Shmt2 serine hydroxymethyltransferase 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Shmt2provided by RGD
Official Full Name: serine hydroxymethyltransferase 2provided by RGD
Primary source: RGD:1308582
See related: EnsemblRapid:ENSRNOG00000008106 AllianceGenome:RGD:1308582
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
Summary: Enables several functions, including L-allo-threonine aldolase activity; glycine hydroxymethyltransferase activity; and pyridoxal phosphate binding activity. Involved in L-serine biosynthetic process; glycine biosynthetic process from serine; and positive regulation of cell population proliferation. Located in mitochondrial inner membrane and mitochondrial matrix. Human ortholog(s) of this gene implicated in neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Liver (RPKM 423.5), Kidney (RPKM 345.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q22

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (65244247..65249580, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (63358961..63364293, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (70824718..70829822, complement)

Chromosome 7 - NC_086025.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2.
Title: Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2.

Submit: New GeneRIF Correction

General gene information

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Markers

RH137111 (e-PCR)
- UniSTS:219199

PMC133987P1 (e-PCR)
- UniSTS:270699

RH125781 (e-PCR)
- UniSTS:162528

Shmt2 (e-PCR), detects polymorphism
- UniSTS:526055

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables L-allo-threonine aldolase activity	IDA Inferred from Direct Assay more info	PubMed
enables amino acid binding	IPI Inferred from Physical Interaction more info	PubMed
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	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 methyltransferase activity	IEA Inferred from Electronic Annotation 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

Process	Evidence Code	Pubs
involved_in L-serine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
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
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 methylation	IEA Inferred from Electronic Annotation more info
involved_in one-carbon metabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitochondrial translation	ISO Inferred from Sequence Orthology more info
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	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
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 microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in microtubule cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial inner membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial matrix	ISO Inferred from Sequence Orthology more info
located_in mitochondrial nucleoid	ISO Inferred from Sequence Orthology more info
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	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, mitochondrial

Names: serine hydroxymethyltransferase 2 (mitochondrial)

NP_001008323.1

EC 2.1.2.1

NP_001380762.1

EC 2.1.2.1

NP_001380763.1

EC 2.1.2.1

XP_038934685.1

EC 2.1.2.1

XP_038934686.1

EC 2.1.2.1

XP_063119310.1

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_001008322.2 → NP_001008323.1 serine hydroxymethyltransferase, mitochondrial isoform 1

See identical proteins and their annotated locations for NP_001008323.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A6HQW0, Q5U3Z7

Related

ENSRNOP00000011082.3, ENSRNOT00000011082.6

Conserved Domains (1) summary

PLN03226
Location:45 → 502

PLN03226; serine hydroxymethyltransferase; Provisional
NM_001393833.1 → NP_001380762.1 serine hydroxymethyltransferase, mitochondrial isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A6HQW0

Related

ENSRNOP00000089446.1, ENSRNOT00000118611.2

Conserved Domains (1) summary

PLN03226
Location:42 → 499

PLN03226; serine hydroxymethyltransferase; Provisional
NM_001393834.1 → NP_001380763.1 serine hydroxymethyltransferase, mitochondrial isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A6HQW0

Conserved Domains (1) summary

PLN03226
Location:45 → 499

PLN03226; serine hydroxymethyltransferase; Provisional

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_086025.1 Reference GRCr8

Range

65244247..65249580 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063263240.1 → XP_063119310.1 serine hydroxymethyltransferase, mitochondrial isoform X1
XM_039078758.2 → XP_038934686.1 serine hydroxymethyltransferase, mitochondrial isoform X3

Conserved Domains (1) summary

cl18945
Location:1 → 251

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 ...
XM_039078757.2 → XP_038934685.1 serine hydroxymethyltransferase, mitochondrial isoform X2

Conserved Domains (1) summary

cl18945
Location:45 → 240

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 ...