Nploc4 NPL4 homolog, ubiquitin recognition factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nploc4provided by RGD
Official Full Name: NPL4 homolog, ubiquitin recognition factorprovided by RGD
Primary source: RGD:620794
See related: Ensembl:ENSRNOG00000036698 AllianceGenome:RGD:620794
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: Npl4
Summary: Enables ATPase binding activity; ubiquitin binding activity; and ubiquitin protein ligase binding activity. Contributes to K48-linked polyubiquitin modification-dependent protein binding activity and K63-linked polyubiquitin modification-dependent protein binding activity. Involved in Golgi organization. Located in cytosol and nucleus. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. Orthologous to human NPLOC4 (NPL4 homolog, ubiquitin recognition factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 118.9), Heart (RPKM 105.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (106152756..106208306, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (105654395..105709958, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (109553518..109610087, complement)

Chromosome 10 - NC_086028.1 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
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.
Results report the solution structure of the NZF domain from Npl4 in complex with ubiquitin.
Title: Ubiquitin interactions of NZF zinc fingers.

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

RH141802 (e-PCR)
- UniSTS:223794

RH136692 (e-PCR)
- UniSTS:218781

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to K48-linked polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to K63-linked polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay 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-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in ERAD pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in Golgi organization	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in membrane fusion	IDA Inferred from Direct Assay more info	PubMed
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 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	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	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	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 cytosol	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: nuclear protein localization protein 4 homolog

Names: homolog of yeast nuclear protein localization 4; 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_080577.2 → NP_542144.1 nuclear protein localization protein 4 homolog

See identical proteins and their annotated locations for NP_542144.1

Status: PROVISIONAL

Source sequence(s)

BC101887

UniProtKB/Swiss-Prot

Q3T1J3, Q9ES54

UniProtKB/TrEMBL

A0A0G2JU66, A6HLC6, F1LQX9

Related

ENSRNOP00000068982.2, ENSRNOT00000080188.2

Conserved Domains (5) summary

COG5100
Location:5 → 560

NPL4; Nuclear pore protein [Nuclear structure]

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:1 → 80

UN_NPL4; Nuclear pore localization protein NPL4

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_086028.1 Reference GRCr8

Range

106152756..106208306 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039085086.2 → XP_038941014.1 nuclear protein localization protein 4 homolog isoform X1

UniProtKB/TrEMBL

A0A0G2JU66, F1LQX9

Conserved Domains (5) summary

smart00547
Location:560 → 582

ZnF_RBZ; Zinc finger domain

sd00029
Location:560 → 579

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

pfam05020
Location:105 → 245

zf-NPL4; NPL4 family, putative zinc binding region

pfam11543
Location:6 → 79

UN_NPL4; Nuclear pore localization protein NPL4

cl13996
Location:249 → 532

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