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SYVN1 synoviolin 1 [ Homo sapiens (human) ]

Gene ID: 84447, updated on 18-Nov-2020

Summary

Official Symbol
SYVN1provided by HGNC
Official Full Name
synoviolin 1provided by HGNC
Primary source
HGNC:HGNC:20738
See related
Ensembl:ENSG00000162298 MIM:608046
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]
Expression
Ubiquitous expression in lymph node (RPKM 27.2), appendix (RPKM 21.7) and 25 other tissues See more
Orthologs

Genomic context

See SYVN1 in Genome Data Viewer
Location:
11q13.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 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 Sharpr-MPRA regulatory region 3974 Neighboring gene zinc finger HIT-type containing 2 Neighboring gene FAU ubiquitin like and ribosomal protein S30 fusion Neighboring gene mitochondrial ribosomal protein L49 Neighboring gene microRNA 6751 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 10 Neighboring gene RNA, U2 small nuclear 23, pseudogene

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
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 NAS
Non-traceable Author Statement
more info
PubMed 
ubiquitin protein ligase activity 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 
Process Evidence Code Pubs
ERAD pathway IDA
Inferred from Direct Assay
more info
PubMed 
ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
IRE1-mediated unfolded protein response TAS
Traceable Author Statement
more info
 
endoplasmic reticulum mannose trimming TAS
Traceable Author Statement
more info
 
immature B cell differentiation ISS
Inferred from Sequence or Structural Similarity
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 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 
retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent ERAD pathway IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent ERAD pathway TAS
Traceable Author Statement
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
Derlin-1 retrotranslocation complex IDA
Inferred from Direct Assay
more info
PubMed 
Hrd1p ubiquitin ligase ERAD-L complex IDA
Inferred from Direct Assay
more info
PubMed 
Hrd1p ubiquitin ligase ERAD-L complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
Hrd1p ubiquitin ligase complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
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 IDA
Inferred from Direct Assay
more info
PubMed 
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 HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
smooth endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase synoviolin
Names
HMG-coA reductase degradation 1 homolog
RING-type E3 ubiquitin transferase synoviolin
synovial apoptosis inhibitor 1, synoviolin
NP_115807.1
NP_757385.1
XP_011543605.1

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.

Genomic

  1. NG_029713.1 RefSeqGene

    Range
    5014..12253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032431.3NP_115807.1  E3 ubiquitin-protein ligase synoviolin isoform a

    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
    ENSP00000294256.8, ENST00000294256.12
    Conserved Domains (3) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:527610
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289330
    zf-RING_2; Ring finger domain
  2. NM_172230.3NP_757385.1  E3 ubiquitin-protein ligase synoviolin isoform b

    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
    ENSP00000366395.3, ENST00000377190.7
    Conserved Domains (3) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:528611
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289330
    zf-RING_2; Ring finger domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011545303.3XP_011543605.1  E3 ubiquitin-protein ligase synoviolin isoform X1

    See identical proteins and their annotated locations for XP_011543605.1

    UniProtKB/Swiss-Prot
    Q86TM6
    Conserved Domains (3) summary
    COG5243
    Location:10333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:528611
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289330
    zf-RING_2; Ring finger domain
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