U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 100144628, updated on 19-May-2025
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, May 2025]
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table
See shmt2 in Genome Data Viewer
Location:
chromosome: 6
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 6 NC_133181.1 (62585275..62649100)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 6 NC_007117.7 (59176470..59230818)

Chromosome 6 - NC_133181.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC141386398 Neighboring gene uncharacterized LOC141386395 Neighboring gene neurexophilin 4 Neighboring gene uncharacterized LOC141386391 Neighboring gene uncharacterized LOC141386389 Neighboring gene cytochrome c oxidase subunit NDUFA4-like Neighboring gene uncharacterized LOC141386399

Go to nucleotide: Graphics FASTA GenBank

  • 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

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 (8) citations in PubMed

GeneRIFs: Gene References Into Functions

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

NEW Try the new Transcript table

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_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

  1. NC_133181.1 Reference GRCz12tu Primary Assembly

    Range
    62585275..62649100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_012407153.1 RNA Sequence

  2. XR_012407154.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials
Tools
Miscellaneous