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Aliases for SYVN1 Gene

Aliases for SYVN1 Gene

  • Synoviolin 1 2 3 5
  • 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 6.3.2.- 4
  • KIAA1810 4
  • EC 6.3.2 61
  • 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. Among its related pathways are Transport to the Golgi and subsequent modification and HIV Life Cycle. 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

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

Genomics for SYVN1 Gene

Regulatory Elements for SYVN1 Gene

Enhancers for SYVN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F065101 0.9 ENCODE 11.8 +32.8 32772 1.1 HDAC1 ATF1 PKNOX1 CREB3L1 INSM2 KLF17 SIN3A FEZF1 RAD21 YY1 CTSW SYVN1 MIR6751 FAU PGAM1P8 CAPN1 LOC728975 SPDYC SAC3D1 ENSG00000254501
GH11F065115 1.2 ENCODE 7.6 +17.8 17815 3.5 HDGF PKNOX1 ARNT MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 LOC105369342 SAC3D1 RPS16P6 ENSG00000231492 CTSW NEAT1 FAU MRPL49 SYVN1 LOC728975
GH11F065082 1.1 ENCODE 7.5 +51.0 51011 2.7 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SNX15 NEAT1 FAU MRPL49 SAC3D1 SYVN1 CDCA5 ZFPL1
GH11F065081 0.8 ENCODE 7.5 +53.7 53675 0.2 ELF3 DRAP1 CTCF PKNOX1 SAP130 ZFP64 ARID4B DMAP1 RAD21 ZNF48 SYVN1 CDCA5 GC11M065079 PIR38481
GH11F065104 0.6 ENCODE 4.9 +29.6 29568 1.7 GATA3 JUND HNF1A PRDM10 ZBTB33 LOC728975 SYVN1 PRDX5 ENSG00000254501 TMEM262
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYVN1 on UCSC Golden Path with GeneCards custom track

Promoters for SYVN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001570814 -722 201 SCRT1 TFDP1 SCRT2 REST YY1
ENSR00001769259 778 2401 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for SYVN1 Gene

Chromosome:
11
Start:
65,121,780 bp from pter
End:
65,135,178 bp from pter
Size:
13,399 bases
Orientation:
Minus strand

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.
    • 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.
    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

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.
  • Contains 1 RING-type zinc finger.
Domain:
  • The RING-type zinc finger is required for E3 ligase activity.
Family:
  • Belongs to the HRD1 family.
Similarity:
  • Contains 1 RING-type zinc finger.
genes like me logo Genes that share domains with SYVN1: view

Function for SYVN1 Gene

Molecular function for SYVN1 Gene

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

Gene Ontology (GO) - Molecular Function for SYVN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17170702
GO:0008270 zinc ion binding IEA --
GO:0016874 ligase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051082 unfolded protein binding IPI 17059562
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

Flow Cytometry 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

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 IEA,TAS 23710284
GO:0018279 protein N-linked glycosylation via asparagine IMP 22607976
GO:0030433 ER-associated ubiquitin-dependent protein catabolic process 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 Nutra 0
Adenosine triphosphate Approved Nutra 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

Flow Cytometry 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 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).
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 and mRNA differential expression in normal tissues 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 34 35
  • 98.59 (n)
cow
(Bos Taurus)
Mammalia SYVN1 34 35
  • 93.64 (n)
dog
(Canis familiaris)
Mammalia SYVN1 34 35
  • 91.82 (n)
mouse
(Mus musculus)
Mammalia Syvn1 34 16 35
  • 89.63 (n)
rat
(Rattus norvegicus)
Mammalia Syvn1 34
  • 88.83 (n)
oppossum
(Monodelphis domestica)
Mammalia SYVN1 35
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYVN1 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYVN1 35
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYVN1 35
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syvn1 34
  • 69.4 (n)
Str.10714 34
zebrafish
(Danio rerio)
Actinopterygii syvn1 34 35
  • 75.54 (n)
Dr.3405 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10009 34
fruit fly
(Drosophila melanogaster)
Insecta sip3 35
  • 47 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea sel-11 34 35
  • 52.86 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HRD1 35 37
  • 18 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G16090 34
  • 51.98 (n)
rice
(Oryza sativa)
Liliopsida Os06g0301000 34
  • 52.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs10088 -- 65,127,730(-) TTTCC(C/T)CTGCA downstream-variant-500B, utr-variant-3-prime
rs1063426 -- 65,127,278(+) CACCA(A/T)TTGTT nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs10895986 -- 65,134,531(+) CACCC(A/C)CTGCG utr-variant-5-prime
rs111304413 -- 65,130,757(+) AGCGA(A/C/T)GCACG upstream-variant-2KB, reference, synonymous-codon
rs111320670 -- 65,135,592(+) TCAAT(C/T)ACTAA upstream-variant-2KB

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)

Relevant External Links 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

Relevant External Links for SYVN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYVN1

No disorders were found for SYVN1 Gene.

No data available for MalaCards , 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. (J. Neurochem. 2006) 3 4 22 64
  2. The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway. (PMID: 16289116) Schulze A. … Seeger M. (J. Mol. Biol. 2005) 3 4 22 64
  3. Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic factor for arthropathy. (PMID: 12975321) Amano T. … Nakajima T. (Genes Dev. 2003) 2 3 4 64
  4. Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L. (PMID: 26471130) Hosokawa N. … Wada I. (FEBS J. 2016) 3 4 64
  5. STT3B-dependent posttranslational N-glycosylation as a surveillance system for secretory protein. (PMID: 22607976) Sato T. … Kai H. (Mol. Cell 2012) 3 4 64

Products for SYVN1 Gene

Sources for SYVN1 Gene

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