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    SNF8 SNF8 subunit of ESCRT-II [ Homo sapiens (human) ]

    Gene ID: 11267, updated on 30-Nov-2024

    Summary

    Official Symbol
    SNF8provided by HGNC
    Official Full Name
    SNF8 subunit of ESCRT-IIprovided by HGNC
    Primary source
    HGNC:HGNC:17028
    See related
    Ensembl:ENSG00000159210 MIM:610904; AllianceGenome:HGNC:17028
    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
    Dot3; EAP30; NEDOA; VPS22; DEE115
    Summary
    The protein encoded by this gene is a component of the endosomal sorting complex required for transport II (ESCRT-II), which regulates the movement of ubiquitinylated transmembrane proteins to the lysosome for degradation. This complex also interacts with the RNA polymerase II elongation factor (ELL) to overcome the repressive effects of ELL on RNA polymerase II activity. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in kidney (RPKM 18.5), fat (RPKM 18.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SNF8 in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48929316..48944842, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (49793036..49808559, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (47006678..47022204, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371814 Neighboring gene ribosomal protein L37 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12348 Neighboring gene ubiquitin conjugating enzyme E2 Z Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8664 Neighboring gene RNA, U1 small nuclear 42, pseudogene Neighboring gene small nucleolar RNA U13

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Developmental and epileptic encephalopathy 115
    MedGen: C5935604 OMIM: 620783 GeneReviews: Not available
    not available
    Neurodevelopmental disorder plus optic atrophy
    MedGen: C5935605 OMIM: 620784 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    shRNA knockdown of SNF8 (ESCRT-II component) impairs intracellular and extracellular (supernatant) HIV-1 CA-p24 production when using VSV-pseudotyped virus; replication is enhanced by SNF8 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Depletion of EAP30 by siRNA leads to a block to HIV-1 genomic RNA trafficking, resulting in the accumulation of genomic RNA in the nucleus and juxtanuclear domains and reduced viral structural protein Gag and virus production levels PubMed
    gag EAP30 interacts with HIV-1 Gag and Staufen1 in live cell tri-molecular fluorescence complementary assay PubMed
    capsid gag Knockdown of SNF8 (ESCRT-II component) decreases extracellular HIV-1 CA-p24 levels when using VSV-pseudotyped virus PubMed
    gag Knockdown of SNF8 (ESCRT-II component) impairs HIV-1 intracellular CA-p24 production when using VSV-pseudotyped virus PubMed

    Go to the HIV-1, Human Interaction Database

    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 channel regulator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipid binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in macroautophagy TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in membrane fission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in multivesicular body assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in multivesicular body assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in multivesicular body assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in multivesicular body sorting pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    NOT involved_in regulation of MAP kinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein complex stability IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of ESCRT II complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of ESCRT II complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ESCRT II complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of ESCRT II complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar-sorting protein SNF8
    Names
    EAP30 subunit of ELL complex
    ELL-associated protein of 30 kDa
    ESCRT-II complex subunit VPS22
    SNF8, ESCRT-II complex subunit, homolog

    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_001317192.2NP_001304121.1  vacuolar-sorting protein SNF8 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
      Source sequence(s)
      AC091133, BC008976, BC038830, BP342490
      Consensus CDS
      CCDS82156.1
      UniProtKB/Swiss-Prot
      Q96H20
      Related
      ENSP00000290330.3, ENST00000290330.7
      Conserved Domains (1) summary
      pfam04157
      Location:6224
      EAP30; EAP30/Vps36 family
    2. NM_001317193.2NP_001304122.1  vacuolar-sorting protein SNF8 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC091133, BC008976, BE818533, BP342490
      UniProtKB/Swiss-Prot
      Q96H20
      Conserved Domains (1) summary
      pfam04157
      Location:16208
      EAP30; EAP30/Vps36 family
    3. NM_001317194.2NP_001304123.1  vacuolar-sorting protein SNF8 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains two additional alternate exons compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC091133, BC008976, BE394098, BP342490
      UniProtKB/Swiss-Prot
      Q96H20
      Conserved Domains (1) summary
      pfam04157
      Location:13121
      EAP30; EAP30/Vps36 family
    4. NM_007241.4NP_009172.2  vacuolar-sorting protein SNF8 isoform 1

      See identical proteins and their annotated locations for NP_009172.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC091133, BC008976, BP342490
      Consensus CDS
      CCDS11541.1
      UniProtKB/Swiss-Prot
      Q8IXY3, Q96H20, Q9UN50
      Related
      ENSP00000421380.1, ENST00000502492.6
      Conserved Domains (1) summary
      pfam04157
      Location:6225
      EAP30; EAP30/Vps36 family

    RNA

    1. NR_133679.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC091133, BC008976, BG248541, BP342490

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      48929316..48944842 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      49793036..49808559 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)