Format

Send to:

Choose Destination

SHMT1 serine hydroxymethyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 6470, updated on 12-Oct-2019

Summary

Official Symbol
SHMT1provided by HGNC
Official Full Name
serine hydroxymethyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:10850
See related
Ensembl:ENSG00000176974 MIM:182144
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SHMT; CSHMT
Summary
This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression
Biased expression in kidney (RPKM 121.9), liver (RPKM 84.9) and 13 other tissues See more
Orthologs

Genomic context

See SHMT1 in Genome Data Viewer
Location:
17p11.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (18327860..18363563, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (18231187..18266856, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase III alpha Neighboring gene ribosomal protein L21 pseudogene 121 Neighboring gene ribosomal protein L7a pseudogene 65 Neighboring gene SMCR8-C9orf72 complex subunit Neighboring gene microRNA 6778 Neighboring gene envoplakin like Neighboring gene TBC1 domain family member 3 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC15229, MGC24556

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-allo-threonine aldolase activity IEA
Inferred from Electronic Annotation
more info
 
amino acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cobalt ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine hydroxymethyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine hydroxymethyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
mRNA 5'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 5'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
serine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
serine binding IDA
Inferred from Direct Assay
more info
PubMed 
translation repressor activity, mRNA regulatory element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
translation repressor activity, mRNA regulatory element binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
L-serine catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
L-serine catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
L-serine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
carnitine biosynthetic process TAS
Traceable Author Statement
more info
 
cellular response to leukemia inhibitory factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to tetrahydrofolate IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to tetrahydrofolate IDA
Inferred from Direct Assay
more info
PubMed 
dTMP biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
folic acid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
folic acid metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
folic acid metabolic process TAS
Traceable Author Statement
more info
 
glycine biosynthetic process from serine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
one-carbon metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homotetramerization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homotetramerization IDA
Inferred from Direct Assay
more info
PubMed 
protein tetramerization IDA
Inferred from Direct Assay
more info
PubMed 
purine nucleobase biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
purine nucleobase biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
tetrahydrofolate interconversion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tetrahydrofolate interconversion IDA
Inferred from Direct Assay
more info
PubMed 
tetrahydrofolate interconversion IEA
Inferred from Electronic Annotation
more info
 
tetrahydrofolate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tetrahydrofolate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
serine hydroxymethyltransferase, cytosolic
Names
cytoplasmic serine hydroxymethyltransferase
glycine hydroxymethyltransferase
serine hydroxymethyltransferase 1 (soluble)
serine methylase
NP_001268715.1
NP_004160.3
NP_683718.1
XP_005256824.1
XP_011522294.1
XP_016880446.1
XP_016880447.1
XP_024306655.1
XP_024306656.1
XP_024306657.1
XP_024306658.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_017111.1 RefSeqGene

    Range
    4993..40670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001281786.1NP_001268715.1  serine hydroxymethyltransferase, cytosolic isoform 3

    See identical proteins and their annotated locations for NP_001268715.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (3) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK298415, AL353997, AU185281, BM792235, DB451683
    Consensus CDS
    CCDS62112.1
    UniProtKB/Swiss-Prot
    P34896
    Related
    ENSP00000345881.7, ENST00000352886.10
    Conserved Domains (1) summary
    cl28184
    Location:1342
    PLN03226; serine hydroxymethyltransferase; Provisional
  2. NM_004169.5NP_004160.3  serine hydroxymethyltransferase, cytosolic isoform 1

    See identical proteins and their annotated locations for NP_004160.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC007979, BC038598, DB451683
    Consensus CDS
    CCDS11196.1
    UniProtKB/Swiss-Prot
    P34896
    Related
    ENSP00000318868.3, ENST00000316694.8
    Conserved Domains (2) summary
    PLN03226
    Location:24480
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:26425
    SHMT; Serine hydroxymethyltransferase
  3. NM_148918.2NP_683718.1  serine hydroxymethyltransferase, cytosolic isoform 2

    See identical proteins and their annotated locations for NP_683718.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL353997, AU185281, BC022874, BM792235, DB451683
    Consensus CDS
    CCDS11197.1
    UniProtKB/Swiss-Prot
    P34896
    Related
    ENSP00000318805.3, ENST00000354098.7
    Conserved Domains (2) summary
    PLN03226
    Location:24441
    PLN03226; serine hydroxymethyltransferase; Provisional
    cl18945
    Location:26386
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    18327860..18363563 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450888.1XP_024306656.1  serine hydroxymethyltransferase, cytosolic isoform X4

    Conserved Domains (1) summary
    cl28184
    Location:1342
    PLN03226; serine hydroxymethyltransferase; Provisional
  2. XM_005256767.3XP_005256824.1  serine hydroxymethyltransferase, cytosolic isoform X1

    See identical proteins and their annotated locations for XP_005256824.1

    UniProtKB/Swiss-Prot
    P34896
    Conserved Domains (2) summary
    PLN03226
    Location:24480
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:26425
    SHMT; Serine hydroxymethyltransferase
  3. XM_017024957.1XP_016880446.1  serine hydroxymethyltransferase, cytosolic isoform X1

    UniProtKB/Swiss-Prot
    P34896
    Conserved Domains (2) summary
    PLN03226
    Location:24480
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:26425
    SHMT; Serine hydroxymethyltransferase
  4. XM_024450889.1XP_024306657.1  serine hydroxymethyltransferase, cytosolic isoform X5

    Conserved Domains (1) summary
    cl28184
    Location:1303
    PLN03226; serine hydroxymethyltransferase; Provisional
  5. XM_017024958.1XP_016880447.1  serine hydroxymethyltransferase, cytosolic isoform X2

    UniProtKB/Swiss-Prot
    P34896
    Conserved Domains (2) summary
    PLN03226
    Location:24441
    PLN03226; serine hydroxymethyltransferase; Provisional
    cl18945
    Location:26386
    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 ...
  6. XM_011523992.3XP_011522294.1  serine hydroxymethyltransferase, cytosolic isoform X3

    See identical proteins and their annotated locations for XP_011522294.1

    UniProtKB/Swiss-Prot
    P34896
    Conserved Domains (1) summary
    cl28184
    Location:24400
    PLN03226; serine hydroxymethyltransferase; Provisional
  7. XM_024450890.1XP_024306658.1  serine hydroxymethyltransferase, cytosolic isoform X6

    Conserved Domains (1) summary
    cl28184
    Location:1262
    PLN03226; serine hydroxymethyltransferase; Provisional
  8. XM_024450887.1XP_024306655.1  serine hydroxymethyltransferase, cytosolic isoform X3

    Conserved Domains (1) summary
    cl28184
    Location:24400
    PLN03226; serine hydroxymethyltransferase; Provisional

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_017363819.1 Reference GRCh38.p13 PATCHES

    Range
    88234..123954 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center