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SYVN1 synoviolin 1 [ Homo sapiens (human) ]

Gene ID: 84447, updated on 8-May-2016
Official Symbol
SYVN1provided by HGNC
Official Full Name
synoviolin 1provided by HGNC
Primary source
HGNC:HGNC:20738
See related
Ensembl:ENSG00000162298 HPRD:07618; MIM:608046; Vega:OTTHUMG00000165607
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
DER3; HRD1
Summary
This gene encodes a protein involved in endoplasmic reticulum (ER)-associated degradation. The encoded protein removes unfolded proteins, accumulated during ER stress, by retrograde transport to the cytosol from the ER. This protein also uses the ubiquitin-proteasome system for additional degradation of unfolded proteins. Sequence analysis identified two transcript variants that encode different isoforms. [provided by RefSeq, May 2011]
Orthologs
Location:
11q13
Exon count:
16
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 11 NC_000011.10 (65127279..65135178, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64894751..64902285, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene zinc finger HIT-type containing 2 Neighboring gene mitochondrial ribosomal protein L49 Neighboring gene Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed Neighboring gene microRNA 6751 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 10 Neighboring gene speedy/RINGO cell cycle regulator family member C

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • Calnexin/calreticulin cycle, organism-specific biosystem (from REACTOME)
    Calnexin/calreticulin cycle, organism-specific biosystemThe unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and P...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • ER Quality Control Compartment (ERQC), organism-specific biosystem (from REACTOME)
    ER Quality Control Compartment (ERQC), organism-specific biosystemProteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to ...
  • HRD1/SEL1 ERAD complex, organism-specific biosystem (from KEGG)
    HRD1/SEL1 ERAD complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • HRD1/SEL1 ERAD complex, conserved biosystem (from KEGG)
    HRD1/SEL1 ERAD complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Hedgehog ligand biogenesis, organism-specific biosystem (from REACTOME)
    Hedgehog ligand biogenesis, organism-specific biosystemMammalian genomes encode three Hedgehog ligands, Sonic Hedgehog (SHH), Indian Hedgehog (IHH) and Desert Hedgehog (DHH). These secreted morphogens can remain associated with lipid rafts on the surfac...
  • Hh mutants abrogate ligand secretion, organism-specific biosystem (from REACTOME)
    Hh mutants abrogate ligand secretion, organism-specific biosystemHh signaling is required for a number of developmental processes, and mutations that disrupt the normal processing and biogenesis of Hh ligand can result in neonatal abnormalities. SHH is one of a n...
  • Hh mutants that don't undergo autocatalytic processing are degraded by ERAD, organism-specific biosystem (from REACTOME)
    Hh mutants that don't undergo autocatalytic processing are degraded by ERAD, organism-specific biosystemHh signaling is required for a number of developmental processes, and mutations that disrupt the normal processing and biogenesis of Hh ligand can result in neonatal abnormalities. SHH is one of a n...
  • IRE1alpha activates chaperones, organism-specific biosystem (from REACTOME)
    IRE1alpha activates chaperones, organism-specific biosystemIRE1-alpha is a single-pass transmembrane protein that resides in the endoplasmic reticulum (ER) membrane. The C-terminus of IRE1-alpha is located in the cytosol; the N-terminus is located in the ER ...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
    N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...
  • Ubiquitin mediated proteolysis, organism-specific biosystem (from KEGG)
    Ubiquitin mediated proteolysis, organism-specific biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • Ubiquitin mediated proteolysis, conserved biosystem (from KEGG)
    Ubiquitin mediated proteolysis, conserved biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
    Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...
  • XBP1(S) activates chaperone genes, organism-specific biosystem (from REACTOME)
    XBP1(S) activates chaperone genes, organism-specific biosystemXbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotri...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA1810, MGC40372

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
chaperone binding IPI
Inferred from Physical Interaction
more info
PubMed 
ligase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
PubMed 
ubiquitin protein ligase activity involved in ERAD pathway IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin protein ligase activity involved in ERAD pathway NAS
Non-traceable Author Statement
more info
PubMed 
ubiquitin protein ligase activity involved in ERAD pathway TAS
Traceable Author Statement
more info
PubMed 
ubiquitin-specific protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
unfolded protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
ER-associated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
ER-associated ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
ER-associated ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
ERAD pathway IDA
Inferred from Direct Assay
more info
PubMed 
IRE1-mediated unfolded protein response TAS
Traceable Author Statement
more info
 
endoplasmic reticulum mannose trimming TAS
Traceable Author Statement
more info
 
endoplasmic reticulum unfolded protein response IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway TAS
Traceable Author Statement
more info
PubMed 
protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein N-linked glycosylation via asparagine IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination TAS
Traceable Author Statement
more info
PubMed 
protein ubiquitination involved in ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination involved in ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Derlin-1 retrotranslocation complex IDA
Inferred from Direct Assay
more info
PubMed 
Hrd1p ubiquitin ligase complex TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum quality control compartment TAS
Traceable Author Statement
more info
PubMed 
integral component of endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
smooth endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
E3 ubiquitin-protein ligase synoviolin
Names
HMG-coA reductase degradation 1 homolog
synovial apoptosis inhibitor 1, synoviolin
NP_115807.1
NP_757385.1

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.

Genomic

  1. NG_029713.1 RefSeqGene

    Range
    5001..12253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032431.2NP_115807.1  E3 ubiquitin-protein ligase synoviolin isoform a precursor

    See identical proteins and their annotated locations for NP_115807.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (a).
    Source sequence(s)
    AA864844, AL834262, BC030530
    Consensus CDS
    CCDS8097.1
    UniProtKB/Swiss-Prot
    Q86TM6
    Related
    ENSP00000294256, OTTHUMP00000230429, ENST00000294256, OTTHUMT00000385273
    Conserved Domains (2) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    cd00162
    Location:291333
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
  2. NM_172230.2NP_757385.1  E3 ubiquitin-protein ligase synoviolin isoform b precursor

    See identical proteins and their annotated locations for NP_757385.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different splice site than variant 1 and encodes the longer isoform (b).
    Source sequence(s)
    AA864844, AL834262, BC030530
    Consensus CDS
    CCDS31605.1
    UniProtKB/Swiss-Prot
    Q86TM6
    Related
    ENSP00000366395, OTTHUMP00000230430, ENST00000377190, OTTHUMT00000385274
    Conserved Domains (2) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    cd00162
    Location:291333
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p2 Primary Assembly

    Range
    65127279..65135178 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545303.1XP_011543605.1  

    See identical proteins and their annotated locations for XP_011543605.1

    UniProtKB/Swiss-Prot
    Q86TM6
    Conserved Domains (2) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    cd00162
    Location:291333
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

Alternate CHM1_1.1

Genomic

  1. NC_018922.2 Alternate CHM1_1.1

    Range
    64778428..64785681 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)