Ufd1 ubiquitin recognition factor in ER-associated degradation 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ufd1provided by MGI
Official Full Name: ubiquitin recognition factor in ER-associated degradation 1provided by MGI
Primary source: MGI:MGI:109353
See related: Ensembl:ENSMUSG00000005262 AllianceGenome:MGI:109353
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ufd1l
Summary: Enables K48-linked polyubiquitin modification-dependent protein binding activity. Predicted to be involved in ERAD pathway; negative regulation of RIG-I signaling pathway; and negative regulation of type I interferon production. Located in cytoplasm. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Is expressed in several structures, including brain; branchial arch; cardiovascular system; forelimb bud; and sensory organ. 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: Ubiquitous expression in testis adult (RPKM 28.2), CNS E14 (RPKM 15.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 16 A3; 16 11.65 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	16	NC_000082.7 (18630486..18654011)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	16	NC_000082.6 (18811736..18835261)

Chromosome 16 - NC_000082.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The study revealed a regulatory role of the p97-Npl4-Ufd1 complex in regulating a partial degradation of the NF-kappaB subunit p100.
Title: The Transitional Endoplasmic Reticulum ATPase p97 Regulates the Alternative Nuclear Factor NF-κB Signaling via Partial Degradation of the NF-κB Subunit p100.
structural analysis of the p97-Npl4-Ufd1 interface
Title: Detailed structural insights into the p97-Npl4-Ufd1 interface.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (1) 1 citation
Endonuclease-mediated (1)

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

Ufd1l (e-PCR), detects polymorphism
- UniSTS:256379

D18S1297 (e-PCR)
- UniSTS:18820

Ufd1l (e-PCR), detects polymorphism
- UniSTS:496815

U64445 (e-PCR)
- UniSTS:163566

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATPase binding	ISO Inferred from Sequence Orthology more info
enables K48-linked polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
enables signaling receptor 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
involved_in ERAD pathway	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type I interferon production	ISO Inferred from Sequence Orthology 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	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 UFD1-NPL4 complex	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
part_of VCP-NPL4-UFD1 AAA ATPase complex	NAS Non-traceable Author Statement more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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_011672.4 → NP_035802.3 ubiquitin recognition factor in ER-associated degradation protein 1

See identical proteins and their annotated locations for NP_035802.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and is the protein-coding transcript.

Source sequence(s)

AK147138, AW544149, CJ085208

Consensus CDS

CCDS28028.1

UniProtKB/Swiss-Prot

P70362, Q923C4

UniProtKB/TrEMBL

Q9CWQ7

Related

ENSMUSP00000005394.7, ENSMUST00000005394.13

Conserved Domains (1) summary

pfam03152
Location:19 → 193

UFD1; Ubiquitin fusion degradation protein UFD1

RNA

NR_028403.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1, that causes a frameshift. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is therefore not thought to encode a protein.

Source sequence(s)

AK147138, AW544149, CJ053815, CJ085208

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000082.7 Reference GRCm39 C57BL/6J

Range

18630486..18654011

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006522006.4 → XP_006522069.1 ubiquitin recognition factor in ER-associated degradation protein 1 isoform X2

See identical proteins and their annotated locations for XP_006522069.1

UniProtKB/TrEMBL

Q9CWQ7

Conserved Domains (1) summary

pfam03152
Location:14 → 188

UFD1; Ubiquitin fusion degradation protein UFD1
XM_006522007.4 → XP_006522070.1 ubiquitin recognition factor in ER-associated degradation protein 1 isoform X3

See identical proteins and their annotated locations for XP_006522070.1

UniProtKB/TrEMBL

Q9CZJ3

Conserved Domains (1) summary

pfam03152
Location:3 → 150

UFD1; Ubiquitin fusion degradation protein UFD1
XM_006522005.4 → XP_006522068.1 ubiquitin recognition factor in ER-associated degradation protein 1 isoform X1

See identical proteins and their annotated locations for XP_006522068.1

UniProtKB/Swiss-Prot

P70362, Q923C4

UniProtKB/TrEMBL

Q9CWQ7

Related

ENSMUSP00000111241.4, ENSMUST00000115578.10

Conserved Domains (1) summary

pfam03152
Location:19 → 193

UFD1; Ubiquitin fusion degradation protein UFD1