Human Gene SHMT1 (ENST00000316694.8_7) from GENCODE V47lift37
  Description: serine hydroxymethyltransferase 1, transcript variant 1 (from RefSeq NM_004169.5)
Gencode Transcript: ENST00000316694.8_7
Gencode Gene: ENSG00000176974.22_16
Transcript (Including UTRs)
   Position: hg19 chr17:18,231,187-18,266,864 Size: 35,678 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr17:18,232,064-18,259,295 Size: 27,232 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:18,231,187-18,266,864)mRNA (may differ from genome)Protein (483 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GLYC_HUMAN
DESCRIPTION: RecName: Full=Serine hydroxymethyltransferase, cytosolic; Short=SHMT; EC=2.1.2.1; AltName: Full=Glycine hydroxymethyltransferase; AltName: Full=Serine methylase;
FUNCTION: Interconversion of serine and glycine.
CATALYTIC ACTIVITY: 5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine.
COFACTOR: Pyridoxal phosphate.
PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
SUBUNIT: Homotetramer.
SUBCELLULAR LOCATION: Cytoplasm.
MISCELLANEOUS: In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.
SIMILARITY: Belongs to the SHMT family.

-  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: SHMT1
Diseases sorted by gene-association score: adult acute lymphocytic leukemia (33), smith-magenis syndrome (22), potocki-luspski syndrome (11), lacrimal gland adenocarcinoma (9), lacrimal system cancer (6), neural tube defects (5), serine deficiency (5)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 136.11 RPKM in Liver
Total median expression: 607.37 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 -93.90198-0.474 Picture PostScript Text
3' UTR -222.00877-0.253 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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015424 - PyrdxlP-dep_Trfase_major_dom
IPR015421 - PyrdxlP-dep_Trfase_major_sub1
IPR015422 - PyrdxlP-dep_Trfase_major_sub2
IPR001085 - Ser_HO-MeTrfase
IPR019798 - Ser_HO-MeTrfase_PLP_BS

Pfam Domains:
PF00155 - Aminotransferase class I and II
PF00464 - Serine hydroxymethyltransferase

SCOP Domains:
53383 - PLP-dependent transferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1BJ4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P34896
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000900 translation repressor activity, nucleic acid binding
GO:0003824 catalytic activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0008732 L-allo-threonine aldolase activity
GO:0016597 amino acid binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0048027 mRNA 5'-UTR binding
GO:0070905 serine binding

Biological Process:
GO:0006231 dTMP biosynthetic process
GO:0006544 glycine metabolic process
GO:0006545 glycine biosynthetic process
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0009113 purine nucleobase biosynthetic process
GO:0017148 negative regulation of translation
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0045329 carnitine biosynthetic process
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
GO:0051262 protein tetramerization
GO:0051289 protein homotetramerization
GO:1904482 cellular response to tetrahydrofolate
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  Y14486 - Homo sapiens mRNA for cytosolic serine hydroxymethyltransferase, clone pUS1206.
BC007979 - Homo sapiens serine hydroxymethyltransferase 1 (soluble), mRNA (cDNA clone MGC:15229 IMAGE:3687873), complete cds.
BC038598 - Homo sapiens serine hydroxymethyltransferase 1 (soluble), mRNA (cDNA clone MGC:46169 IMAGE:4523709), complete cds.
AK223552 - Homo sapiens mRNA for serine hydroxymethyltransferase 1 (soluble) isoform 1 variant, clone: FCC126F02.
JD097993 - Sequence 79017 from Patent EP1572962.
JD319934 - Sequence 300958 from Patent EP1572962.
JD295307 - Sequence 276331 from Patent EP1572962.
AK298415 - Homo sapiens cDNA FLJ55740 complete cds, highly similar to Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1).
JD074286 - Sequence 55310 from Patent EP1572962.
BC022874 - Homo sapiens serine hydroxymethyltransferase 1 (soluble), mRNA (cDNA clone MGC:24556 IMAGE:4108106), complete cds.
Y14485 - Homo sapiens mRNA for cytosolic serine hydroxymethyltransferase, clone pUS1217.
L11931 - Human cytosolic serine hydroxymethyltransferase (SHMT) mRNA, complete cds.
L23928 - Homo sapiens serine hydroxymethyltransferase mRNA, complete cds.
JD399687 - Sequence 380711 from Patent EP1572962.
DQ893242 - Synthetic construct clone IMAGE:100005872; FLH195540.01X; RZPDo839D07152D serine hydroxymethyltransferase 1 (soluble) (SHMT1) gene, encodes complete protein.
KJ897552 - Synthetic construct Homo sapiens clone ccsbBroadEn_06946 SHMT1 gene, encodes complete protein.
KR710122 - Synthetic construct Homo sapiens clone CCSBHm_00009895 SHMT1 (SHMT1) mRNA, encodes complete protein.
EU176779 - Synthetic construct Homo sapiens clone IMAGE:100011554; FLH195539.01L; RZPDo839H04256D serine hydroxymethyltransferase 1 (soluble) (SHMT1) gene, encodes complete protein.
KJ905917 - Synthetic construct Homo sapiens clone ccsbBroadEn_15587 SHMT1 gene, encodes complete protein.
AB527874 - Synthetic construct DNA, clone: pF1KB0441, Homo sapiens SHMT1 gene for serine hydroxymethyltransferase 1, without stop codon, in Flexi system.
AK091498 - Homo sapiens cDNA FLJ34179 fis, clone FCBBF3016622, weakly similar to SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1).
AX747021 - Sequence 546 from Patent EP1308459.
Y14487 - Homo sapiens mRNA for cytosolic serine hydroxymethyltransferase, partial, clone pUS1214.
AK302834 - Homo sapiens cDNA FLJ60988 complete cds, highly similar to Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1).
CU675881 - Synthetic construct Homo sapiens gateway clone IMAGE:100019616 5' read SHMT1 mRNA.
CU692746 - Synthetic construct Homo sapiens gateway clone IMAGE:100022008 5' read SHMT1 mRNA.
Y14488 - Homo sapiens mRNA for putative 14kD protein containing SHMT homology, clone pUS1215.
AF017065 - Homo sapiens cytoplasmic serine hydroxymethyltransferase mRNA, 5'UTR.

-  Biochemical and Signaling 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)
PWY-6100 - L-carnitine biosynthesis
PWY66-414 - superpathway of choline degradation to L-serine
SER-GLYSYN-PWY - serine and glycine biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein P34896 (Reactome details) participates in the following event(s):

R-HSA-71249 SHMT1 tetramer cleaves HTMLYS to yield TEABL and Gly
R-HSA-200651 5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine
R-HSA-200735 Tetrahydrofolate polyglutamate (THF polyglutamate) + serine <=> 5,10-methyleneTHF polyglutamate + glycine
R-HSA-71262 Carnitine synthesis
R-HSA-196757 Metabolism of folate and pterines
R-HSA-70895 Branched-chain amino acid catabolism
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B4DPM9, D3DXD0, ENST00000316694.1, ENST00000316694.2, ENST00000316694.3, ENST00000316694.4, ENST00000316694.5, ENST00000316694.6, ENST00000316694.7, GLYC_HUMAN, NM_004169, P34896, Q96HY0, Q9UMD1, Q9UMD2, uc317qbq.1, uc317qbq.2
UCSC ID: ENST00000316694.8_7
RefSeq Accession: NM_004169.5
Protein: P34896 (aka GLYC_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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