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Shmt2 serine hydroxymethyltransferase 2 (mitochondrial) [ Mus musculus (house mouse) ]

Gene ID: 108037, updated on 23-Mar-2024

Summary

Official Symbol
Shmt2provided by MGI
Official Full Name
serine hydroxymethyltransferase 2 (mitochondrial)provided by MGI
Primary source
MGI:MGI:1277989
See related
Ensembl:ENSMUSG00000025403 AllianceGenome:MGI:1277989
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; 2700043D08Rik
Summary
Enables glycine hydroxymethyltransferase activity. Involved in regulation of mitochondrial translation; regulation of oxidative phosphorylation; and tetrahydrofolate interconversion. Located in nucleus. Is expressed in several structures, including brain; neural retina; placenta; skeleton; and submandibular gland primordium. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver adult (RPKM 102.9), kidney adult (RPKM 81.2) and 27 other tissues See more
Orthologs
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Genomic context

See Shmt2 in Genome Data Viewer
Location:
10 D3; 10 74.51 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (127352992..127358313, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (127517123..127522444, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene R3H domain containing 2 Neighboring gene predicted gene, 23819 Neighboring gene STARR-positive B cell enhancer mm9_chr10:126945421-126945721 Neighboring gene STARR-positive B cell enhancer ABC_E10656 Neighboring gene STARR-positive B cell enhancer ABC_E2342 Neighboring gene Ndufa4, mitochondrial complex associated like 2 Neighboring gene STARR-positive B cell enhancer ABC_E1132 Neighboring gene SH3 and cysteine rich domain 3 Neighboring gene neurexophilin 4 Neighboring gene low density lipoprotein receptor-related protein 1 Neighboring gene STARR-seq mESC enhancer starr_28231 Neighboring gene predicted gene 16217

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)
  • Gene trapped (1) 
  • Endonuclease-mediated (6)  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 chromatin 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 pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables pyridoxal phosphate 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 biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in L-serine 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 one-carbon metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in protein K63-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
 
involved_in protein homotetramerization ISO
Inferred from Sequence Orthology
more info
 
involved_in protein tetramerization ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of aerobic respiration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of aerobic respiration ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mitochondrial translation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of oxidative phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of oxidative phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in response to type I interferon ISO
Inferred from Sequence Orthology
more info
 
involved_in tetrahydrofolate interconversion IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
part_of BRISC complex ISO
Inferred from Sequence Orthology
more info
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in microtubule cytoskeleton ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrial inner membrane HDA PubMed 
located_in mitochondrial inner membrane ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrial matrix ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrial nucleoid 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 mitochondrion ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
serine hydroxymethyltransferase, mitochondrial
Names
glycine hydroxymethyltransferase
serine methylase
NP_001239245.1
NP_082506.1

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_001252316.1NP_001239245.1  serine hydroxymethyltransferase, mitochondrial isoform 2

    See identical proteins and their annotated locations for NP_001239245.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus when it is compared to isoform 1.
    Source sequence(s)
    AK162421, AK169192
    Consensus CDS
    CCDS88105.1
    UniProtKB/TrEMBL
    Q3TFD0, Q9CZN7
    Related
    ENSMUSP00000151616.2, ENSMUST00000219239.2
    Conserved Domains (1) summary
    PLN03226
    Location:42499
    PLN03226; serine hydroxymethyltransferase; Provisional
  2. NM_028230.4NP_082506.1  serine hydroxymethyltransferase, mitochondrial isoform 1

    See identical proteins and their annotated locations for NP_082506.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
    Source sequence(s)
    AK162421, BY760884
    Consensus CDS
    CCDS24244.1
    UniProtKB/Swiss-Prot
    Q3TFD0, Q99K87, Q9CZN7
    Related
    ENSMUSP00000026470.5, ENSMUST00000026470.6
    Conserved Domains (1) summary
    PLN03226
    Location:45502
    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_000076.7 Reference GRCm39 C57BL/6J

    Range
    127352992..127358313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)