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    shmt2 serine hydroxymethyltransferase 2 (mitochondrial) [ Danio rerio (zebrafish) ]

    Gene ID: 100144628, updated on 2-Nov-2024

    Summary

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    Official Symbol
    shmt2provided by ZNC
    Official Full Name
    serine hydroxymethyltransferase 2 (mitochondrial)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-071213-1
    See related
    Ensembl:ENSDARG00000104414 AllianceGenome:ZFIN:ZDB-GENE-071213-1
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Summary
    Enables glycine hydroxymethyltransferase activity and pyridoxal phosphate binding activity. Predicted to be involved in glycine biosynthetic process from serine and tetrahydrofolate metabolic process. Predicted to act upstream of or within methylation and one-carbon metabolic process. Located in mitochondrion. Is expressed in digestive system; heart; muscle; nervous system; and pleuroperitoneal region. Used to study schizophrenia. Human ortholog(s) of this gene implicated in neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See shmt2 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (59176470..59230818)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (59182239..59235373)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 9 Neighboring gene neurexophilin 4 Neighboring gene family with sequence similarity 210 member B Neighboring gene protein phosphatase 1, regulatory subunit 16B

    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 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. Serine hydroxymethyltransferase isoforms are differentially inhibited by leucovorin: characterization and comparison of recombinant zebrafish serine hydroxymethyltransferases. Chang WN, et al. Drug Metab Dispos, 2007 Nov. PMID 17664250
    2. The TCA cycle transferase DLST is important for MYC-mediated leukemogenesis. Anderson NM, et al. Leukemia, 2016 Jun. PMID 26876595, Free PMC Article
    3. The Incoherent Fluctuation of Folate Pools and Differential Regulation of Folate Enzymes Prioritize Nucleotide Supply in the Zebrafish Model Displaying Folate Deficiency-Induced Microphthalmia and Visual Defects. Hsiao TH, et al. Front Cell Dev Biol, 2021. PMID 34268314, Free PMC Article
    4. Dynamic Editome of Zebrafish under Aminoglycosides Treatment and Its Potential Involvement in Ototoxicity. Yan S, et al. Front Pharmacol, 2017. PMID 29213239, Free PMC Article
    5. Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions. Thyme SB, et al. Cell, 2019 Apr 4. PMID 30929901, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables glycine hydroxymethyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycine hydroxymethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycine hydroxymethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase 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 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in glycine biosynthetic process from serine IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within glycine biosynthetic process from serine IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within one-carbon metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tetrahydrofolate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    serine hydroxymethyltransferase, mitochondrial
    Names
    mitochondrial serine hydroxymethyltransferase
    NP_001116846.1

    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_001123374.1 → NP_001116846.1  serine hydroxymethyltransferase, mitochondrial

      See identical proteins and their annotated locations for NP_001116846.1

      Status: PROVISIONAL

      Source sequence(s)
      EF213101
      UniProtKB/TrEMBL
      A0A0R4IBM1, A0A8M1NG89, A9LDD9
      Related
      ENSDARP00000132340.2, ENSDART00000161720.2
      Conserved Domains (2) summary
      PLN03226
      Location:34 → 489
      PLN03226; serine hydroxymethyltransferase; Provisional
      pfam00464
      Location:38 → 436
      SHMT; Serine hydroxymethyltransferase

    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_007117.7 Reference GRCz11 Primary Assembly

      Range
      59176470..59230818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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