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    Gldc glycine decarboxylase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309312, updated on 6-Jun-2024

    Summary

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    Symbol
    Gldcprovided by RGD
    Full Name
    glycine decarboxylaseprovided by RGD
    Primary source
    RGD:1308660
    See related
    Ensembl:ENSRNOG00000011599 AllianceGenome:RGD:1308660
    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
    Enables anion binding activity; enzyme binding activity; and glycine dehydrogenase (decarboxylating) activity. Involved in glycine decarboxylation via glycine cleavage system and protein-containing complex assembly. Located in mitochondrion. Part of glycine cleavage complex. Human ortholog(s) of this gene implicated in glycine encephalopathy. Orthologous to human GLDC (glycine decarboxylase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 189.6), Kidney (RPKM 170.4) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Gldc in Genome Data Viewer
    Location:
    1q52
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (237296753..237375620, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (227883249..227962119, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (248295140..248377122, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 beta 2, pseudogene 3 Neighboring gene ubiquitin like with PHD and ring finger domains 2 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4, pseudogene 1 Neighboring gene cytochrome c, somatic, pseudogene 1

    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
    • 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. Epigenetic Silencing of the Putative Tumor Suppressor Gene GLDC (Glycine Dehydrogenase) in Gastric Carcinoma. Min HL, et al. Anticancer Res, 2016 Jan. PMID 26722042
    2. Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease. Bravo-Alonso I, et al. Hum Mutat, 2017 Jun. PMID 28244183
    3. Glycine decarboxylase deficiency causes neural tube defects and features of non-ketotic hyperglycinemia in mice. Pai YJ, et al. Nat Commun, 2015 Mar 4. PMID 25736695, Free PMC Article
    4. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. Kanno J, et al. J Med Genet, 2007 Mar. PMID 17361008, Free PMC Article
    5. Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. Flusser H, et al. Neurology, 2005 Apr 26. PMID 15851735

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables glycine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycine dehydrogenase (decarboxylating) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycine dehydrogenase (decarboxylating) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycine dehydrogenase (decarboxylating) activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pyridoxal phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pyridoxal phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in glycine catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in glycine decarboxylation via glycine cleavage system IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glycine decarboxylation via glycine cleavage system IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of glycine cleavage complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of glycine cleavage complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    glycine dehydrogenase (decarboxylating), mitochondrial
    Names
    glycine decarboxylase, glycine cleavage system protein P)
    glycine dehydrogenase (decarboxylating)
    glycine dehydrogenase (decarboxylating), mitochondrial-like
    glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)
    glycine dehydrogenase [decarboxylating], mitochondrial
    glycine dehydrogenase [decarboxylating], mitochondrial-like
    NP_001402873.1
    XP_006231273.1

    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_001415944.1 → NP_001402873.1  glycine dehydrogenase (decarboxylating), mitochondrial

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A0G2JUZ5
      Related
      ENSRNOP00000069291.2, ENSRNOT00000089073.2

    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_086019.1 Reference GRCr8

      Range
      237296753..237375620 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006231211.5 → XP_006231273.1  glycine dehydrogenase (decarboxylating), mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A0G2JUZ5
      Conserved Domains (3) summary
      PRK05367
      Location:61 → 823
      PRK05367; glycine dehydrogenase; Provisional
      pfam02347
      Location:69 → 492
      GDC-P; Glycine cleavage system P-protein
      cl18945
      Location:522 → 837
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107583.1: Suppressed sequence

      Description
      NM_001107583.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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