Human Gene VPS41 (ENST00000310301.9_9) from GENCODE V47lift37

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Description: VPS41 subunit of HOPS complex, transcript variant 1 (from RefSeq NM_014396.4)
Gencode Transcript: ENST00000310301.9_9
Gencode Gene: ENSG00000006715.16_13
Transcript (Including UTRs)
Position: hg19 chr7:38,762,574-38,948,791 Size: 186,218 Total Exon Count: 29 Strand: -
Coding Region
Position: hg19 chr7:38,765,846-38,948,774 Size: 182,929 Coding Exon Count: 29

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr7:38,762,574-38,948,791)			mRNA (may differ from genome)		Protein (854 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	UniProtKB
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

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 D001564 Benzo(a)pyrene C006780 bisphenol A C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine C009505 4,4'-diaminodiphenylmethane D002110 Caffeine D019327 Copper Sulfate D003375 Coumestrol D003993 Dibutyl Phthalate D006861 Hydrogen Peroxide more ... click here to view the complete list

Common Gene Haplotype Alleles


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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


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	0.00	17	0.000	Picture	PostScript	Text
3' UTR	-1074.10	3272	-0.328	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
48452 - TPR-like
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50978 - WD40 repeat-like
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on P49754


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	Genome Browser
Gene Details	Gene Details		Gene Details	Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase	SGD
				Protein Sequence	Protein Sequence
				Alignment	Alignment

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. JD094189 - Sequence 75213 from Patent EP1572962. JD419810 - Sequence 400834 from Patent EP1572962. JD285431 - Sequence 266455 from Patent EP1572962. JD505164 - Sequence 486188 from Patent EP1572962. JD505165 - Sequence 486189 from Patent EP1572962. JD505163 - Sequence 486187 from Patent EP1572962. 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: E9PF36, ENST00000310301.1, ENST00000310301.2, ENST00000310301.3, ENST00000310301.4, ENST00000310301.5, ENST00000310301.6, ENST00000310301.7, ENST00000310301.8, NM_014396, P49754, Q86TP8, Q99851, Q99852, uc317osl.1, uc317osl.2, VPS41_HUMAN UCSC ID: ENST00000310301.9_9 RefSeq Accession: NM_014396.4 Protein: P49754 (aka VPS41_HUMAN or VP41_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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