Shmt1 serine hydroxymethyltransferase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Shmt1provided by RGD
Official Full Name: serine hydroxymethyltransferase 1provided by RGD
Primary source: RGD:1312011
See related: EnsemblRapid:ENSRNOG00000005275 AllianceGenome:RGD:1312011
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Shmt; mShmt; LRRGT00032
Summary: Enables several functions, including L-allo-threonine aldolase activity; glycine hydroxymethyltransferase activity; and pyridoxal phosphate binding activity. Involved in glycine biosynthetic process from serine. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in mitochondrion and nucleus. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Liver (RPKM 409.4), Kidney (RPKM 384.7) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q22

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (45968959..45990341, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (45468698..45490833, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (47030813..47059216, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of AGXT2, SHMT1, and ACO2 as important biomarkers of acute kidney injury by WGCNA.
Title: Identification of AGXT2, SHMT1, and ACO2 as important biomarkers of acute kidney injury by WGCNA.
The low activity of SHMT in the human and rat placenta suggests that, unlike in the sheep, placental conversion of serine to glycine is not a major source of fetal glycine in these species.
Title: Low serine hydroxymethyltransferase activity in the human placenta has important implications for fetal glycine supply.
Vitamin B 6 intake affects level of serine hydroxymethyltransferase in rat liver cytosol and mitochondria.
Title: Activities of hepatic cytosolic and mitochondrial forms of serine hydroxymethyltransferase and hepatic glycine concentration are affected by vitamin B-6 intake in rats.
SHMT enzymes are the major source of the one-carbon unit required for folate metabolism and for the biosynthesis of nucleotides and amino acids. Our data establish a novel functional link between Myc and the regulation of cellular metabolism.
Title: A functional screen for Myc-responsive genes reveals serine hydroxymethyltransferase, a major source of the one-carbon unit for cell metabolism.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH128681 (e-PCR)
- UniSTS:211989

RH142767 (e-PCR)
- UniSTS:232014

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

AI385541 (e-PCR)
- UniSTS:180217

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables L-allo-threonine aldolase activity	IDA Inferred from Direct Assay more info	PubMed
enables aldehyde-lyase activity	ISO Inferred from Sequence Orthology more info
enables amino acid binding	IPI Inferred from Physical Interaction more info	PubMed
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	ISO Inferred from Sequence Orthology more info
enables glycine hydroxymethyltransferase activity	TAS Traceable Author Statement more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA 5'-UTR binding	ISO Inferred from Sequence Orthology more info
enables mRNA regulatory element binding translation repressor activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
enables pyridoxal phosphate binding	TAS Traceable Author Statement more info	PubMed
enables serine binding	ISO Inferred from Sequence Orthology more info
enables small molecule binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in L-serine catabolic process	ISO Inferred from Sequence Orthology more info
involved_in L-serine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in L-serine metabolic process	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tetrahydrofolate	ISO Inferred from Sequence Orthology more info
involved_in dTMP biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in folic acid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine biosynthetic process from serine	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine biosynthetic process from serine	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycine metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	ISO Inferred from Sequence Orthology more info
involved_in purine nucleobase biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in tetrahydrofolate interconversion	IEA Inferred from Electronic Annotation more info
involved_in tetrahydrofolate interconversion	ISO Inferred from Sequence Orthology more info
involved_in tetrahydrofolate metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in tetrahydrofolate metabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: serine hydroxymethyltransferase, cytosolic

Names: serine hydroxymethyltransferase 1 (soluble)

NP_001400080.1

EC 2.1.2.1

XP_038941332.1

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.

mRNA and Protein(s)

NM_001413151.1 → NP_001400080.1 serine hydroxymethyltransferase, cytosolic

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A8I5ZKU9

Related

ENSRNOP00000105844.1, ENSRNOT00000156060.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

45968959..45990341 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039085404.2 → XP_038941332.1 serine hydroxymethyltransferase, cytosolic isoform X1

UniProtKB/TrEMBL

A6HF57, Q4KLG7

Conserved Domains (1) summary

cl18945
Location:1 → 343

AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001047842.1: Suppressed sequence

Description

NM_001047842.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.