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

Gene ID: 11267, updated on 17-Jun-2019

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
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; VPS22
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

Genomic context

See SNF8 in Genome Data Viewer
Location:
17q21.32
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (48929316..48944842, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (47007458..47022484, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371814 Neighboring gene ribosomal protein L37 pseudogene Neighboring gene ubiquitin conjugating enzyme E2 Z Neighboring gene RNA, U1 small nuclear 42, pseudogene Neighboring gene gastric inhibitory polypeptide

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA 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 BioSystems

  • ESCRT-II complex, organism-specific biosystem (from KEGG)
    ESCRT-II complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • ESCRT-II complex, conserved biosystem (from KEGG)
    ESCRT-II complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystem (from REACTOME)
    Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystemMany plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to th...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
channel regulator activity IDA
Inferred from Direct Assay
more info
PubMed 
protein C-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
early endosome to late endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
endocytic recycling IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosomal transport TAS
Traceable Author Statement
more info
 
macroautophagy TAS
Traceable Author Statement
more info
PubMed 
multivesicular body assembly TAS
Traceable Author Statement
more info
PubMed 
multivesicular body sorting pathway TAS
Traceable Author Statement
more info
PubMed 
positive regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
NOT regulation of MAP kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of multivesicular body size involved in endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein complex stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of viral budding via host ESCRT complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
ESCRT II complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ESCRT II complex IDA
Inferred from Direct Assay
more info
PubMed 
ESCRT II complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
late endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor 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)

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
    Q96H20
    Related
    ENSP00000421380.1, ENST00000502492.5
    Conserved Domains (1) summary
    pfam04157
    Location:6225
    EAP30; EAP30/Vps36 family

RNA

  1. NR_133679.1 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)
    BC008976, BG248541, BP342490

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017024075.2XP_016879564.1  vacuolar-sorting protein SNF8 isoform X1

    Conserved Domains (1) summary
    pfam04157
    Location:13121
    EAP30; EAP30/Vps36 family
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