hVps41p (HVPS41) mRNA, complete cds.
AK074325 - Homo sapiens cDNA FLJ23745 fis, clone HEP15778, highly similar to VACUOLAR ASSEMBLY PROTEIN VPS41 HOMOLOG.
BC044851 - Homo sapiens vacuolar protein sorting 41 homolog (S. cerevisiae), mRNA (cDNA clone MGC:42423 IMAGE:4822048), complete cds.
AF135593 - Homo sapiens hVps41p (HVPS41) mRNA, alternative splice variant, complete cds.
AK299143 - Homo sapiens cDNA FLJ58251 complete cds, highly similar to Vacuolar assembly protein VPS41 homolog.
AK314556 - Homo sapiens cDNA, FLJ95380, highly similar to Homo sapiens vacuolar protein sorting 41 (yeast) (VPS41), transcript variant 1, mRNA.
KJ893595 - Synthetic construct Homo sapiens clone ccsbBroadEn_02989 VPS41 gene, encodes complete protein.
HQ257912 - Synthetic construct Homo sapiens clone IMAGE:100072221 vacuolar protein sorting 41 homolog (S. cerevisiae) (VPS41) gene, encodes complete protein.
MA445272 - JP 2018138019-A/17198: Polycomb-Associated Non-Coding RNAs.
JD051476 - Sequence 32500 from Patent EP1572962.
JD303115 - Sequence 284139 from Patent EP1572962.
JD038877 - Sequence 19901 from Patent EP1572962.
JD326285 - Sequence 307309 from Patent EP1572962.
JD347555 - Sequence 328579 from Patent EP1572962.
JD120851 - Sequence 101875 from Patent EP1572962.
JD552958 - Sequence 533982 from Patent EP1572962.
JD390416 - Sequence 371440 from Patent EP1572962.
JD054835 - Sequence 35859 from Patent EP1572962.
JD561896 - Sequence 542920 from Patent EP1572962.
JD551712 - Sequence 532736 from Patent EP1572962.
JD360984 - Sequence 342008 from Patent EP1572962.
JD264343 - Sequence 245367 from Patent EP1572962.
JD557961 - Sequence 538985 from Patent EP1572962.
JD144705 - Sequence 125729 from Patent EP1572962.
JD144704 - Sequence 125728 from Patent EP1572962.
JD425823 - Sequence 406847 from Patent EP1572962.
JD119122 - Sequence 100146 from Patent EP1572962.
JD211746 - Sequence 192770 from Patent EP1572962.
JD278368 - Sequence 259392 from Patent EP1572962.
JD036371 - Sequence 17395 from Patent EP1572962.
JD294031 - Sequence 275055 from Patent EP1572962.
JD481494 - Sequence 462518 from Patent EP1572962.
JD212615 - Sequence 193639 from Patent EP1572962.
JD246744 - Sequence 227768 from Patent EP1572962.
JD112374 - Sequence 93398 from Patent EP1572962.
JD542665 - Sequence 523689 from Patent EP1572962.
JD497722 - Sequence 478746 from Patent EP1572962.
JD222883 - Sequence 203907 from Patent EP1572962.
JD112373 - Sequence 93397 from Patent EP1572962.
JD356512 - Sequence 337536 from Patent EP1572962.
JD536407 - Sequence 517431 from Patent EP1572962.
JD455002 - Sequence 436026 from Patent EP1572962.
JD565719 - Sequence 546743 from Patent EP1572962.
JD049155 - Sequence 30179 from Patent EP1572962.
JD230595 - Sequence 211619 from Patent EP1572962.
JD548803 - Sequence 529827 from Patent EP1572962.
L40398 - Homo sapiens hypothetical protein mRNA, partial cds.
U87281 - Human hVps41p (hVPS41) mRNA, alternative splice variant, partial cds.
AK026848 - Homo sapiens cDNA: FLJ23195 fis, clone REC00843, highly similar to HSU87309 Human hVps41p (HVPS41) mRNA.
JD353646 - Sequence 334670 from Patent EP1572962.
JD224105 - Sequence 205129 from Patent EP1572962.
LF331146 - JP 2014500723-A/138649: Polycomb-Associated Non-Coding RNAs.
JD502236 - Sequence 483260 from Patent EP1572962.
JD041016 - Sequence 22040 from Patent EP1572962.
JD465338 - Sequence 446362 from Patent EP1572962.
JD109471 - Sequence 90495 from Patent EP1572962.
JD313511 - Sequence 294535 from Patent EP1572962.
LF331145 - JP 2014500723-A/138648: Polycomb-Associated Non-Coding RNAs.
MA566723 - JP 2018138019-A/138649: Polycomb-Associated Non-Coding RNAs.
MA566722 - JP 2018138019-A/138648: Polycomb-Associated Non-Coding RNAs.
LF331144 - JP 2014500723-A/138647: Polycomb-Associated Non-Coding RNAs.
LF331143 - JP 2014500723-A/138646: Polycomb-Associated Non-Coding RNAs.
LF331141 - JP 2014500723-A/138644: Polycomb-Associated Non-Coding RNAs.
LF331137 - JP 2014500723-A/138640: Polycomb-Associated Non-Coding RNAs.
LF331126 - JP 2014500723-A/138629: Polycomb-Associated Non-Coding RNAs.
JD187504 - Sequence 168528 from Patent EP1572962.
MA566721 - JP 2018138019-A/138647: Polycomb-Associated Non-Coding RNAs.
MA566720 - JP 2018138019-A/138646: Polycomb-Associated Non-Coding RNAs.
MA566718 - JP 2018138019-A/138644: Polycomb-Associated Non-Coding RNAs.
MA566714 - JP 2018138019-A/138640: Polycomb-Associated Non-Coding RNAs.
MA566703 - JP 2018138019-A/138629: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_014396, NP_055211, P49754, Q86TP8, Q99851, Q99852, VPS41_HUMAN
UCSC ID: uc003tgy.3
RefSeq Accession: NM_014396
Protein: P49754 (aka VPS41_HUMAN or VP41_HUMAN)
CCDS: CCDS5457.1, CCDS5458.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014396.3
exon count: 29CDS single in 3' UTR: no RNA size: 4894
ORF size: 2565CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5330.00frame shift in genome: no % Coverage: 100.00
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.