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

    Gene ID: 20425, updated on 3-Dec-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 mitochondrion. Is active 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, Nov 2024]
    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

    See Shmt1 in Genome Data Viewer
    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) 
    • Gene trapped (2) 
    • Targeted (5)  1 citation

    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 glycine hydroxymethyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables mRNA 5'-UTR binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables mRNA 5'-UTR binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables mRNA regulatory element binding translation repressor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables mRNA regulatory element binding translation repressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    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 pyridoxal phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables serine binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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 ISS
    Inferred from Sequence or Structural Similarity
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    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 glycine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of translation IEA
    Inferred from Electronic Annotation
    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 protein homotetramerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in purine nucleobase biosynthetic process IEA
    Inferred from Electronic Annotation
    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 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
     
    involved_in tetrahydrofolate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    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 cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in mitochondrion HDA PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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)

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

      Status: VALIDATED

      Source sequence(s)
      AL596215
      UniProtKB/Swiss-Prot
      P50431, Q64508, Q8R0X9
      UniProtKB/TrEMBL
      Q9CWR5
      Related
      ENSMUSP00000134269.2, ENSMUST00000174214.2
    2. NM_001425411.1NP_001412340.1  serine hydroxymethyltransferase, cytosolic isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL596215
      UniProtKB/TrEMBL
      G3UZ26
      Related
      ENSMUSP00000134318.2, ENSMUST00000174719.8
    3. NM_001425412.1NP_001412341.1  serine hydroxymethyltransferase, cytosolic isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL596215
      UniProtKB/TrEMBL
      Q9CWR5
    4. NM_001425413.1NP_001412342.1  serine hydroxymethyltransferase, cytosolic isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL596215
      UniProtKB/TrEMBL
      Q9CWR5
    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)