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    phgdh phosphoglycerate dehydrogenase [ Danio rerio (zebrafish) ]

    Gene ID: 321928, updated on 9-Dec-2024

    Summary

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    Official Symbol
    phgdhprovided by ZNC
    Official Full Name
    phosphoglycerate dehydrogenaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-647
    See related
    Ensembl:ENSDARG00000001873 AllianceGenome:ZFIN:ZDB-GENE-030131-647
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fb38f06; zgc:65956; wu:fb38f06
    Summary
    Predicted to enable phosphoglycerate dehydrogenase activity. Predicted to act upstream of or within L-serine biosynthetic process. Is expressed in annular ligament. Human ortholog(s) of this gene implicated in Neu-Laxova syndrome 1; PHGDH deficiency; and amino acid metabolic disorder. Orthologous to human PHGDH (phosphoglycerate dehydrogenase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See phgdh in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (48185936..48214218, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (48488541..48516823, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene kelch-like family member 23 Neighboring gene transfer RNA arginine (anticodon CCU) Neighboring gene transfer RNA methionine (anticodon CAU) Neighboring gene cilia and flagella associated protein 210 Neighboring gene FAST kinase domains 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. INPP5K and SIL1 associated pathologies with overlapping clinical phenotypes converge through dysregulation of PHGDH. Hathazi D, et al. Brain, 2021 Sep 4. PMID 33792664, Free PMC Article
    2. Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle. Li Y, et al. PLoS Comput Biol, 2015 Feb. PMID 25714999, Free PMC Article
    3. Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin. Higdon CW, et al. PLoS One, 2013. PMID 23874447, Free PMC Article
    4. The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. Schüttler A, et al. Toxicol Sci, 2017 Jun 1. PMID 28329862, Free PMC Article
    5. Malate enhances survival of zebrafish against Vibrio alginolyticus infection in the same manner as taurine. Yang MJ, et al. Virulence, 2020 Dec. PMID 32316833, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoglycerate dehydrogenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphoglycerate dehydrogenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within L-serine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within amino acid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    D-3-phosphoglycerate dehydrogenase
    NP_955871.2

    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_199577.2 → NP_955871.2  D-3-phosphoglycerate dehydrogenase

      Status: VALIDATED

      Source sequence(s)
      BX321905, EH435992, EH460654, EH592171, EH600120, EH609675
      UniProtKB/TrEMBL
      A0A8M1PFH7, F1QEY8
      Related
      ENSDARP00000020860.6, ENSDART00000012938.7
      Conserved Domains (2) summary
      cd12173
      Location:8 → 310
      PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
      TIGR01327
      Location:8 → 499
      PGDH; D-3-phosphoglycerate dehydrogenase

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      48185936..48214218 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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