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shmt1 serine hydroxymethyltransferase 1 (soluble) [ Danio rerio (zebrafish) ]

Gene ID: 394021, updated on 11-Apr-2024

Summary

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Official Symbol
shmt1provided by ZNC
Official Full Name
serine hydroxymethyltransferase 1 (soluble)provided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-1558
See related
Ensembl:ENSDARG00000052816 AllianceGenome:ZFIN:ZDB-GENE-040426-1558
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
Also known as
zgc:66171; zgc:77524
Summary
Enables glycine hydroxymethyltransferase activity. Predicted to be involved in several processes, including L-serine metabolic process; folic acid-containing compound metabolic process; and protein homotetramerization. Predicted to act upstream of or within methylation. Located in cytosol and nucleus. Is expressed in several structures, including digestive system; immature eye; midbrain; neural tube; and oocyte. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See shmt1 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
12
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (40260974..40276034, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (40119113..40136184, complement)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase III alpha Neighboring gene Smith-Magenis syndrome chromosome region, candidate 8a Neighboring gene pdgfa associated protein 1b Neighboring gene BUD31 homolog

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. 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. Cloning, expression, purification, and characterization of zebrafish cytosolic serine hydroxymethyltransferase. Chang WN, et al. Protein Expr Purif, 2006 Apr. PMID 16242955
  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. Brief embryonic strychnine exposure in zebrafish causes long-term adult behavioral impairment with indications of embryonic synaptic changes. Roy NM, et al. Neurotoxicol Teratol, 2012 Nov-Dec. PMID 23022260, Free PMC Article
  5. Dynamics of Zebrafish Heart Regeneration Using an HPLC-ESI-MS/MS Approach. Ma D, et al. J Proteome Res, 2018 Mar 2. PMID 29369637

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC66171

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 glycine hydroxymethyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
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 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
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
serine hydroxymethyltransferase, cytosolic
Names
zSHMT-1
NP_957340.1

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_201046.1 → NP_957340.1  serine hydroxymethyltransferase, cytosolic

    See identical proteins and their annotated locations for NP_957340.1

    Status: PROVISIONAL

    Source sequence(s)
    BC055527
    UniProtKB/TrEMBL
    Q7SXN1
    Related
    ENSDARP00000069223.4, ENSDART00000074737.6
    Conserved Domains (2) summary
    PLN03226
    Location:22 → 478
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:23 → 422
    SHMT; Serine hydroxymethyltransferase

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007114.7 Reference GRCz11 Primary Assembly

    Range
    40260974..40276034 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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