Human Gene SHMT2 (ENST00000328923.8) from GENCODE V44
  Description: Homo sapiens serine hydroxymethyltransferase 2 (SHMT2), transcript variant 1, mRNA; nuclear gene for mitochondrial product. (from RefSeq NM_005412)
RefSeq Summary (NM_005412): This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009].
Gencode Transcript: ENST00000328923.8
Gencode Gene: ENSG00000182199.11
Transcript (Including UTRs)
   Position: hg38 chr12:57,229,711-57,234,935 Size: 5,225 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg38 chr12:57,229,779-57,234,361 Size: 4,583 Coding Exon Count: 12 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:57,229,711-57,234,935)mRNA (may differ from genome)Protein (504 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SHMT2
Diseases sorted by gene-association score: pyridoxine deficiency (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 80.66 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 717.34 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -16.2068-0.238 Picture PostScript Text
3' UTR -183.30574-0.319 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  LF208936 - JP 2014500723-A/16439: Polycomb-Associated Non-Coding RNAs.
MA444513 - JP 2018138019-A/16439: Polycomb-Associated Non-Coding RNAs.
AK298231 - Homo sapiens cDNA FLJ57275 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
AK301339 - Homo sapiens cDNA FLJ58288 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
AK055053 - Homo sapiens cDNA FLJ30491 fis, clone BRAWH2000177.
AK223555 - Homo sapiens mRNA for serine hydroxymethyltransferase 2 (mitochondrial) variant, clone: FCC127B09.
AK303827 - Homo sapiens cDNA FLJ57281 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
BC032584 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone MGC:45240 IMAGE:5499481), complete cds.
BC044211 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone MGC:49833 IMAGE:5521082), complete cds.
BC013677 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone MGC:9375 IMAGE:3863368), complete cds.
AK295941 - Homo sapiens cDNA FLJ58534 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
BC008066 - Homo sapiens cDNA clone IMAGE:3010445, containing frame-shift errors.
BC012833 - Homo sapiens cDNA clone IMAGE:3529453, **** WARNING: chimeric clone ****.
BC011911 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone MGC:20325 IMAGE:4139001), complete cds.
EU668344 - Homo sapiens epididymis secretory sperm binding protein Li 51e (HEL-S-51e) mRNA, complete cds.
BC091501 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone IMAGE:30378499), partial cds.
CU689432 - Synthetic construct Homo sapiens gateway clone IMAGE:100019660 5' read SHMT2 mRNA.
CU680112 - Synthetic construct Homo sapiens gateway clone IMAGE:100017375 5' read SHMT2 mRNA.
KJ905918 - Synthetic construct Homo sapiens clone ccsbBroadEn_15588 SHMT2 gene, encodes complete protein.
KJ897553 - Synthetic construct Homo sapiens clone ccsbBroadEn_06947 SHMT2 gene, encodes complete protein.
KJ904558 - Synthetic construct Homo sapiens clone ccsbBroadEn_13952 SHMT2 gene, encodes complete protein.
JD537801 - Sequence 518825 from Patent EP1572962.
AB527799 - Synthetic construct DNA, clone: pF1KB5913, Homo sapiens SHMT2 gene for serine hydroxymethyltransferase 2, without stop codon, in Flexi system.
KU178333 - Homo sapiens serine hydroxymethyltransferase 2 isoform 1 (SHMT2) mRNA, partial cds.
KU178334 - Homo sapiens serine hydroxymethyltransferase 2 isoform 2 (SHMT2) mRNA, complete cds, alternatively spliced.
BT006866 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) mRNA, complete cds.
DQ891309 - Synthetic construct clone IMAGE:100003939; FLH170976.01X; RZPDo839D09100D serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2) gene, encodes complete protein.
DQ894430 - Synthetic construct Homo sapiens clone IMAGE:100008890; FLH170972.01L; RZPDo839D0999D serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2) gene, encodes complete protein.
BX647711 - Homo sapiens mRNA; cDNA DKFZp686P09201 (from clone DKFZp686P09201).
AK301443 - Homo sapiens cDNA FLJ58289 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
BX648847 - Homo sapiens mRNA; cDNA DKFZp686P05153 (from clone DKFZp686P05153).
BC004215 - Homo sapiens cDNA clone IMAGE:2964623, **** WARNING: chimeric clone ****.
BC008711 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone IMAGE:3530697), partial cds.
AK296183 - Homo sapiens cDNA FLJ58535 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
AK315916 - Homo sapiens cDNA, FLJ78815 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
AK297173 - Homo sapiens cDNA FLJ58585 complete cds, highly similar to Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1).
L11932 - Human nuclear-encoded mitochondrial serine hydroxymethyltransferase (SHMT) mRNA, 3' end.
LF324208 - JP 2014500723-A/131711: Polycomb-Associated Non-Coding RNAs.
MA559785 - JP 2018138019-A/131711: Polycomb-Associated Non-Coding RNAs.
LF208938 - JP 2014500723-A/16441: Polycomb-Associated Non-Coding RNAs.
MA444515 - JP 2018138019-A/16441: Polycomb-Associated Non-Coding RNAs.
JD022557 - Sequence 3581 from Patent EP1572962.
JD021669 - Sequence 2693 from Patent EP1572962.
LF324205 - JP 2014500723-A/131708: Polycomb-Associated Non-Coding RNAs.
MA559782 - JP 2018138019-A/131708: Polycomb-Associated Non-Coding RNAs.
JD021714 - Sequence 2738 from Patent EP1572962.
JD021522 - Sequence 2546 from Patent EP1572962.
LF324204 - JP 2014500723-A/131707: Polycomb-Associated Non-Coding RNAs.
MA559781 - JP 2018138019-A/131707: Polycomb-Associated Non-Coding RNAs.
JD031348 - Sequence 12372 from Patent EP1572962.
BC025355 - Homo sapiens serine hydroxymethyltransferase 2 (mitochondrial), mRNA (cDNA clone IMAGE:4905540).
JD029941 - Sequence 10965 from Patent EP1572962.
LF324203 - JP 2014500723-A/131706: Polycomb-Associated Non-Coding RNAs.
MA559780 - JP 2018138019-A/131706: Polycomb-Associated Non-Coding RNAs.
LF324201 - JP 2014500723-A/131704: Polycomb-Associated Non-Coding RNAs.
MA559778 - JP 2018138019-A/131704: Polycomb-Associated Non-Coding RNAs.
JD267815 - Sequence 248839 from Patent EP1572962.
LF324200 - JP 2014500723-A/131703: Polycomb-Associated Non-Coding RNAs.
MA559777 - JP 2018138019-A/131703: Polycomb-Associated Non-Coding RNAs.
JD533237 - Sequence 514261 from Patent EP1572962.
JD499155 - Sequence 480179 from Patent EP1572962.
JD546453 - Sequence 527477 from Patent EP1572962.
LF324199 - JP 2014500723-A/131702: Polycomb-Associated Non-Coding RNAs.
MA559776 - JP 2018138019-A/131702: Polycomb-Associated Non-Coding RNAs.
JD096187 - Sequence 77211 from Patent EP1572962.
JD382142 - Sequence 363166 from Patent EP1572962.
JD545374 - Sequence 526398 from Patent EP1572962.
LF324197 - JP 2014500723-A/131700: Polycomb-Associated Non-Coding RNAs.
MA559774 - JP 2018138019-A/131700: Polycomb-Associated Non-Coding RNAs.
JD223238 - Sequence 204262 from Patent EP1572962.
JD479638 - Sequence 460662 from Patent EP1572962.
JD167157 - Sequence 148181 from Patent EP1572962.
LF208934 - JP 2014500723-A/16437: Polycomb-Associated Non-Coding RNAs.
MA444511 - JP 2018138019-A/16437: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00260 - Glycine, serine and threonine metabolism
hsa00460 - Cyanoamino acid metabolism
hsa00670 - One carbon pool by folate
hsa00680 - Methane metabolism
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
GLYSYN-PWY - glycine/serine biosynthesis
PWY-2161 - folate polyglutamylation
PWY-2201-1 - folate transformations I
PWY-3661-1 - glycine betaine degradation II (mammalian)
PWY66-385 - dTMP de novo biosynthesis (mitochondrial)
PWY66-414 - superpathway of choline degradation to L-serine
SER-GLYSYN-PWY - serine and glycine biosynthesis

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000328923.1, ENST00000328923.2, ENST00000328923.3, ENST00000328923.4, ENST00000328923.5, ENST00000328923.6, ENST00000328923.7, NM_005412, uc001snf.1, uc001snf.2, uc001snf.3, uc001snf.4, V9HW06
UCSC ID: ENST00000328923.8
RefSeq Accession: NM_005412
CCDS: CCDS53805.1, CCDS8934.1, CCDS55837.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.