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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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