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
Data last updated at UCSC: 2023-08-18 00:09:47
Sequence and Links to Tools and Databases
Primer design for this transcript
MalaCards Disease Associations
Comparative Toxicogenomics Database (CTD)
RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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.
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 metabolismhsa00460 - Cyanoamino acid metabolismhsa00670 - One carbon pool by folatehsa00680 - Methane metabolismhsa01100 - 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, V9HW06UCSC ID: ENST00000328923.8RefSeq Accession: NM_005412
CCDS: CCDS53805.1 , CCDS8934.1 , CCDS55837.1
Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.