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

Gene ID: 55666, updated on 6-Jan-2019

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
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
Expression
Ubiquitous expression in testis (RPKM 14.2), esophagus (RPKM 10.3) and 25 other tissues See more
Orthologs

Genomic context

See NPLOC4 in Genome Data Viewer
Location:
17q25.3
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (81556885..81637153, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79523913..79604138, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene fascin actin-bundling protein 2, retinal Neighboring gene FA core complex associated protein 100 Neighboring gene tetraspanin 10 Neighboring gene phosphodiesterase 6G

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Digital quantification of human eye color highlights genetic association of three new loci.
NHGRI GWA 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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14336, FLJ20657, FLJ23742, KIAA1499

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
Golgi organization ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
error-free translesion synthesis TAS
Traceable Author Statement
more info
 
negative regulation of RIG-I signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of type I interferon production IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent ERAD pathway ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
UFD1-NPL4 complex IPI
Inferred from Physical Interaction
more info
PubMed 
VCP-NPL4-UFD1 AAA ATPase complex IDA
Inferred from Direct Assay
more info
PubMed 
VCP-NPL4-UFD1 AAA ATPase complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nuclear outer membrane-endoplasmic reticulum membrane network ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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_017921.4NP_060391.2  nuclear protein localization protein 4 homolog

    See identical proteins and their annotated locations for NP_060391.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein.
    Source sequence(s)
    AB040932, AC137896, AK000664, BC025930, HY116973
    Consensus CDS
    CCDS45812.1
    UniProtKB/Swiss-Prot
    Q8TAT6
    UniProtKB/TrEMBL
    A0A024R8R4
    Related
    ENSP00000331487.5, ENST00000331134.10
    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

    Description
    Transcript Variant: This variant (2) 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, BU542911, CK903591, HY179409
  2. NR_130140.1 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, CK903591, DA998574

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    81556885..81637153 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524981.1XP_011523283.1  nuclear protein localization protein 4 homolog isoform X3

    Conserved Domains (5) summary
    COG5100
    Location:5565
    NPL4; Nuclear pore protein [Nuclear structure]
    sd00029
    Location:589608
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    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
  2. XM_011524980.1XP_011523282.1  nuclear protein localization protein 4 homolog isoform X2

    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_011524982.2XP_011523284.1  nuclear protein localization protein 4 homolog isoform X4

    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
  4. XM_011524979.1XP_011523281.1  nuclear protein localization protein 4 homolog isoform X1

    See identical proteins and their annotated locations for XP_011523281.1

    UniProtKB/Swiss-Prot
    Q8TAT6
    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

RNA

  1. XR_934501.1 RNA Sequence

  2. XR_934502.1 RNA Sequence

  3. XR_001752557.1 RNA Sequence

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