Ufd1 ubiquitin recognition factor in ER associated degradation 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ufd1provided by RGD
Official Full Name: ubiquitin recognition factor in ER associated degradation 1provided by RGD
Primary source: RGD:619822
See related: Ensembl:ENSRNOG00000047394 AllianceGenome:RGD:619822
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables ATPase binding activity and signaling receptor binding activity. Predicted to be involved in ERAD pathway; negative regulation of RIG-I signaling pathway; and negative regulation of type I interferon production. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Human ortholog(s) of this gene implicated in DiGeorge syndrome and schizophrenia. Orthologous to human UFD1 (ubiquitin recognition factor in ER associated degradation 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 283.3), Adrenal (RPKM 213.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 11q23

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	11	NC_086029.1 (95665971..95689423, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	11	NC_051346.1 (82161618..82185107, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	11	NC_005110.4 (86304836..86328478, complement)

Chromosome 11 - NC_086029.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: 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?

the p97-Ufd1-Npl4 complex couples ubiquitinated IP(3) receptors to proteasomal degradation and, thus, plays a key role in IP(3) receptor processing
Title: Involvement of the p97-Ufd1-Npl4 complex in the regulated endoplasmic reticulum-associated degradation of inositol 1,4,5-trisphosphate receptors.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Ufd1l (e-PCR), detects polymorphism
- UniSTS:265766

D11Rat89 (e-PCR), detects polymorphism
- UniSTS:226432

D18S1297 (e-PCR)
- UniSTS:18820

RH134555 (e-PCR)
- UniSTS:217835

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables K48-linked polyubiquitin modification-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables K48-linked polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables polyubiquitin modification-dependent protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor 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
involved_in ERAD pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to misfolded protein	IEA Inferred from Electronic Annotation more info
involved_in cellular response to misfolded protein	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of RIG-I signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of RIG-I signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of RIG-I signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of type I interferon production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of type I interferon production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type I interferon production	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in retrograde protein transport, ER to cytosol	EXP Inferred from Experiment more info	PubMed
involved_in retrograde protein transport, ER to cytosol	IEA Inferred from Electronic Annotation more info
involved_in retrograde protein transport, ER to cytosol	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of UFD1-NPL4 complex	IDA Inferred from Direct Assay more info	PubMed
part_of UFD1-NPL4 complex	IEA Inferred from Electronic Annotation more info
part_of UFD1-NPL4 complex	ISO Inferred from Sequence Orthology more info
part_of VCP-NPL4-UFD1 AAA ATPase complex	EXP Inferred from Experiment more info	PubMed
part_of VCP-NPL4-UFD1 AAA ATPase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of VCP-NPL4-UFD1 AAA ATPase complex	IDA Inferred from Direct Assay more info	PubMed
part_of VCP-NPL4-UFD1 AAA ATPase complex	IEA Inferred from Electronic Annotation more info
part_of VCP-NPL4-UFD1 AAA ATPase complex	IPI Inferred from Physical Interaction more info	PubMed
part_of VCP-NPL4-UFD1 AAA ATPase complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin recognition factor in ER-associated degradation protein 1

Names: UB fusion protein 1; ubiquitin fusion degradation 1 like; ubiquitin fusion degradation protein 1 homolog

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_053418.2 → NP_445870.1 ubiquitin recognition factor in ER-associated degradation protein 1

See identical proteins and their annotated locations for NP_445870.1

Status: VALIDATED

Source sequence(s)

AF234601, BC061998, CK599711

UniProtKB/Swiss-Prot

Q9ES53

UniProtKB/TrEMBL

A0A8I6A8U7

Related

ENSRNOP00000084640.1, ENSRNOT00000100452.1

Conserved Domains (1) summary

pfam03152
Location:19 → 193

UFD1; Ubiquitin fusion degradation protein UFD1

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_086029.1 Reference GRCr8

Range

95665971..95689423 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008768904.4 → XP_008767126.1 ubiquitin recognition factor in ER-associated degradation protein 1 isoform X1

UniProtKB/TrEMBL

A0A8I6A8U7

Conserved Domains (1) summary

pfam03152
Location:3 → 150

UFD1; Ubiquitin fusion degradation protein UFD1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001034834.1: Suppressed sequence

Description

NM_001034834.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.