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

    Gene ID: 6944, updated on 14-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001271087.2NP_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:2278
      LTV; Low temperature viability protein
      pfam05764
      Location:6216
      YL1; YL1 nuclear protein
      pfam08265
      Location:302330
      YL1_C; YL1 nuclear protein C-terminal domain
    2. NM_001271088.2NP_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:7193
      YL1; YL1 nuclear protein
    3. NM_005997.3NP_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:2278
      LTV; Low temperature viability protein
      pfam05764
      Location:6216
      YL1; YL1 nuclear protein
      pfam08265
      Location:291319
      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_017002205.2XP_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_054338527.1XP_054194502.1  vacuolar protein sorting-associated protein 72 homolog isoform X1