Nploc4 NPL4 homolog, ubiquitin recognition factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nploc4provided by MGI
Official Full Name: NPL4 homolog, ubiquitin recognition factorprovided by MGI
Primary source: MGI:MGI:2679787
See related: Ensembl:ENSMUSG00000039703 AllianceGenome:MGI:2679787
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: Npl4; mKIAA1499
Summary: Predicted to enable ATPase binding activity; ubiquitin binding activity; and ubiquitin protein ligase binding activity. Predicted to contribute to K48-linked polyubiquitin modification-dependent protein binding activity and K63-linked polyubiquitin modification-dependent protein binding activity. Involved in retrograde protein transport, ER to cytosol. Part of VCP-NPL4-UFD1 AAA ATPase complex. Is expressed in lens. Orthologous to human NPLOC4 (NPL4 homolog, ubiquitin recognition factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis adult (RPKM 28.6), ovary adult (RPKM 21.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 E2; 11 84.09 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (120270624..120328526, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (120379798..120437700, complement)

Chromosome 11 - NC_000077.7 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.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:236785

NoName (e-PCR)
- UniSTS:236795

UniSTS:236796 (e-PCR)
- UniSTS:236796

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATPase binding	ISO Inferred from Sequence Orthology more info
contributes_to K48-linked polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
contributes_to K63-linked polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in ERAD pathway	EXP Inferred from Experiment more info	PubMed
involved_in Golgi organization	ISO Inferred from Sequence Orthology more info
involved_in Golgi organization	ISS Inferred from Sequence or Structural Similarity 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	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	ISO Inferred from Sequence Orthology more info
involved_in retrograde protein transport, ER to cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor 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	ISO Inferred from Sequence Orthology more info
part_of UFD1-NPL4 complex	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
part_of VCP-NPL4-UFD1 AAA ATPase complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear outer membrane-endoplasmic reticulum membrane network	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nuclear protein localization protein 4 homolog

Names: nuclear protein localization 4 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_001195023.1 → NP_001181952.1 nuclear protein localization protein 4 homolog isoform A

See identical proteins and their annotated locations for NP_001181952.1

Status: VALIDATED

Description

Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A).

Source sequence(s)

AK149912, AL669855

Consensus CDS

CCDS56827.1

UniProtKB/Swiss-Prot

B1ATY4, B1ATY5, P60670

UniProtKB/TrEMBL

Q3UDU9, Q3UE06

Related

ENSMUSP00000035851.9, ENSMUST00000044271.15

Conserved Domains (5) summary

smart00547
Location:584 → 606

ZnF_RBZ; Zinc finger domain

sd00029
Location:584 → 603

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam05020
Location:105 → 245

zf-NPL4; NPL4 family, putative zinc binding region

pfam05021
Location:249 → 556

NPL4; NPL4 family

pfam11543
Location:6 → 79

UN_NPL4; Nuclear pore localization protein NPL4
NM_199469.2 → NP_955763.1 nuclear protein localization protein 4 homolog isoform B

See identical proteins and their annotated locations for NP_955763.1

Status: VALIDATED

Description

Transcript Variant: This variant (B) lacks an in-frame exon in the coding region, compared to variant A. This results in a shorter protein (isoform B), compared to isoform A.

Source sequence(s)

AL669855, BC065156

Consensus CDS

CCDS25732.1

UniProtKB/TrEMBL

Q3UDU9, Q3UE06

Related

ENSMUSP00000099306.4, ENSMUST00000103017.4

Conserved Domains (5) summary

COG5100
Location:5 → 528

NPL4; Nuclear pore protein [Nuclear structure]

sd00029
Location:552 → 571

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam05020
Location:105 → 245

zf-NPL4; NPL4 family, putative zinc binding region

pfam11543
Location:1 → 80

UN_NPL4; Nuclear pore localization protein NPL4

cl13996
Location:249 → 524

MPN; Mpr1p, Pad1p N-terminal (MPN) domains

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_000077.7 Reference GRCm39 C57BL/6J

Range

120270624..120328526 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006533134.3 → XP_006533197.1 nuclear protein localization protein 4 homolog isoform X1

UniProtKB/TrEMBL

Q3UDU9, Q3UE06

Conserved Domains (3) summary

sd00029
Location:496 → 515

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam05020
Location:17 → 157

zf-NPL4; NPL4 family, putative zinc binding region

pfam05021
Location:161 → 468

NPL4; NPL4 family
XM_036156619.1 → XP_036012512.1 nuclear protein localization protein 4 homolog isoform X1

UniProtKB/TrEMBL

Q3UDU9, Q3UE06

Conserved Domains (3) summary

sd00029
Location:496 → 515

zf-RanBP2; RanBP2-type Zn finger [structural motif]

pfam05020
Location:17 → 157

zf-NPL4; NPL4 family, putative zinc binding region

pfam05021
Location:161 → 468

NPL4; NPL4 family