SYVN1 synoviolin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYVN1provided by HGNC
Official Full Name: synoviolin 1provided by HGNC
Primary source: HGNC:HGNC:20738
See related: Ensembl:ENSG00000162298 MIM:608046; AllianceGenome:HGNC:20738
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: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (65127279..65134519, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (65120558..65127829, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (64894751..64901990, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of hepatic inclusions and fibrinogen biogenesis by SEL1L-HRD1 ERAD.
Title: Regulation of hepatic inclusions and fibrinogen biogenesis by SEL1L-HRD1 ERAD.
ER-associated degradation ligase HRD1 links ER stress to DNA damage repair by modulating the activity of DNA-PKcs.
Title: ER-associated degradation ligase HRD1 links ER stress to DNA damage repair by modulating the activity of DNA-PKcs.
HRD1-induced TMEM2 ubiquitination promotes ER stress-mediated apoptosis through a non-canonical pathway in intestinal ischemia/reperfusion.
Title: HRD1-induced TMEM2 ubiquitination promotes ER stress-mediated apoptosis through a non-canonical pathway in intestinal ischemia/reperfusion.
Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.
Title: Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.
Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders.
Title: Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders.
Exogenous H2 S promotes ubiquitin-mediated degradation of SREBP1 to alleviate diabetic cardiomyopathy via SYVN1 S-sulfhydration.
Title: Exogenous H(2) S promotes ubiquitin-mediated degradation of SREBP1 to alleviate diabetic cardiomyopathy via SYVN1 S-sulfhydration.
SYVN1-mediated ubiquitylation directs localization of MCT4 in the plasma membrane to promote the progression of lung adenocarcinoma.
Title: SYVN1-mediated ubiquitylation directs localization of MCT4 in the plasma membrane to promote the progression of lung adenocarcinoma.
SLC35F2-SYVN1-TRIM59 axis critically regulates ferroptosis of pancreatic cancer cells by inhibiting endogenous p53.
Title: SLC35F2-SYVN1-TRIM59 axis critically regulates ferroptosis of pancreatic cancer cells by inhibiting endogenous p53.
Association between SYVN1 and SEL1 genetic polymorphisms and remission in rheumatoid arthritis patients treated with TNF-alpha inhibitors: a machine learning approach.
Title: Association between SYVN1 and SEL1 genetic polymorphisms and remission in rheumatoid arthritis patients treated with TNF-α inhibitors: a machine learning approach.
SYVN1 Promotes STAT3 Protein Ubiquitination and Exerts Antiangiogenesis Effects in Retinopathy of Prematurity Development.
Title: SYVN1 Promotes STAT3 Protein Ubiquitination and Exerts Antiangiogenesis Effects in Retinopathy of Prematurity Development.

Submit: New GeneRIF Correction See all GeneRIFs (87)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70269 (e-PCR)
- UniSTS:64004

RH36465 (e-PCR)
- UniSTS:65118

RH70124 (e-PCR)
- UniSTS:69056

RH18051 (e-PCR)
- UniSTS:92647

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-folding chaperone binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ubiquitin protein ligase activity	NAS Non-traceable Author Statement more info	PubMed
enables ubiquitin protein ligase activity	TAS Traceable Author Statement more info	PubMed
enables ubiquitin-specific protease binding	IPI Inferred from Physical Interaction more info	PubMed
enables unfolded protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ERAD pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ERAD pathway	TAS Traceable Author Statement more info	PubMed
involved_in endoplasmic reticulum mannose trimming	TAS Traceable Author Statement more info
involved_in immature B cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	TAS Traceable Author Statement more info	PubMed
involved_in retrograde protein transport, ER to cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of Derlin-1 retrotranslocation complex	IDA Inferred from Direct Assay more info	PubMed
part_of Hrd1p ubiquitin ligase ERAD-L complex	IDA Inferred from Direct Assay more info	PubMed
part_of Hrd1p ubiquitin ligase ERAD-L complex	IMP Inferred from Mutant Phenotype more info	PubMed
part_of Hrd1p ubiquitin ligase complex	TAS Traceable Author Statement more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	TAS Traceable Author Statement more info	PubMed
located_in endoplasmic reticulum membrane	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in endoplasmic reticulum quality control compartment	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum quality control compartment	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum quality control compartment	TAS Traceable Author Statement more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in smooth endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

EC 2.3.2.27

NP_757385.1

EC 2.3.2.27

XP_011543605.1

EC 2.3.2.27

XP_047283667.1

EC 2.3.2.27

XP_047283668.1

EC 2.3.2.27

XP_047283669.1

EC 2.3.2.27

XP_054226165.1

EC 2.3.2.27

XP_054226166.1

EC 2.3.2.27

XP_054226167.1

EC 2.3.2.27

XP_054226168.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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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

NG_029713.2 RefSeqGene

Range

5000..12240

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_032431.3 → NP_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/TrEMBL

B3KX82

Related

ENSP00000294256.8, ENST00000294256.12

Conserved Domains (3) summary

COG5243
Location:10 → 333

HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

pfam08619
Location:527 → 610

Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus

pfam13639
Location:289 → 330

zf-RING_2; Ring finger domain
NM_172230.3 → NP_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, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3

UniProtKB/TrEMBL

B3KX82

Related

ENSP00000366395.3, ENST00000377190.8

Conserved Domains (3) summary

COG5243
Location:10 → 333

HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

pfam08619
Location:528 → 611

Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus

pfam13639
Location:289 → 330

zf-RING_2; Ring finger domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

65127279..65134519 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047427713.1 → XP_047283669.1 E3 ubiquitin-protein ligase synoviolin isoform X4

Related

ENSP00000436984.1, ENST00000526060.5
XM_047427712.1 → XP_047283668.1 E3 ubiquitin-protein ligase synoviolin isoform X2
XM_011545303.4 → XP_011543605.1 E3 ubiquitin-protein ligase synoviolin isoform X3

See identical proteins and their annotated locations for XP_011543605.1

UniProtKB/Swiss-Prot

Q86TM6, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3

UniProtKB/TrEMBL

B3KX82

Conserved Domains (3) summary

COG5243
Location:10 → 333

HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

pfam08619
Location:528 → 611

Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus

pfam13639
Location:289 → 330

zf-RING_2; Ring finger domain
XM_047427711.1 → XP_047283667.1 E3 ubiquitin-protein ligase synoviolin isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

65120558..65127829 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370193.1 → XP_054226168.1 E3 ubiquitin-protein ligase synoviolin isoform X4
XM_054370192.1 → XP_054226167.1 E3 ubiquitin-protein ligase synoviolin isoform X3

UniProtKB/Swiss-Prot

Q86TM6, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3
XM_054370191.1 → XP_054226166.1 E3 ubiquitin-protein ligase synoviolin isoform X2
XM_054370190.1 → XP_054226165.1 E3 ubiquitin-protein ligase synoviolin isoform X1