Syvn1 synoviolin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Syvn1provided by RGD
Official Full Name: synoviolin 1provided by RGD
Primary source: RGD:1310488
See related: EnsemblRapid:ENSRNOG00000020950 AllianceGenome:RGD:1310488
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1310488
Summary: Predicted to enable several functions, including enzyme binding activity; protein-folding chaperone binding activity; and unfolded protein binding activity. Predicted to be involved in several processes, including proteasomal protein catabolic process; protein K48-linked ubiquitination; and protein stabilization. Predicted to act upstream of or within in utero embryonic development and negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway. Predicted to be located in nucleoplasm and smooth endoplasmic reticulum. Predicted to be part of Derlin-1 retrotranslocation complex and Hrd1p ubiquitin ligase ERAD-L complex. Predicted to be active in endoplasmic reticulum quality control compartment. Orthologous to human SYVN1 (synoviolin 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 113.8), Kidney (RPKM 74.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (212766736..212775426)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (203339235..203346137)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (221409281..221416229)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SYVN1 attenuates ferroptosis and alleviates spinal cord ischemia-reperfusion injury in rats by regulating the HMGB1/NRF2/HO-1 axis.
Title: SYVN1 attenuates ferroptosis and alleviates spinal cord ischemia-reperfusion injury in rats by regulating the HMGB1/NRF2/HO-1 axis.
The E3 Ubiquitin Ligase SYVN1 Plays an Antiapoptotic Role in Polycystic Ovary Syndrome by Regulating Mitochondrial Fission.
Title: The E3 Ubiquitin Ligase SYVN1 Plays an Antiapoptotic Role in Polycystic Ovary Syndrome by Regulating Mitochondrial Fission.
Hrd1 might mediate the ubiquitination of IGF-1R through sema3a and then participate in the regulation of cardiomyocyte apoptosis.
Title: Hrd1 induces cardiomyocyte apoptosis via regulating the degradation of IGF-1R by sema3a.
Endoplasmic reticulum stress induces HRD1 to protect alveolar type II epithelial cells from apoptosis induced by cigarette smoke extract.
Title: Endoplasmic Reticulum Stress Induces HRD1 to Protect Alveolar Type II Epithelial Cells from Apoptosis Induced by Cigarette Smoke Extract.
our study reveals Icariin-induced Synoviolin expression through NFE2L1 as a previously unappreciated molecular mechanism underlying the neuronal protective function of Icariin.
Title: Icariin induces synoviolin expression through NFE2L1 to protect neurons from ER stress-induced apoptosis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATPase binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein-folding chaperone binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-specific protease binding	ISO Inferred from Sequence Orthology more info
enables unfolded protein binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ERAD pathway	ISO Inferred from Sequence Orthology more info
involved_in ERAD pathway	ISO Inferred from Sequence Orthology more info
involved_in immature B cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in retrograde protein transport, ER to cytosol	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Derlin-1 retrotranslocation complex	ISO Inferred from Sequence Orthology more info
part_of Hrd1p ubiquitin ligase ERAD-L complex	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in smooth endoplasmic reticulum	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase synoviolin

Names: HRD1 protein; synovial apoptosis inhibitor 1, synoviolin

NP_001094209.1

EC 2.3.2.27

EC 6.3.2.-

XP_006230914.1

EC 2.3.2.27

EC 6.3.2.-

XP_038939886.1

EC 2.3.2.27

EC 6.3.2.-

XP_063124320.1

EC 2.3.2.27

EC 6.3.2.-

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.

mRNA and Protein(s)

NM_001100739.1 → NP_001094209.1 E3 ubiquitin-protein ligase synoviolin

See identical proteins and their annotated locations for NP_001094209.1

Status: PROVISIONAL

Source sequence(s)

BC166727

UniProtKB/TrEMBL

A6HZC0, B2RYC4, F7FG68

Related

ENSRNOP00000079621.1, ENSRNOT00000112643.2

Conserved Domains (2) summary

COG5243
Location:10 → 333

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

pfam13639
Location:289 → 330

zf-RING_2; Ring finger domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

212766736..212775426

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268250.1 → XP_063124320.1 E3 ubiquitin-protein ligase synoviolin isoform X2

UniProtKB/TrEMBL

B2RYC4, F7FG68
XM_006230852.5 → XP_006230914.1 E3 ubiquitin-protein ligase synoviolin isoform X1

See identical proteins and their annotated locations for XP_006230914.1

UniProtKB/TrEMBL

A6HZC0, A6HZC1

Related

ENSRNOP00000028462.7, ENSRNOT00000028462.8

Conserved Domains (2) summary

COG5243
Location:10 → 333

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

NF033913
Location:524 → 597

fibronec_FbpA; LPXTG-anchored fibronectin-binding protein FbpA
XM_039083958.2 → XP_038939886.1 E3 ubiquitin-protein ligase synoviolin isoform X1

UniProtKB/TrEMBL

A6HZC0, A6HZC1

Conserved Domains (2) summary

COG5243
Location:10 → 333

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

NF033913
Location:524 → 597

fibronec_FbpA; LPXTG-anchored fibronectin-binding protein FbpA