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Ngly1 N-glycanase 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 361014, updated on 2-Nov-2024

Summary

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Symbol
Ngly1provided by RGD
Full Name
N-glycanase 1provided by RGD
Primary source
RGD:1308518
See related
EnsemblRapid:ENSRNOG00000006143 AllianceGenome:RGD:1308518
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity. Predicted to be involved in glycoprotein catabolic process and positive regulation of BMP signaling pathway. Predicted to be located in cytoplasm. Predicted to be active in cytosol and nucleus. Used to study congenital disorder of deglycosylation 1. Human ortholog(s) of this gene implicated in congenital disorder of deglycosylation 1. Orthologous to human NGLY1 (N-glycanase 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Liver (RPKM 267.0), Kidney (RPKM 237.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ngly1 in Genome Data Viewer
Location:
15p16
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (11584475..11640977, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (9153738..9210228, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (10405453..10455973, complement)

Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene retinoic acid receptor, beta Neighboring gene DNA topoisomerase II beta Neighboring gene uncharacterized LOC120097102 Neighboring gene 3-oxoacyl-ACP synthase, mitochondrial

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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Related articles in PubMed

  1. Ngly1 -/- rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems. Asahina M, et al. Hum Mol Genet, 2020 Jun 27. PMID 32259258, Free PMC Article
  2. Tissue-specific regulation of BMP signaling by Drosophila N-glycanase 1. Galeone A, et al. Elife, 2017 Aug 4. PMID 28826503, Free PMC Article
  3. A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins. Katiyar S, et al. Proc Natl Acad Sci U S A, 2004 Sep 21. PMID 15358861, Free PMC Article
  4. Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis. Na CH, et al. J Proteome Res, 2012 Sep 7. PMID 22871113, Free PMC Article
  5. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, et al. Nature, 2004 Apr 1. PMID 15057822

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ngly1 -/- rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems.
    Title: Ngly1 -/- rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems.
Submit: New GeneRIF Correction

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in glycoprotein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycoprotein catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in glycoprotein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycoprotein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of BMP signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Names
PNGase
peptide:N-glycanase
NP_001014158.1
NP_001401916.1
XP_038949378.1
XP_038949379.1
XP_038949380.1
XP_038949381.1

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_001014136.2 → NP_001014158.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 1

    See identical proteins and their annotated locations for NP_001014158.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015
    UniProtKB/TrEMBL
    A0A8I5ZUV9
    Related
    ENSRNOP00000008289.7, ENSRNOT00000008289.8
    Conserved Domains (5) summary
    cd10459
    Location:19 → 109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    COG1305
    Location:290 → 351
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:272 → 351
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:335 → 419
    Rad4; Rad4 transglutaminase-like domain
    pfam04721
    Location:454 → 603
    PAW; PNGase C-terminal domain, mannose-binding module PAW

  2. NM_001414987.1 → NP_001401916.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015
    UniProtKB/Swiss-Prot
    Q5XI55
    UniProtKB/TrEMBL
    A6K047
    Related
    ENSRNOP00000083143.1, ENSRNOT00000104278.2

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

  1. NC_086033.1 Reference GRCr8

    Range
    11584475..11640977 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039093451.2 → XP_038949379.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X2

    UniProtKB/TrEMBL
    A0A8I5ZUV9
    Conserved Domains (4) summary
    pfam01841
    Location:195 → 274
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:377 → 571
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl10615
    Location:258 → 325
    sm_acid_XPC-like; small acidic domain of Xeroderma pigmentosum group C complementing protein and similar proteins
    cl15262
    Location:1 → 32
    PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins

  2. XM_039093450.2 → XP_038949378.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZUV9, A0A8I6A5T0
    Related
    ENSRNOP00000086683.1, ENSRNOT00000116474.2
    Conserved Domains (4) summary
    cd10459
    Location:19 → 109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    pfam01841
    Location:272 → 351
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:454 → 586
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl10615
    Location:335 → 402
    sm_acid_XPC-like; small acidic domain of Xeroderma pigmentosum group C complementing protein and similar proteins

  3. XM_039093452.2 → XP_038949380.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X3

    UniProtKB/TrEMBL
    A0A8I5ZUV9
    Conserved Domains (4) summary
    pfam01841
    Location:193 → 272
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:375 → 569
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl10615
    Location:256 → 323
    sm_acid_XPC-like; small acidic domain of Xeroderma pigmentosum group C complementing protein and similar proteins
    cl15262
    Location:19 → 110
    PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins

  4. XM_039093453.2 → XP_038949381.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X4

    Conserved Domains (3) summary
    pfam01841
    Location:130 → 209
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:312 → 506
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl10615
    Location:193 → 260
    sm_acid_XPC-like; small acidic domain of Xeroderma pigmentosum group C complementing protein and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5XI55.2 GenPept UniProtKB/Swiss-Prot:Q5XI55

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