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    VPS72 vacuolar protein sorting 72 homolog [ Homo sapiens (human) ]

    Gene ID: 6944, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VPS72provided by HGNC
    Official Full Name
    vacuolar protein sorting 72 homologprovided by HGNC
    Primary source
    HGNC:HGNC:11644
    See related
    Ensembl:ENSG00000163159 MIM:600607; AllianceGenome:HGNC:11644
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    YL1; CFL1; Swc2; YL-1; TCFL1
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 14.7), prostate (RPKM 14.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS72 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151176304..151190197, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150300033..150313938, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151148780..151162673, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene sodium channel modifier 1 Neighboring gene tropomodulin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1711 Neighboring gene uncharacterized LOC124904419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1713 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr1:151183035-151183192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151183741-151184733 Neighboring gene MPRA-validated peak410 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1316 Neighboring gene Sharpr-MPRA regulatory region 10214 Neighboring gene proteasome 26S subunit ubiquitin receptor, non-ATPase 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Forced expression of YL-1 protein suppresses the anchorage-independent growth of Kirsten sarcoma virus-transformed NIH3T3 cells. Horikawa I, et al. Exp Cell Res, 1995 Sep. PMID 7664828
    2. Prognostic marker VPS72 could promote the malignant progression of prostate cancer. Xu X, et al. BMC Cancer, 2024 Jun 10. PMID 38858662, Free PMC Article
    3. Molecular cloning of a novel human cDNA on chromosome 1q21 and its mouse homolog encoding a nuclear protein with DNA-binding ability. Horikawa I, et al. Biochem Biophys Res Commun, 1995 Mar 28. PMID 7702631
    4. VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis. Moreno-Andrés D, et al. Cells, 2020 Jul 16. PMID 32708675, Free PMC Article
    5. Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway. Chen T, et al. Bioengineered, 2022 Apr. PMID 35383533, Free PMC Article

    See all (67) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Prognostic marker VPS72 could promote the malignant progression of prostate cancer.
      Title: Prognostic marker VPS72 could promote the malignant progression of prostate cancer.
    2. Targeting VPS72 inhibits ACTL6A/MYC axis activity in HCC progression.
      Title: Targeting VPS72 inhibits ACTL6A/MYC axis activity in HCC progression.
    3. Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway.
      Title: Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway.
    4. VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis.
      Title: VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis.
    5. The 2.7-A-resolution crystal structure of the human YL1-H2A.Z-H2B complex shows that YL1 binding, similarly to ANP32E binding, triggers an extension of the H2A.Z alphaC helix.
      Title: Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1.
    6. Results identify YL1 as a subunit of the TRRAP/TIP60 HAT complex, and also as a component of a novel mammalian multiprotein complex that includes the SNF2-related helicase SRCAP.
      Title: The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone chaperone activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair via homologous recombination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of apoptotic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in somatic stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of NuA4 histone acetyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of nucleosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nucleosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 72 homolog
    Names
    transcription factor-like 1
    transformation suppressor gene YL-1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001271087.2 → NP_001258016.1  vacuolar protein sorting-associated protein 72 homolog isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA128103, AW194498, BU539181, CX163016, DQ655941
      Consensus CDS
      CCDS59201.1
      UniProtKB/Swiss-Prot
      Q15906
      Related
      ENSP00000346464.4, ENST00000354473.4
      Conserved Domains (3) summary
      pfam04180
      Location:22 → 78
      LTV; Low temperature viability protein
      pfam05764
      Location:6 → 216
      YL1; YL1 nuclear protein
      pfam08265
      Location:302 → 330
      YL1_C; YL1 nuclear protein C-terminal domain

    2. NM_001271088.2 → NP_001258017.1  vacuolar protein sorting-associated protein 72 homolog isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites in the 3' coding region that result in a frameshift, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL592424, CT003766, DQ655941
      UniProtKB/TrEMBL
      B4DMP5
      Conserved Domains (1) summary
      pfam05764
      Location:7 → 193
      YL1; YL1 nuclear protein

    3. NM_005997.3 → NP_005988.1  vacuolar protein sorting-associated protein 72 homolog isoform 2

      See identical proteins and their annotated locations for NP_005988.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AA128103, AW194498, D43642, DQ655941
      Consensus CDS
      CCDS989.1
      UniProtKB/Swiss-Prot
      A6NLK9, A6PW55, Q15906, Q53GJ2, Q5U0R4
      Related
      ENSP00000357887.5, ENST00000368892.9
      Conserved Domains (3) summary
      pfam04180
      Location:22 → 78
      LTV; Low temperature viability protein
      pfam05764
      Location:6 → 216
      YL1; YL1 nuclear protein
      pfam08265
      Location:291 → 319
      YL1_C; YL1 nuclear protein C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      151176304..151190197 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002205.2 → XP_016857694.1  vacuolar protein sorting-associated protein 72 homolog isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150300033..150313938 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338527.1 → XP_054194502.1  vacuolar protein sorting-associated protein 72 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15906.1 GenPept UniProtKB/Swiss-Prot:Q15906

    Gene LinkOut

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