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NPLOC4 NPL4 homolog, ubiquitin recognition factor [ Homo sapiens (human) ]

Gene ID: 55666, updated on 4-Jan-2025

Summary

Official Symbol
NPLOC4provided by HGNC
Official Full Name
NPL4 homolog, ubiquitin recognition factorprovided by HGNC
Primary source
HGNC:HGNC:18261
See related
Ensembl:ENSG00000182446 MIM:606590; AllianceGenome:HGNC:18261
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPL4
Summary
Predicted to enable 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 negative regulation of RIG-I signaling pathway; negative regulation of type I interferon production; and proteolysis involved in protein catabolic process. Located in nucleus. Part of UFD1-NPL4 complex and VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Jan 2025]
Expression
Ubiquitous expression in testis (RPKM 14.2), esophagus (RPKM 10.3) and 25 other tissues See more
Orthologs
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Genomic context

See NPLOC4 in Genome Data Viewer
Location:
17q25.3
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81556885..81637112, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82474164..82554047, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79523911..79604138, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482073-79482696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482697-79483322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79483947-79484572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79484573-79485196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495325-79495851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495852-79496377 Neighboring gene fascin actin-bundling protein 2, retinal Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79504525-79505496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79507853-79508353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79516844-79517639 Neighboring gene FA core complex associated protein 100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9136 Neighboring gene uncharacterized LOC124904085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79520435-79521010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79525737-79526238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79526239-79526738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12972 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:79537592-79537800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79585853-79586396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:79586397-79586940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9140 Neighboring gene tetraspanin 10 Neighboring gene phosphodiesterase 6G

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Digital quantification of human eye color highlights genetic association of three new loci.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpu vpu The VCP-UFD1L-NPL4 complex is required for HIV-1 Vpu-induced CD4 degradation in the ER-associated degradation pathway. The ATPase activity of VCP and ubiquitin binding to UFD1L are important for CD4 degradation by Vpu PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Clone Names

  • FLJ14336, FLJ20657, FLJ23742, KIAA1499

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase binding  
enables K48-linked polyubiquitin modification-dependent protein binding  
enables K63-linked polyubiquitin modification-dependent protein binding  
enables metal ion binding  
enables protein binding PubMed 
enables protein-containing complex binding  
enables ubiquitin binding  
enables ubiquitin protein ligase binding  
Component Evidence Code Pubs
part_of UFD1-NPL4 complex PubMed 
part_of VCP-NPL4-UFD1 AAA ATPase complex PubMed 
part_of VCP-NPL4-UFD1 AAA ATPase complex PubMed 
part_of VCP-NPL4-UFD1 AAA ATPase complex  
located_in cytosol  
located_in endoplasmic reticulum PubMed 
located_in nuclear outer membrane-endoplasmic reticulum membrane network PubMed 
located_in nucleoplasm  
located_in nucleus PubMed 
is_active_in nucleus  

General protein information

Preferred Names
nuclear protein localization protein 4 homolog
Names
NPLOC4 ubiquitin recognition factor
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)

  1. NM_001369698.1NP_001356627.1  nuclear protein localization protein 4 homolog isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC137896, AC139530
    UniProtKB/TrEMBL
    A0A994J7H4
    Conserved Domains (5) summary
    smart00547
    Location:589611
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:589608
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam05021
    Location:249561
    NPL4; NPL4 family
    pfam05020
    Location:105245
    zf-NPL4; NPL4 family, putative zinc binding region
    pfam11543
    Location:180
    UN_NPL4; Nuclear pore localization protein NPL4
  2. NM_017921.4NP_060391.2  nuclear protein localization protein 4 homolog isoform 1

    See identical proteins and their annotated locations for NP_060391.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AB040932, AC137896, AK000664, BC025930, HY116973
    Consensus CDS
    CCDS45812.1
    UniProtKB/Swiss-Prot
    Q8N3J1, Q8TAT6, Q9H8V2, Q9H964, Q9NWR5, Q9P229
    UniProtKB/TrEMBL
    A0A994J7H4
    Related
    ENSP00000331487.5, ENST00000331134.11
    Conserved Domains (5) summary
    COG5100
    Location:5560
    NPL4; Nuclear pore protein [Nuclear structure]
    sd00029
    Location:584603
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam05020
    Location:105245
    zf-NPL4; NPL4 family, putative zinc binding region
    pfam05021
    Location:249556
    NPL4; NPL4 family
    pfam11543
    Location:180
    UN_NPL4; Nuclear pore localization protein NPL4

RNA

  1. NR_130139.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC137896, AK000664, BU542911, CK903591, HY179409
  2. NR_130140.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks multiple 5' exons and contains an alternate 5' terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC137896, AK000664, DA998574

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81556885..81637112 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436365.1XP_047292321.1  nuclear protein localization protein 4 homolog isoform X3

    UniProtKB/TrEMBL
    A0A994J7H4
  2. XM_011524980.2XP_011523282.1  nuclear protein localization protein 4 homolog isoform X2

    UniProtKB/TrEMBL
    A0A994J7H4
    Conserved Domains (4) summary
    COG5100
    Location:5564
    NPL4; Nuclear pore protein [Nuclear structure]
    pfam05020
    Location:105245
    zf-NPL4; NPL4 family, putative zinc binding region
    pfam05021
    Location:249561
    NPL4; NPL4 family
    pfam11543
    Location:180
    UN_NPL4; Nuclear pore localization protein NPL4
  3. XM_047436368.1XP_047292324.1  nuclear protein localization protein 4 homolog isoform X7

  4. XM_011524982.3XP_011523284.1  nuclear protein localization protein 4 homolog isoform X4

    UniProtKB/TrEMBL
    A0A994J7H4
    Conserved Domains (4) summary
    COG5100
    Location:5564
    NPL4; Nuclear pore protein [Nuclear structure]
    pfam05020
    Location:105245
    zf-NPL4; NPL4 family, putative zinc binding region
    pfam05021
    Location:249561
    NPL4; NPL4 family
    pfam11543
    Location:180
    UN_NPL4; Nuclear pore localization protein NPL4
  5. XM_047436366.1XP_047292322.1  nuclear protein localization protein 4 homolog isoform X5

    UniProtKB/TrEMBL
    A0A994J7H4
  6. XM_011524979.2XP_011523281.1  nuclear protein localization protein 4 homolog isoform X1

    See identical proteins and their annotated locations for XP_011523281.1

    UniProtKB/TrEMBL
    A0A994J7H4
    Related
    ENSP00000363879.5, ENST00000374747.9
    Conserved Domains (4) summary
    COG5100
    Location:5558
    NPL4; Nuclear pore protein [Nuclear structure]
    pfam05020
    Location:105245
    zf-NPL4; NPL4 family, putative zinc binding region
    pfam05021
    Location:249556
    NPL4; NPL4 family
    pfam11543
    Location:180
    UN_NPL4; Nuclear pore localization protein NPL4
  7. XM_047436367.1XP_047292323.1  nuclear protein localization protein 4 homolog isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82474164..82554047 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316630.1XP_054172605.1  nuclear protein localization protein 4 homolog isoform X3

    UniProtKB/TrEMBL
    A0A994J7H4
  2. XM_054316629.1XP_054172604.1  nuclear protein localization protein 4 homolog isoform X2

    UniProtKB/TrEMBL
    A0A994J7H4
  3. XM_054316635.1XP_054172610.1  nuclear protein localization protein 4 homolog isoform X7

  4. XM_054316631.1XP_054172606.1  nuclear protein localization protein 4 homolog isoform X8

    UniProtKB/TrEMBL
    A0A994J7H4
  5. XM_054316632.1XP_054172607.1  nuclear protein localization protein 4 homolog isoform X4

    UniProtKB/TrEMBL
    A0A994J7H4
  6. XM_054316633.1XP_054172608.1  nuclear protein localization protein 4 homolog isoform X5

    UniProtKB/TrEMBL
    A0A994J7H4
  7. XM_054316628.1XP_054172603.1  nuclear protein localization protein 4 homolog isoform X1

    UniProtKB/TrEMBL
    A0A994J7H4
  8. XM_054316634.1XP_054172609.1  nuclear protein localization protein 4 homolog isoform X6

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