Shmt1 serine hydroxymethyltransferase 1 (soluble) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Shmt1provided by MGI
Official Full Name: serine hydroxymethyltransferase 1 (soluble)provided by MGI
Primary source: MGI:MGI:98299
See related: Ensembl:ENSMUSG00000020534 Vega:OTTMUSG00000007760
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Shmt; mshmt; C81125; mshmt1; mshmt2; AI324848; AI385541
Expression: Broad expression in liver adult (RPKM 76.7), kidney adult (RPKM 33.5) and 15 other tissues See more
Orthologs: human all

Genomic context

Location:: 11; 11 B2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
106	current	GRCm38.p4 (GCF_000001635.24)	11	NC_000077.6 (60788886..60811265, complement)
Build 37.2	previous assembly	MGSCv37 (GCF_000001635.18)	11	NC_000077.5 (60602399..60624767, complement)

Chromosome 11 - NC_000077.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Shmt1 and dietary folate deficiency influence metabolic markers of homocysteine remethylation in mice.
Title: Disruption of shmt1 impairs hippocampal neurogenesis and mnemonic function in mice.
SHMT1 and TYMS localization to the nucleus is essential to prevent uracil accumulation in DNA
Title: Nuclear localization of de novo thymidylate biosynthesis pathway is required to prevent uracil accumulation in DNA.
Data show that Shmt1 hemizygosity was associated with increased risk for intestinal cancer in Apc(min)(/+) mice through a gene-by-diet interaction.
Title: Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk.
These results provide evidence that disruption of Shmt1 expression causes NTDs by impairing thymidylate biosynthesis and shows that changes in the expression of genes that encode folate-dependent enzymes may be key determinates of NTD risk.
Title: Shmt1 and de novo thymidylate biosynthesis underlie folate-responsive neural tube defects in mice.
It is one of the genetic components regulating PPI in mice and is relevant to schizophrenia susceptibility in humans. (review)
Title: [Analysis of mouse strain-dependent prepulse inhibition points to a role for Shmt1 (SHMT1) in mice and in schizophrenia].
Shmt1 (SHMT1), but not Srr, is likely to be one of the genetic components regulating prepulse inhibition in mice and possibly relevant to human schizophrenia.
Title: Analysis of strain-dependent prepulse inhibition points to a role for Shmt1 (SHMT1) in mice and in schizophrenia.
SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis
Title: SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis.
mitochondrial SHMT-derived one-carbon units are essential for folate-mediated one-carbon metabolism in the cytoplasm
Title: Cytoplasmic serine hydroxymethyltransferase regulates the metabolic partitioning of methylenetetrahydrofolate but is not essential in mice.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (2)
Targeted (4) 1 citation

Pathways from BioSystems

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Antifolate resistance, organism-specific biosystem (from KEGG)
Antifolate resistance, organism-specific biosystemSince the 1940s, antifolates have played a pivotal role in drug treatment of malignant, microbial, parasitic and chronic inflammatory diseases. The molecular basis of the anti-proliferative activity ...
Antifolate resistance, conserved biosystem (from KEGG)
Antifolate resistance, conserved biosystemSince the 1940s, antifolates have played a pivotal role in drug treatment of malignant, microbial, parasitic and chronic inflammatory diseases. The molecular basis of the anti-proliferative activity ...
Biosynthesis of amino acids, organism-specific biosystem (from KEGG)
Biosynthesis of amino acids, organism-specific biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
Biosynthesis of amino acids, conserved biosystem (from KEGG)
Biosynthesis of amino acids, conserved biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
Branched-chain amino acid catabolism, organism-specific biosystem (from REACTOME)
Branched-chain amino acid catabolism, organism-specific biosystemcomputationally inferred pathway (not manually curated)
C1-unit interconversion, eukaryotes, organism-specific biosystem (from KEGG)
C1-unit interconversion, eukaryotes, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Cofactor and vitamin biosynthesis
C1-unit interconversion, eukaryotes, conserved biosystem (from KEGG)
C1-unit interconversion, eukaryotes, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Cofactor and vitamin biosynthesis
Carbon metabolism, organism-specific biosystem (from KEGG)
Carbon metabolism, organism-specific biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
Carbon metabolism, conserved biosystem (from KEGG)
Carbon metabolism, conserved biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
Carnitine synthesis, organism-specific biosystem (from REACTOME)
Carnitine synthesis, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Glutathione and one carbon metabolism, organism-specific biosystem (from WikiPathways)
Glutathione and one carbon metabolism, organism-specific biosystemThis pathway provides a combined view on the one-carbon and glutathione metabolism pathways. Based on existing pathways: * [[Pathway:WP435|WP435]] * [[Pathway:WP164|WP164]]
Glycine, serine and threonine metabolism, organism-specific biosystem (from KEGG)
Glycine, serine and threonine metabolism, organism-specific biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
Glycine, serine and threonine metabolism, conserved biosystem (from KEGG)
Glycine, serine and threonine metabolism, conserved biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
Glyoxylate and dicarboxylate metabolism, organism-specific biosystem (from KEGG)
Glyoxylate and dicarboxylate metabolism, organism-specific biosystem
Glyoxylate and dicarboxylate metabolism
Glyoxylate and dicarboxylate metabolism, conserved biosystem (from KEGG)
Glyoxylate and dicarboxylate metabolism, conserved biosystem
Glyoxylate and dicarboxylate metabolism
Metabolic pathways, organism-specific biosystem (from KEGG)
Metabolic pathways, organism-specific biosystem
Metabolic pathways
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Metabolism of amino acids and derivatives, organism-specific biosystem (from REACTOME)
Metabolism of amino acids and derivatives, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Metabolism of folate and pterines, organism-specific biosystem (from REACTOME)
Metabolism of folate and pterines, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
Metabolism of vitamins and cofactors, organism-specific biosystemcomputationally inferred pathway (not manually curated)
Metabolism of water-soluble vitamins and cofactors, organism-specific biosystem (from REACTOME)
Metabolism of water-soluble vitamins and cofactors, organism-specific biosystemcomputationally inferred pathway (not manually curated)
One Carbon Metabolism, organism-specific biosystem (from WikiPathways)
One Carbon Metabolism, organism-specific biosystemThis one-carbon metabolism pathway is centered around folate. Folate is the primary methyl-group donor for processes such as DNA methylation reactions, nucleotide synthesis and DNA repair mechanisms....
One carbon metabolism and related pathways, organism-specific biosystem (from WikiPathways)
One carbon metabolism and related pathways, organism-specific biosystemThis pathway shows the carbon metabolism over grey and related pathways around it.
One carbon pool by folate, organism-specific biosystem (from KEGG)
One carbon pool by folate, organism-specific biosystem
One carbon pool by folate
One carbon pool by folate, conserved biosystem (from KEGG)
One carbon pool by folate, conserved biosystem
One carbon pool by folate
Serine degradation II, organism-specific biosystem (from BIOCYC)
Serine degradation II, organism-specific biosystem
Serine degradation II
folate polyglutamylation, organism-specific biosystem (from BIOCYC)
folate polyglutamylation, organism-specific biosystem
folate polyglutamylation
folate transformations I, organism-specific biosystem (from BIOCYC)
folate transformations I, organism-specific biosystem
folate transformations I
folate transformations II (plants), organism-specific biosystem (from BIOCYC)
folate transformations II (plants), organism-specific biosystem
folate transformations II (plants)
glycine betaine degradation, organism-specific biosystem (from BIOCYC)
glycine betaine degradation, organism-specific biosystem
glycine betaine degradation
glycine biosynthesis I, organism-specific biosystem (from BIOCYC)
glycine biosynthesis I, organism-specific biosystem
glycine biosynthesis I
superpathway of serine and glycine biosynthesis I, organism-specific biosystem (from BIOCYC)
superpathway of serine and glycine biosynthesis I, organism-specific biosystem
superpathway of serine and glycine biosynthesis I

General gene information

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Markers

NoName (e-PCR)
- UniSTS:224581

AI324848 (e-PCR)
- UniSTS:160102

RH127015 (e-PCR)
- UniSTS:209774

Shmt1 (e-PCR), detects polymorphism
- UniSTS:546986

AI385541 (e-PCR)
- UniSTS:180217

Homology

Homologs of the Shmt1 gene: The Shmt1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, and frog.
Orthologs from Annotation Pipeline: 238 organisms have orthologs with human gene Shmt1
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
L-allo-threonine aldolase activity	ISO Inferred from Sequence Orthology more info
amino acid binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
amino acid binding	ISO Inferred from Sequence Orthology more info
catalytic activity	IEA Inferred from Electronic Annotation more info
cobalt ion binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
glycine hydroxymethyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
glycine hydroxymethyltransferase activity	ISO Inferred from Sequence Orthology more info
identical protein binding	ISO Inferred from Sequence Orthology more info
mRNA 5'-UTR binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA 5'-UTR binding	ISO Inferred from Sequence Orthology more info
protein homodimerization activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein homodimerization activity	ISO Inferred from Sequence Orthology more info
pyridoxal phosphate binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
pyridoxal phosphate binding	ISO Inferred from Sequence Orthology more info
serine binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
serine binding	ISO Inferred from Sequence Orthology more info
transferase activity	IEA Inferred from Electronic Annotation more info
translation repressor activity, mRNA regulatory element binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
translation repressor activity, mRNA regulatory element binding	ISO Inferred from Sequence Orthology more info
zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
L-serine catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
L-serine catabolic process	ISO Inferred from Sequence Orthology more info
L-serine metabolic process	ISO Inferred from Sequence Orthology more info
cellular response to leukemia inhibitory factor	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
cellular response to tetrahydrofolate	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cellular response to tetrahydrofolate	ISO Inferred from Sequence Orthology more info
dTMP biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
folic acid metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
folic acid metabolic process	ISO Inferred from Sequence Orthology more info
glycine biosynthetic process	ISO Inferred from Sequence Orthology more info
glycine biosynthetic process from serine	IBA Inferred from Biological aspect of Ancestor more info	PubMed
glycine biosynthetic process from serine	ISO Inferred from Sequence Orthology more info
glycine metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
glycine metabolic process	ISO Inferred from Sequence Orthology more info
negative regulation of translation	ISO Inferred from Sequence Orthology more info
one-carbon metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
one-carbon metabolic process	IC Inferred by Curator more info	PubMed
protein homotetramerization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein homotetramerization	ISO Inferred from Sequence Orthology more info
protein tetramerization	ISO Inferred from Sequence Orthology more info
purine nucleobase biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
purine nucleobase biosynthetic process	ISO Inferred from Sequence Orthology more info
tetrahydrofolate interconversion	IBA Inferred from Biological aspect of Ancestor more info	PubMed
tetrahydrofolate interconversion	ISO Inferred from Sequence Orthology more info
tetrahydrofolate metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
tetrahydrofolate metabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
cytoplasm	IEA Inferred from Electronic Annotation more info
cytosol	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytosol	ISO Inferred from Sequence Orthology more info
mitochondrion	HDA more info	PubMed
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: serine hydroxymethyltransferase, cytosolic

Names: glycine hydroxymethyltransferase; serine methylase

NP_033197.2

EC 2.1.2.1

XP_006532707.1

EC 2.1.2.1

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.