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Aliases for SYVN1 Gene

Aliases for SYVN1 Gene

  • Synoviolin 1 2 3 5
  • RING-Type E3 Ubiquitin Transferase Synoviolin 3 4
  • Synovial Apoptosis Inhibitor 1, Synoviolin 2 3
  • HRD1 3 4
  • HMG-CoA Reductase Degradation 1 Homolog (S. Cerevisiae) 2
  • HMG-CoA Reductase Degradation 1 Homolog 3
  • E3 Ubiquitin-Protein Ligase Synoviolin 3
  • Synovial Apoptosis Inhibitor 1 4
  • EC 2.3.2.27 4
  • KIAA1810 4
  • EC 6.3.2 56
  • DER3 3

External Ids for SYVN1 Gene

Previous GeneCards Identifiers for SYVN1 Gene

  • GC11M064651
  • GC11M064894
  • GC11M061221

Summaries for SYVN1 Gene

Entrez Gene Summary for SYVN1 Gene

  • 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]

GeneCards Summary for SYVN1 Gene

SYVN1 (Synoviolin 1) is a Protein Coding gene. Diseases associated with SYVN1 include Wolfram Syndrome 1 and Wolfram Syndrome. Among its related pathways are Metabolism of proteins and Transport to the Golgi and subsequent modification. Gene Ontology (GO) annotations related to this gene include ubiquitin protein ligase activity and acid-amino acid ligase activity. An important paralog of this gene is AMFR.

UniProtKB/Swiss-Prot for SYVN1 Gene

  • Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation. Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis.

Gene Wiki entry for SYVN1 Gene

Additional gene information for SYVN1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYVN1 Gene

Genomics for SYVN1 Gene

GeneHancer (GH) Regulatory Elements for SYVN1 Gene

Promoters and enhancers for SYVN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I065129 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.9 1905 7.2 CLOCK ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC SYVN1 SPDYC LOC728975 SSSCA1 PGAM1P8 CAPN1 ZNHIT2 SF1 POLA2 SCYL1
GH11I065470 Promoter/Enhancer 2.9 VISTA FANTOM5 Ensembl ENCODE dbSUPER 59.8 -354.9 -354906 40 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 LOC105369346 SF1 PCNX3 POLA2 ZFPL1 EIF1AD SART1 MUS81 LOC105369352 KAT5
GH11I065414 Promoter/Enhancer 2.4 FANTOM5 Ensembl ENCODE dbSUPER 23 -289.0 -289003 18.8 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 NEAT1 ENSG00000277599 ENSG00000278050 ENSG00000278144 GC11P065529 SF1 ZFPL1 EIF1AD POLA2 PCNX3
GH11I066000 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.9 -867.1 -867105 3 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 EIF1AD BANF1 ENSG00000258297 ZFPL1 PCNX3 POLA2 SART1 RBM14 RBM4 SF3B2
GH11I065377 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13 -247.3 -247304 10.3 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 FRMD8 SLC25A45 SF1 PCNX3 POLA2 MUS81 NEAT1 SART1 EIF1AD RELA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYVN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYVN1 gene promoter:

Genomic Locations for SYVN1 Gene

Genomic Locations for SYVN1 Gene
chr11:65,121,780-65,135,178
(GRCh38/hg38)
Size:
13,399 bases
Orientation:
Minus strand
chr11:64,889,252-64,902,004
(GRCh37/hg19)

Genomic View for SYVN1 Gene

Genes around SYVN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYVN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYVN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYVN1 Gene

Proteins for SYVN1 Gene

  • Protein details for SYVN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TM6-SYVN1_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase synoviolin
    Protein Accession:
    Q86TM6
    Secondary Accessions:
    • Q8N3K3
    • Q8N6E8
    • Q96JL5
    • Q96PK3

    Protein attributes for SYVN1 Gene

    Size:
    617 amino acids
    Molecular mass:
    67685 Da
    Quaternary structure:
    • Homodimer. Interacts with p53/TP53 and HTT. Interacts with VCP, HERPUD1 and DERL1. Part of a complex containing SYVN1, HERPUD1, VIMP and DERL1; which probably transfer misfolded proteins from the ER to VCP. Part of a complex containing SYVN1, SEL1L and DERL2. Interacts with UBXN6. Interacts (via N-terminal loop) with SEL1L; recruits ERLEC1 and OS9. May form a complex with ERLEC1; HSPA5; OS9 AND SEL1L (PubMed:16186509, PubMed:16186510, PubMed:16289116, PubMed:17141218, PubMed:17170702, PubMed:18264092, PubMed:18502753, PubMed:18656546, PubMed:26471130). Interacts with BAG6 (PubMed:21636303).
    SequenceCaution:
    • Sequence=BAB47439.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SYVN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYVN1 Gene

Selected DME Specific Peptides for SYVN1 Gene

Q86TM6:
  • PRFVALFT
  • KCFHWLA
  • CLRSWFQRQQTCPTCR
  • LPPFPPGMFPLWPPMG
  • KVHTFPLFAIRPMYLAMRQFKKAVTDA
  • LYIQAFVLVFLLGK
  • RVDFMERSP
  • MSRRAIRNMNTLYPDAT
  • KVFFGQLRAAEMEHL
  • QFYPTVVYLTKSSPSMA
  • RGASVQLVFGFEYAILMT

Post-translational modifications for SYVN1 Gene

Domains & Families for SYVN1 Gene

Gene Families for SYVN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for SYVN1 Gene

Suggested Antigen Peptide Sequences for SYVN1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86TM6

UniProtKB/Swiss-Prot:

SYVN1_HUMAN :
  • The RING-type zinc finger is required for E3 ligase activity.
  • Belongs to the HRD1 family.
Domain:
  • The RING-type zinc finger is required for E3 ligase activity.
Family:
  • Belongs to the HRD1 family.
genes like me logo Genes that share domains with SYVN1: view

Function for SYVN1 Gene

Molecular function for SYVN1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation. Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis.
UniProtKB/Swiss-Prot Induction:
By endoplasmic reticulum stress-inducing agents such as thapsigargin, tunicamycin or brefeldin A, but not by heat shock.

Enzyme Numbers (IUBMB) for SYVN1 Gene

Phenotypes From GWAS Catalog for SYVN1 Gene

Gene Ontology (GO) - Molecular Function for SYVN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17170702
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051082 unfolded protein binding IPI 17059562
GO:0051087 chaperone binding IPI 21636303
genes like me logo Genes that share ontologies with SYVN1: view
genes like me logo Genes that share phenotypes with SYVN1: view

Animal Models for SYVN1 Gene

MGI Knock Outs for SYVN1:

Animal Model Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYVN1 Gene

Localization for SYVN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYVN1 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYVN1 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
plasma membrane 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
  • Nucleoplasm (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYVN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000836 Hrd1p ubiquitin ligase complex TAS 21454652
GO:0000839 Hrd1p ubiquitin ligase ERAD-L complex IMP 26471130
GO:0005654 nucleoplasm IDA --
GO:0005783 endoplasmic reticulum TAS 23710284
GO:0005789 endoplasmic reticulum membrane TAS --
genes like me logo Genes that share ontologies with SYVN1: view

Pathways & Interactions for SYVN1 Gene

genes like me logo Genes that share pathways with SYVN1: view

UniProtKB/Swiss-Prot Q86TM6-SYVN1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for SYVN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination TAS,IEA 23710284
GO:0018279 protein N-linked glycosylation via asparagine IMP 22607976
GO:0030433 ubiquitin-dependent ERAD pathway IEA,TAS 22013210
GO:0030968 endoplasmic reticulum unfolded protein response IBA --
GO:0030970 retrograde protein transport, ER to cytosol IMP 25660456
genes like me logo Genes that share ontologies with SYVN1: view

No data available for SIGNOR curated interactions for SYVN1 Gene

Drugs & Compounds for SYVN1 Gene

(3) Drugs for SYVN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for SYVN1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with SYVN1: view

Transcripts for SYVN1 Gene

Unigene Clusters for SYVN1 Gene

Synovial apoptosis inhibitor 1, synoviolin:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYVN1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c ^ 13 ^ 14 ^
SP1: - - -
SP2: - -
SP3: - - - - -
SP4: - - - -
SP5: - -
SP6: - - -
SP7: -
SP8:
SP9:
SP10: - - -
SP11:
SP12:
SP13:

ExUns: 15a · 15b · 15c · 15d · 15e ^ 16
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9: - -
SP10:
SP11:
SP12: -
SP13:

Relevant External Links for SYVN1 Gene

GeneLoc Exon Structure for
SYVN1
ECgene alternative splicing isoforms for
SYVN1

Expression for SYVN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYVN1 Gene

Protein differential expression in normal tissues from HIPED for SYVN1 Gene

This gene is overexpressed in Nasal epithelium (44.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SYVN1 Gene



Protein tissue co-expression partners for SYVN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYVN1 Gene:

SYVN1

SOURCE GeneReport for Unigene cluster for SYVN1 Gene:

Hs.75859

mRNA Expression by UniProt/SwissProt for SYVN1 Gene:

Q86TM6-SYVN1_HUMAN
Tissue specificity: Ubiquitously expressed, with highest levels in liver and kidney (at protein level). Up-regulated in synovial tissues from patients with rheumatoid arthritis (at protein level).

Evidence on tissue expression from TISSUES for SYVN1 Gene

  • Liver(4.6)
  • Nervous system(4.4)
  • Blood(4.2)
  • Skin(3.1)
  • Intestine(2.4)
  • Muscle(2.4)
  • Stomach(2.4)
  • Heart(2.3)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with SYVN1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYVN1 Gene

Orthologs for SYVN1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SYVN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYVN1 33 34
  • 98.59 (n)
cow
(Bos Taurus)
Mammalia SYVN1 33 34
  • 93.64 (n)
dog
(Canis familiaris)
Mammalia SYVN1 33 34
  • 91.82 (n)
mouse
(Mus musculus)
Mammalia Syvn1 33 16 34
  • 89.63 (n)
rat
(Rattus norvegicus)
Mammalia Syvn1 33
  • 88.83 (n)
oppossum
(Monodelphis domestica)
Mammalia SYVN1 34
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYVN1 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYVN1 34
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYVN1 34
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syvn1 33
  • 69.4 (n)
Str.10714 33
zebrafish
(Danio rerio)
Actinopterygii syvn1 33 34
  • 75.54 (n)
Dr.3405 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10009 33
fruit fly
(Drosophila melanogaster)
Insecta sip3 34
  • 47 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea sel-11 33 34
  • 52.86 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HRD1 34 36
  • 18 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G16090 33
  • 51.98 (n)
rice
(Oryza sativa)
Liliopsida Os06g0301000 33
  • 52.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
OneToOne
Species where no ortholog for SYVN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SYVN1 Gene

ENSEMBL:
Gene Tree for SYVN1 (if available)
TreeFam:
Gene Tree for SYVN1 (if available)

Paralogs for SYVN1 Gene

Paralogs for SYVN1 Gene

(1) SIMAP similar genes for SYVN1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with SYVN1: view

Variants for SYVN1 Gene

Sequence variations from dbSNP and Humsavar for SYVN1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs756191256 benign, not specified 65,130,692(-) T/A/G coding_sequence_variant, missense_variant
rs1000144991 -- 65,134,953(-) A/T 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000433292 -- 65,135,202(-) A/C upstream_transcript_variant
rs1000502807 -- 65,134,850(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1001874421 -- 65,134,434(-) G/C 5_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SYVN1 Gene

Variant ID Type Subtype PubMed ID
nsv526181 CNV gain 19592680

Variation tolerance for SYVN1 Gene

Residual Variation Intolerance Score: 35.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.55; 72.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYVN1 Gene

Human Gene Mutation Database (HGMD)
SYVN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYVN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYVN1 Gene

Disorders for SYVN1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SYVN1 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
wolfram syndrome 1
  • wfs1
wolfram syndrome
  • wfs
- elite association - COSMIC cancer census association via MalaCards
Search SYVN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYVN1

genes like me logo Genes that share disorders with SYVN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYVN1 Gene

Publications for SYVN1 Gene

  1. A ubiquitin ligase HRD1 promotes the degradation of Pael receptor, a substrate of Parkin. (PMID: 17059562) Omura T … Nomura Y (Journal of neurochemistry 2006) 3 4 22 58
  2. The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway. (PMID: 16289116) Schulze A … Seeger M (Journal of molecular biology 2005) 3 4 22 58
  3. Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic factor for arthropathy. (PMID: 12975321) Amano T … Nakajima T (Genes & development 2003) 2 3 4 58
  4. Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L. (PMID: 26471130) Hosokawa N … Wada I (The FEBS journal 2016) 3 4 58
  5. STT3B-dependent posttranslational N-glycosylation as a surveillance system for secretory protein. (PMID: 22607976) Sato T … Kai H (Molecular cell 2012) 3 4 58

Products for SYVN1 Gene