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

Gene ID: 20425, updated on 18-Apr-2024

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 AllianceGenome:MGI:98299
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; mshmt1; mshmt2
Summary
Enables glycine hydroxymethyltransferase activity. Involved in dTMP biosynthetic process and tetrahydrofolate interconversion. Acts upstream of or within cellular response to leukemia inhibitory factor. Located in nucleus. Is expressed in several structures, including alimentary system; brain ventricular layer; genitourinary system; liver and biliary system; and skin. 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]
Expression
Broad expression in liver adult (RPKM 76.7), kidney adult (RPKM 33.5) and 15 other tissues See more
Orthologs
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Genomic context

Location:
11 B2; 11 37.84 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (60679723..60702062, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (60788897..60811265, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_29657 Neighboring gene topoisomerase (DNA) III alpha Neighboring gene STARR-seq mESC enhancer starr_29659 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 8 homolog (human) Neighboring gene STARR-positive B cell enhancer ABC_E6992 Neighboring gene phosphoserine aminotransferase 1 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E8411 Neighboring gene dehydrogenase/reductase 7B

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (5)  1 citation
  • Gene trapped (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables L-allo-threonine aldolase activity ISO
Inferred from Sequence Orthology
more info
 
enables amino acid binding ISO
Inferred from Sequence Orthology
more info
 
enables glycine hydroxymethyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables glycine hydroxymethyltransferase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
enables glycine hydroxymethyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables glycine hydroxymethyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
enables serine binding ISO
Inferred from Sequence Orthology
more info
 
enables small molecule binding ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
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
 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to tetrahydrofolate ISO
Inferred from Sequence Orthology
more info
 
involved_in dTMP biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in folic acid metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in glycine biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in glycine biosynthetic process from serine IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in glycine biosynthetic process from serine ISO
Inferred from Sequence Orthology
more info
 
involved_in glycine metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of translation ISO
Inferred from Sequence Orthology
more info
 
involved_in one-carbon metabolic process IC
Inferred by Curator
more info
PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
located_in mitochondrion HDA PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IGI
Inferred from Genetic Interaction
more info
PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
serine hydroxymethyltransferase, cytosolic
Names
glycine hydroxymethyltransferase
serine methylase
NP_001412339.1
NP_001412340.1
NP_001412341.1
NP_001412342.1
NP_001412343.1
NP_033197.2

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_001425410.1NP_001412339.1  serine hydroxymethyltransferase, cytosolic isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL596215
    UniProtKB/Swiss-Prot
    P50431, Q64508, Q8R0X9
  2. NM_001425411.1NP_001412340.1  serine hydroxymethyltransferase, cytosolic isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL596215
  3. NM_001425412.1NP_001412341.1  serine hydroxymethyltransferase, cytosolic isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL596215
  4. NM_001425413.1NP_001412342.1  serine hydroxymethyltransferase, cytosolic isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL596215
  5. NM_001425414.1NP_001412343.1  serine hydroxymethyltransferase, cytosolic isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL596215
  6. NM_009171.3NP_033197.2  serine hydroxymethyltransferase, cytosolic isoform 1

    See identical proteins and their annotated locations for NP_033197.2

    Status: VALIDATED

    Source sequence(s)
    AL596215
    Consensus CDS
    CCDS24799.1
    UniProtKB/Swiss-Prot
    P50431, Q64508, Q8R0X9
    UniProtKB/TrEMBL
    Q9CWR5
    Related
    ENSMUSP00000018744.9, ENSMUST00000018744.15
    Conserved Domains (1) summary
    PLN03226
    Location:13475
    PLN03226; serine hydroxymethyltransferase; Provisional

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    60679723..60702062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)