The protein encoded by this gene is a shared subunit of two multi-component complexes, the histone acetyltransferase complex TRRAP/TIP60 as well as the chromatin remodeling SRCAP-containing complex. The TRRAP/TIP60 complex acetylates nucleosomal histones important for transcriptional regulation, double strand DNA break repair and apoptosis. The SRCAP-containing complex catalyze... See more...

Aliases for VPS72 Gene

Aliases for VPS72 Gene

  • Vacuolar Protein Sorting 72 Homolog 2 3 5
  • Transcription Factor-Like 1 2 3 4
  • Vacuolar Protein Sorting-Associated Protein 72 Homolog 3 4
  • TCFL1 3 4
  • YL1 3 4
  • Vacuolar Protein Sorting 72 Homolog (S. Cerevisiae) 2
  • Transformation Suppressor Gene YL-1 3
  • Vacuolar Protein Sorting 72 (Yeast) 2
  • Protein YL-1 4
  • CFL1 3
  • Swc2 3
  • YL-1 3

External Ids for VPS72 Gene

Previous HGNC Symbols for VPS72 Gene

  • TCFL1

Previous GeneCards Identifiers for VPS72 Gene

  • GC01M147963
  • GC01M149415
  • GC01M151143
  • GC01M122527

Summaries for VPS72 Gene

Entrez Gene Summary for VPS72 Gene

  • The protein encoded by this gene is a shared subunit of two multi-component complexes, the histone acetyltransferase complex TRRAP/TIP60 as well as the chromatin remodeling SRCAP-containing complex. The TRRAP/TIP60 complex acetylates nucleosomal histones important for transcriptional regulation, double strand DNA break repair and apoptosis. The SRCAP-containing complex catalyzes the exchange of histone H2A with the histone variant Htz1 (H2AFZ) into nucleosomes. This protein may be responsible for binding H2AFZ, which has a role in chromosome segregation. This protein may also have a role in regulating long-term hematopoietic stem cell activity. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Aug 2012]

GeneCards Summary for VPS72 Gene

VPS72 (Vacuolar Protein Sorting 72 Homolog) is a Protein Coding gene. Diseases associated with VPS72 include Meckel Syndrome, Type 6. Among its related pathways are Chromatin organization.

UniProtKB/Swiss-Prot Summary for VPS72 Gene

  • Deposition-and-exchange histone chaperone specific for H2AFZ, specifically chaperones H2AFZ and deposits it into nucleosomes. As component of the SRCAP complex, mediates the ATP-dependent exchange of histone H2AFZ/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling.

Gene Wiki entry for VPS72 Gene

Additional gene information for VPS72 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS72 Gene

Genomics for VPS72 Gene

GeneHancer (GH) Regulatory Elements for VPS72 Gene

Promoters and enhancers for VPS72 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J151188 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 750.4 +5.7 5727 2.9 PPP1R10 SIN3A SP1 ZBTB40 LCORL ZBTB6 MLX RBPJ POLR2A CTBP1 VPS72 SETDB1 PIP5K1A PRPF3 ARNT UBE2D3P3 ZNF687 GOLPH3L PI4KB MRPL9
GH01J151142 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 +50.1 50112 6.1 SP1 FOXA1 MIXL1 NFYC L3MBTL2 MNT POLR2A ZFX SP5 ZNF704 SEMA6C BNIPL LYSMD1 GABPB2 PRUNE1 TMOD4 VPS72 PIP5K1A RNU6-884P C1orf56
GH01J151099 Enhancer 0.6 ENCODE 10.7 +95.3 95341 0.2 CTCF RAD21 ZNF384 ARID2 REST ZBTB33 TARDBP TRIM22 SCRT2 RFX5 piR-45035-013 TNFAIP8L2 SEMA6C GABPB2 MINDY1 PRUNE1 TMOD4 SCNM1 LYSMD1 PIP5K1A
GH01J151124 Enhancer 0.6 Ensembl 10.2 +70.3 70320 0.8 NR2F1 NR2F6 ZNF644 GATAD2A SOX13 SAP130 POLR2A SMAD4 BCL6 RARA lnc-GABPB2-1 GABPB2 SEMA6C TNFAIP8L2 C1orf56 BNIPL SCNM1 LYSMD1 MINDY1 PRUNE1
GH01J151134 Enhancer 0.5 dbSUPER 10.4 +59.4 59399 2.7 PRDM10 ZBTB33 RFX1 RUNX3 CTCF GLIS1 lnc-LYSMD1-2 BNIPL GABPB2 SEMA6C TNFAIP8L2 TMOD4 MINDY1 PRUNE1 SCNM1 LYSMD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS72 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS72 gene promoter:
  • C/EBPalpha
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HOXA5
  • MAZR
  • Pax-4a
  • RSRFC4
  • SEF-1 (1)
  • Sp1

Genomic Locations for VPS72 Gene

Genomic Locations for VPS72 Gene
chr1:151,169,987-151,195,321
(GRCh38/hg38)
Size:
25,335 bases
Orientation:
Minus strand
chr1:151,142,463-151,167,797
(GRCh37/hg19)
Size:
25,335 bases
Orientation:
Minus strand

Genomic View for VPS72 Gene

Genes around VPS72 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS72 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS72 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS72 Gene

Proteins for VPS72 Gene

  • Protein details for VPS72 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15906-VPS72_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 72 homolog
    Protein Accession:
    Q15906
    Secondary Accessions:
    • A6NLK9
    • A6PW55
    • Q53GJ2
    • Q5U0R4

    Protein attributes for VPS72 Gene

    Size:
    364 amino acids
    Molecular mass:
    40594 Da
    Quaternary structure:
    • Component of the NuA4 histone acetyltransferase complex which contains the catalytic subunit KAT5/TIP60 and the subunits EP400, TRRAP/PAF400, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, ING3, actin, ACTL6A/BAF53A, MORF4L1/MRG15, MORF4L2/MRGX, MRGBP, YEATS4/GAS41 and VPS72/YL1. Component of a NuA4-related complex which contains EP400, TRRAP/PAF400, SRCAP, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, actin, ACTL6A/BAF53A, VPS72 and YEATS4/GAS41. Also part of a multiprotein complex which contains SRCAP and which binds to H2AFZ/H2AZ. Interacts (via N-terminal domain) with heterodimer HIST1H2BJ and H2AFZ (PubMed:26974126).

    Three dimensional structures from OCA and Proteopedia for VPS72 Gene

    Alternative splice isoforms for VPS72 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS72 Gene

Post-translational modifications for VPS72 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS72 Gene

No data available for DME Specific Peptides for VPS72 Gene

Domains & Families for VPS72 Gene

Gene Families for VPS72 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VPS72 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VPS72 Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar protein sorting 72 homolog (S. cerevisiae) (A6PW55_HUMAN)
  • Transcription factor-like 1 (VPS72_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15906

UniProtKB/Swiss-Prot:

VPS72_HUMAN :
  • Belongs to the VPS72/YL1 family.
Family:
  • Belongs to the VPS72/YL1 family.
genes like me logo Genes that share domains with VPS72: view

Function for VPS72 Gene

Molecular function for VPS72 Gene

UniProtKB/Swiss-Prot Function:
Deposition-and-exchange histone chaperone specific for H2AFZ, specifically chaperones H2AFZ and deposits it into nucleosomes. As component of the SRCAP complex, mediates the ATP-dependent exchange of histone H2AFZ/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling.

Phenotypes From GWAS Catalog for VPS72 Gene

Gene Ontology (GO) - Molecular Function for VPS72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 15647280
GO:0042393 histone binding IPI 26974126
genes like me logo Genes that share ontologies with VPS72: view
genes like me logo Genes that share phenotypes with VPS72: view

Animal Models for VPS72 Gene

MGI Knock Outs for VPS72:
  • Vps72 Vps72<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS72

Clone Products

  • Addgene plasmids for VPS72

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS72 Gene

Localization for VPS72 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS72 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS72 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IEA 21873635
GO:0005654 nucleoplasm TAS --
GO:0016607 nuclear speck IDA --
GO:0032991 protein-containing complex IDA 14966270
genes like me logo Genes that share ontologies with VPS72: view

Pathways & Interactions for VPS72 Gene

PathCards logo

SuperPathways for VPS72 Gene

genes like me logo Genes that share pathways with VPS72: view

Pathways by source for VPS72 Gene

Gene Ontology (GO) - Biological Process for VPS72 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II TAS 7702631
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0035019 somatic stem cell population maintenance IEA --
genes like me logo Genes that share ontologies with VPS72: view

No data available for SIGNOR curated interactions for VPS72 Gene

Drugs & Compounds for VPS72 Gene

No Compound Related Data Available

Transcripts for VPS72 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS72

Clone Products

  • Addgene plasmids for VPS72

Alternative Splicing Database (ASD) splice patterns (SP) for VPS72 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c
SP1: -
SP2:
SP3:

Relevant External Links for VPS72 Gene

GeneLoc Exon Structure for
VPS72
ECgene alternative splicing isoforms for
VPS72

Expression for VPS72 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS72 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VPS72 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.5), Blymphocyte (8.4), CD8 Tcells (6.9), and Fetal Brain (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS72 Gene



Protein tissue co-expression partners for VPS72 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS72 Gene:

VPS72

SOURCE GeneReport for Unigene cluster for VPS72 Gene:

Hs.2430

Evidence on tissue expression from TISSUES for VPS72 Gene

  • Kidney(4.4)
  • Liver(4.2)
  • Nervous system(4)
  • Muscle(2.4)
genes like me logo Genes that share expression patterns with VPS72: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS72 Gene

Orthologs for VPS72 Gene

This gene was present in the common ancestor of animals.

Orthologs for VPS72 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS72 33 32
  • 99.45 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS72 33
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS72 33 32
  • 91.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS72 33 32
  • 90.84 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps72 32
  • 87.09 (n)
mouse
(Mus musculus)
Mammalia Vps72 17 33 32
  • 86.9 (n)
chicken
(Gallus gallus)
Aves VPS72 33
  • 72 (a)
OneToOne
LOC100859689 32
  • 67.96 (n)
lizard
(Anolis carolinensis)
Reptilia VPS72 33
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps72 32
  • 63.74 (n)
Str.9975 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.11940 32
zebrafish
(Danio rerio)
Actinopterygii vps72 33 32
  • 63.14 (n)
OneToMany
VPS72 (2 of 2) 33
  • 57 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.871 32
fruit fly
(Drosophila melanogaster)
Insecta YL-1 33 32
  • 50.66 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001565 32
  • 46.75 (n)
worm
(Caenorhabditis elegans)
Secernentea C17E4.6 33
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10900 33
  • 42 (a)
OneToOne
Species where no ortholog for VPS72 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS72 Gene

ENSEMBL:
Gene Tree for VPS72 (if available)
TreeFam:
Gene Tree for VPS72 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS72: view image

Paralogs for VPS72 Gene

No data available for Paralogs for VPS72 Gene

Variants for VPS72 Gene

Sequence variations from dbSNP and Humsavar for VPS72 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1182821166 A breast cancer sample 151,176,787(-) T/C 3_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000210359 -- 151,182,667(-) C/T intron_variant
rs1000224725 -- 151,190,160(-) A/G 5_prime_UTR_variant
rs1000338835 -- 151,189,837(-) C/T intron_variant
rs1000496608 -- 151,178,325(-) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS72 Gene

Variant ID Type Subtype PubMed ID
dgv2n68 CNV loss 17160897
nsv522840 CNV gain 19592680

Variation tolerance for VPS72 Gene

Residual Variation Intolerance Score: 25% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.01; 20.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS72 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS72

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS72 Gene

Disorders for VPS72 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS72 Gene - From: DISEASES

Disorder Aliases PubMed IDs
meckel syndrome, type 6
  • mks6
- elite association - COSMIC cancer census association via MalaCards
Search VPS72 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS72

genes like me logo Genes that share disorders with VPS72: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS72 Gene

Publications for VPS72 Gene

  1. Molecular cloning of a novel human cDNA on chromosome 1q21 and its mouse homolog encoding a nuclear protein with DNA-binding ability. (PMID: 7702631) Horikawa I … Oshimura M (Biochemical and biophysical research communications 1995) 2 3 4 56
  2. Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1. (PMID: 26974126) Latrick CM … Hamiche A (Nature structural & molecular biology 2016) 3 4 56
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 56
  4. The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. (PMID: 15647280) Cai Y … Conaway JW (The Journal of biological chemistry 2005) 3 4 56
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 56

Products for VPS72 Gene

Sources for VPS72 Gene