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SHMT1 Gene

protein-coding   GIFtS: 67
GCID: GC17M018231

Serine Hydroxymethyltransferase 1 (Soluble)

  See SHMT1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Serine Hydroxymethyltransferase 1 (Soluble)1 2     EC 2.1.2.13 8
Cytoplasmic Serine Hydroxymethyltransferase1 2     14 KDa Protein1
Glycine Hydroxymethyltransferase2 3     CSHMT2
Serine Methylase2 3     Serine Hydroxymethyltransferase, Cytosolic2
SHMT2 3     

External Ids:    HGNC: 108501   Entrez Gene: 64702   Ensembl: ENSG000001769747   OMIM: 1821445   UniProtKB: P348963   

Export aliases for SHMT1 gene to outside databases

Previous GC identifers: GC17M018476 GC17M019823 GC17M018174 GC17M018431 GC17M018171 GC17M017984


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SHMT1 Gene:
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)

GeneCards Summary for SHMT1 Gene:
SHMT1 (serine hydroxymethyltransferase 1 (soluble)) is a protein-coding gene. Diseases associated with SHMT1 include adult acute lymphocytic leukemia, and pediatric osteosarcoma. GO annotations related to this gene include amino acid binding and protein homodimerization activity. An important paralog of this gene is SHMT2.

UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
Function: Interconversion of serine and glycine




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NT_010718.17  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SHMT1 gene promoter:
         AhR   CHOP-10   CBF-B   CBF-A   NF-YA   c-Myb   CP1A   NF-Y   CBF(2)   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SHMT1 promoter sequence
   Search Chromatin IP Primers for SHMT1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SHMT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

SHMT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHMT1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M018231:  view genomic region     (about GC identifiers)

Start:
18,231,187 bp from pter      End:
18,266,856 bp from pter
Size:
35,670 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896 (See protein sequence)
Recommended Name: Serine hydroxymethyltransferase, cytosolic  
Size: 483 amino acids; 53083 Da
Cofactor: Pyridoxal phosphate
Subunit: Homotetramer
Miscellaneous: In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one
1 PDB 3D structure from and Proteopedia for SHMT1:
1BJ4 (3D)    
Secondary accessions: D3DXD0 Q96HY0 Q9UMD1 Q9UMD2
Alternative splicing: 3 isoforms:  P34896-1   P34896-2   P34896-3   (Contains a N6-acetyllysine at position 271)

Explore the universe of human proteins at neXtProt for SHMT1: NX_P34896

Explore proteomics data for SHMT1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys72, Lys98, Lys105, Lys375, Lys386, Lys416, Lys420, Lys456
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SHMT1 (P34896) (see all 28)
     LCQKRAL  VTTTTHK  SGSPANF  LIASENF 


    See SHMT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001268715.1  NP_004160.3  NP_683718.1  

    ENSEMBL proteins: 
     ENSP00000318868   ENSP00000462043   ENSP00000318805   ENSP00000462227   ENSP00000462041  
     ENSP00000345881   ENSP00000440089  
    Reactome Protein details: P34896

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    Novus Biologicals SHMT1 Proteins
    Novus Biologicals SHMT1 Lysates
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    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for SHMT1
    Cloud-Clone Corp. Proteins for SHMT1

     
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    Cloud-Clone Corp. ELISAs for SHMT1
    Cloud-Clone Corp. CLIAs for SHMT1
    Search eBioscience for ELISAs for SHMT1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    5 InterPro protein domains:
     IPR019798 Ser_HO-MeTrfase_PLP_BS
     IPR001085 Ser_HO-MeTrfase
     IPR015422 PyrdxlP-dep_Trfase_major_sub2
     IPR015424 PyrdxlP-dep_Trfase
     IPR015421 PyrdxlP-dep_Trfase_major_sub1

    Graphical View of Domain Structure for InterPro Entry P34896

    ProtoNet protein and cluster: P34896

    1 Blocks protein domain: IPB001085 Glycine hydroxymethyltransferase

    UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
    Similarity: Belongs to the SHMT family


    Find genes that share domains with SHMT1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: GLYC_HUMAN, P34896
    Function: Interconversion of serine and glycine
    Catalytic activity: 5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine

         Genatlas biochemistry entry for SHMT1:
    serine hydroxy-methyltransferase,cytosolic,with several alternatively spliced isoforms,catalyzing serine
    synthesis,"one-carbone" metabolism,constantly deleted in Smith-Magenis syndrome,putative regulator of cell growth
    and proliferation

         Enzyme Number (IUBMB): EC 2.1.2.11 2

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004372glycine hydroxymethyltransferase activity TAS--
    GO:0008168methyltransferase activity ----
    GO:0008242omega peptidase activity ----
    GO:0008732L-allo-threonine aldolase activity IEA--
    GO:0016597amino acid binding IEA--
         
    Find genes that share ontologies with SHMT1           About GenesLikeMe


    Phenotypes:
         4 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Shmt1):
     homeostasis/metabolism  liver/biliary system  mortality/aging  tumorigenesis 

    Find genes that share phenotypes with SHMT1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Shmt1tm1.1Stov for SHMT1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SHMT1
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SHMT1

    miRNA
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    miRTarBase miRNAs that target SHMT1:
    hsa-mir-125b-5p (MIRT045899), hsa-mir-193b-3p (MIRT016266)

    Block miRNA regulation of human, mouse, rat SHMT1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SHMT1 (see all 28):
    hsa-miR-320a hsa-miR-2052 hsa-miR-4307 hsa-miR-19b-2* hsa-miR-522 hsa-miR-3653 hsa-miR-578 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidSHMT1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SHMT1
    Predesigned siRNA for gene silencing in human, mouse, rat SHMT1

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for SHMT1

    Clone
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    OriGene ORF clones in mouse, rat for SHMT1
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    GenScript: all cDNA clones in your preferred vector (see all 2): SHMT1 (NM_004169)
    Sino Biological Human cDNA Clone for SHMT1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SHMT1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SHMT1

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for SHMT1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHMT1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    GLYC_HUMAN, P34896: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol5
    nucleus4
    chloroplast2
    mitochondrion2
    extracellular1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005739mitochondrion IEA--
    GO:0005829cytosol TAS--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with SHMT1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SHMT1 About   (see all 12)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1One carbon pool by folate
    One carbon pool by folate0.53
    Methotrexate Pathway (Cancer Cell), Pharmacodynamics0.35
    One Carbon Metabolism0.53
    Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics0.34
    Trans-sulfuration and one carbon metabolism0.43
    Antimetabolite Pathway - Folate Cycle, Pharmacodynamics0.00
    2folate polyglutamylation
    folate polyglutamylation0.50
    folate transformations0.43
    Glycine Metabolism0.50
    glycine biosynthesis I0.00
    3Glycine, serine and threonine metabolism
    Glycine, serine and threonine metabolism
    glycine biosynthesis0.00
    serine and glycine biosynthesis0.00
    glycine betaine degradation0.00
    4Metabolism
    Metabolism0.38
    Metabolic pathways0.38
    5Defective BTD causes biotidinase deficiency
    Defective BTD causes biotidinase deficiency1.00
    Metabolism of vitamins and cofactors1.00
    Defective AMN causes hereditary megaloblastic anemia 11.00
    Defective MMACHC causes methylmalonic aciduria and homocystinuria type cblC1.00
    Defective MMAA causes methylmalonic aciduria type cblA1.00
    Defective MUT causes methylmalonic aciduria mut type1.00
    Defective CD320 causes methylmalonic aciduria1.00
    Defects in cobalamin (B12) metabolism1.00


    Find genes that share SuperPaths with SHMT1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SHMT1
        Glucose / Energy Metabolism

    Selected BioSystems Pathways for SHMT1 (see all 10)
        One Carbon Metabolism
    folate transformations
    folate polyglutamylation
    glycine biosynthesis I
    Validated targets of C-MYC transcriptional activation


    2 Reactome Pathways for SHMT1
        Metabolism of folate and pterines
    Carnitine synthesis

    3 PharmGKB Pathways for SHMT1
        Antimetabolite Pathway - Folate Cycle, Pharmacodynamics
    Methotrexate Pathway (Cancer Cell), Pharmacodynamics
    Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics

    Selected Kegg Pathways  (Kegg details for SHMT1) (see all 7):
        Glycine, serine and threonine metabolism
    Cyanoamino acid metabolism
    Glyoxylate and dicarboxylate metabolism
    One carbon pool by folate
    Metabolic pathways

    UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
    Pathway: One-carbon metabolism; tetrahydrofolate interconversion

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SHMT1
    Interactions:

        GeneGlobe Interaction Network for SHMT1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SHMT1 (P348963 ENSP000003188684) via UniProtKB, MINT, STRING, and/or I2D (see all 108)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    CSNK2BP678703, ENSP000003650254I2D: score=2 STRING: ENSP00000365025
    ENSG00000206406P678703I2D: score=2 
    ENSG00000224398P678703I2D: score=2 
    ENSG00000224774P678703I2D: score=2 
    ENSG00000228875P678703I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006544glycine metabolic process ----
    GO:0006545glycine biosynthetic process ----
    GO:0006563L-serine metabolic process ----
    GO:0006565L-serine catabolic process IDA17482557
    GO:0006766vitamin metabolic process TAS--

    Find genes that share ontologies with SHMT1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SHMT1 (GLYC)

    6 HMDB Compounds for SHMT1    About this table
    CompoundSynonyms CAS #PubMed Ids
    5,10-Methylene-THF5,10-methylene-THF (see all 8)31690-11-6--
    Glycine2-Aminoacetate (see all 15)56-40-6--
    L-Serine(-)-Serine (see all 26)56-45-1--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--
    Tetrahydrofolic acid(6S)-Tetrahydrofolate (see all 10)135-16-0--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    7 DrugBank Compounds for SHMT1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor9305893 17139284 3143355 17016423 10592235 7526359
    Tetrahydrofolic acid5,6,7,8-tetrahydrofolate (see all 3)135-16-0targetcofactor12668769 11752472 10656824 11386852 10592235 10998057
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17664250 17150100 16876889 17142057 17355947
    MimosineL-Mimosine (see all 6)500-44-7targetinhibitor11936838 8576220 15531579 10766749
    5-Hydroxymethylene-6-Hydrofolic Acid-- --target--17139284 17016423 10592235
    N-Pyridoxyl-Glycine-5-Monophosphate-- --target--17139284 17016423 10592235
    Triglu-5-Formyl-Tetrahydrofolate-- --target--17139284 17016423 10592235

    Selected Novoseek inferred chemical compound relationships for SHMT1 gene (see all 18)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tetrahydrofolate 87.3 9 11305908 (1), 11386852 (1), 12514178 (1), 9753690 (1) (see all 5)
    thymidylate 84 47 12161434 (3), 19513116 (3), 18067453 (3), 11516159 (1) (see all 18)
    serine 78.8 109 12161434 (4), 8527925 (3), 9675060 (3), 9753690 (3) (see all 53)
    folate 78.6 23 11386852 (2), 15122597 (1), 16536979 (1), 12161434 (1) (see all 16)
    pyridoxal 5-phosphate 75.3 21 17482557 (3), 12514178 (3), 8527925 (1), 9753690 (1) (see all 5)
    methionine 67.9 12 16536979 (1), 16410450 (1), 12161434 (1), 11986237 (1) (see all 8)
    mimosine 63.1 13 10766749 (4), 15531579 (4)
    deoxyribonucleotide 60.1 2 12161434 (1), 15531579 (1)
    dihydrofolate 55.4 8 19513116 (1), 18067453 (1), 11197757 (1), 17446168 (1)
    homocysteine 54.5 2 11386852 (1), 14656021 (1)

    5 PharmGKB related drug/compound annotations for SHMT1 gene    About this table
    Drug/compound PharmGKB Annotation
    bevacizumabCA  
    fluorouracilCA  
    irinotecanCA  
    leucovorinCA  
    methotrexateCA  



    Find genes that share compounds with SHMT1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SHMT1 gene (3 alternative transcripts): 
    NM_001281786.1  NM_004169.4  NM_148918.2  

    Unigene Clusters for SHMT1:

    Serine hydroxymethyltransferase 1 (soluble)
    Hs.513987  [show with all ESTs], Hs.636044
    Unigene Representative Sequences: AK091498, Y14488
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000395684(uc002gsz.3) ENST00000316694(uc002gta.3 uc002gtb.3 uc010vxt.2)
    ENST00000580002 ENST00000354098 ENST00000582352(uc002gtc.1) ENST00000579558(uc010vxu.1)
    ENST00000582653 ENST00000395682 ENST00000583780 ENST00000352886 ENST00000539052

    miRNA
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    Block miRNA regulation of human, mouse, rat SHMT1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SHMT1 (see all 28):
    hsa-miR-320a hsa-miR-2052 hsa-miR-4307 hsa-miR-19b-2* hsa-miR-522 hsa-miR-3653 hsa-miR-578 hsa-miR-218
    SwitchGear 3'UTR luciferase reporter plasmidSHMT1 3' UTR sequence
    Inhib. RNA
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    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SHMT1 (NM_004169)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SHMT1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SHMT1
    Primer
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    OriGene qPCR primer pairs and template standards for SHMT1
    OriGene qSTAR qPCR primer pairs in human, mouse for SHMT1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SHMT1
      QuantiTect SYBR Green Assays in human, mouse, rat SHMT1
      QuantiFast Probe-based Assays in human, mouse, rat SHMT1

    Additional mRNA sequence: Y14488.1 

    17 DOTS entries:

    DT.418980  DT.100817283  DT.100817277  DT.100697358  DT.95237322  DT.97847235  DT.99938562  DT.95333677 
    DT.100817274  DT.421797  DT.92065961  DT.95237302  DT.100817271  DT.100834637  DT.120915249  DT.95237308 
    DT.100817278 

    Selected AceView cDNA sequences (see all 453):

    AA236270 BI767164 BX956375 AI796271 AA380329 AI763304 AW151761 AU122696 
    BX486945 BM831133 BM455243 AV648239 BF434238 AA854873 AI078054 AA005356 
    BM551497 BE047626 BM976745 AV648296 N63677 BC022874 AA553682 N63726 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SHMT1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
    SP1:                          -                 -     -                                                               
    SP2:                          -                 -     -                                   -                           
    SP3:                                            -     -                                                               
    SP4:                          -                 -                                                                     
    SP5:                          -                                                                                       


    ECgene alternative splicing isoforms for SHMT1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SHMT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCAAAGGAGA
    SHMT1 Expression
    About this image


    SHMT1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Trophoblast (Extraembryonic Tissues)    fully expand to see all 2 entries
             Trophoblast Cells Trophoblast
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Ovary (Reproductive System)
             Oviduct
    SHMT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SHMT1 Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.513987 Hs.636044
        Custom PCR Arrays for SHMT1
    Primer
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHMT1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SHMT1 gene from Selected species (see all 29)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shmt11 , 5 serine hydroxymethyltransferase 1 (soluble)1, 5 85.22(n)1
    91.6(a)1
      11 (37.84 cM)5
    204251  NM_009171.21  NP_033197.21 
     607881045 
    chicken
    (Gallus gallus)
    Aves SHMT11 serine hydroxymethyltransferase 1 (soluble) 74.67(n)
    81.68(a)
      416520  XM_004945203.1  XP_004945260.1 
    lizard
    (Anolis carolinensis)
    Reptilia SHMT16
    serine hydroxymethyltransferase 1 (soluble)
    82(a)
    1 ↔ 1
    GL343618.1(206498-225361)
    African clawed frog
    (Xenopus laevis)
    Amphibia shmt1-prov2 serine hydroxymethyltransferase 1 (soluble) 81.3(n)    BC042276.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc661712 similar to serine hydroxymethyl transferase 1 (soluble) 75.95(n)   394021  BC055527.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG30111 , 3 glycine hydroxymethyltransferase3
    CG30111
    60(a)3
    61.04(n)1
    60.39(a)1
      5C73
    315241  NM_132050.21  NP_572278.11 
    worm
    (Caenorhabditis elegans)
    Secernentea mel-321 , 3 mel-321 61(a)3
    60.73(n)1
    61.8(a)1
      III(6512024-6514577)3
    1759151  NM_171169.41  NP_741197.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SHM21 SHM2 56.57(n)
    55.84(a)
      850747   NP_013159.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SHM21 SHM2 58.15(n)
    60.17(a)
      832736  NM_122560.2  NP_568488.2 
    barley
    (Hordeum vulgare)
    Liliopsida Hv.24162 Transcribed sequence with moderate similarity to protein more 76.39(n)    CA006934.1 


    ENSEMBL Gene Tree for SHMT1 (if available)
    TreeFam Gene Tree for SHMT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SHMT1 gene
    SHMT22  
    3 SIMAP similar genes for SHMT1 using alignment to 5 protein entries:     GLYC_HUMAN (see all proteins):
    SHMT    SHMT2    DKFZp686P09201

    Find genes that share paralogs with SHMT1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SHMT1
    PGOHUM00000243989


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SHMT1 (see all 833)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1381949581,2
    C--18218863(+) GCCCTA/GGAGAT 2 -- ds50010--------
    rs802239401,2
    C,F--18218892(+) GGGGAG/AGGGTC 2 -- ds50012Minor allele frequency- A:0.04WA 120
    rs1900452701,2
    --18219039(+) CCTACA/GAGGTG 2 -- ds50010--------
    rs1491589131,2
    --18219135(+) TGCAGA/TGAAAA 2 -- ds50010--------
    rs1450722561,2
    --18219209(+) TTCCCA/GTCCCG 2 -- ds50010--------
    rs1831942591,2
    --18219243(+) ACCACA/GTGAGG 2 -- ds50010--------
    rs1380139791,2
    --18219294(+) CGTGTA/GTGATA 2 -- ds50010--------
    rs1426090601,2
    --18219569(+) GATTAC/TGGGAG 2 -- ut310--------
    rs1136408811,2
    C--18219594(+) CAGGTA/GGAGCA 2 -- ut310--------
    rs20454631,2
    C,H--18219683(+) ACTTTG/AAGCTA 2 -- ut316Minor allele frequency- A:0.00NS EA NA 424

    HapMap Linkage Disequilibrium report for SHMT1 (18231187 - 18266856 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for SHMT1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1004827CNV Deletion20482838
    nsv1998CNV Insertion18451855
    nsv509653CNV Insertion20534489
    nsv833387CNV Loss17160897
    nsv428333CNV Gain18775914
    nsv827913CNV Gain20364138
    nsv833386CNV Gain17160897
    dgv932e1CNV Complex17122850
    nsv155OTHER Inversion15895083
    nsv499114OTHER Inversion21111241

    Human Gene Mutation Database (HGMD): SHMT1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SHMT1
    DNA2.0 Custom Variant and Variant Library Synthesis for SHMT1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 182144    OMIM disorders: --

    6 diseases for SHMT1:    
    About MalaCards
    adult acute lymphocytic leukemia    pediatric osteosarcoma    autonomic dysfunction    acute lymphocytic leukemia
    neural tube defects    non-hodgkin lymphoma


    Find genes that share disorders with SHMT1           About GenesLikeMe

    8 Novoseek inferred disease relationships for SHMT1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    adult acute lymphocytic leukemia 77.4 1 12604405 (1)
    neural tube defects 54.6 1 11386852 (1)
    cancer 15 7 9753690 (2), 16049973 (2), 16410450 (1), 9757129 (1) (see all 5)
    breast cancer 13.7 18 19707223 (5), 17896178 (3), 16049973 (2), 17311260 (1)
    colorectal cancer 13.3 2 15902326 (1), 17216011 (1)
    cancer lung 0 6 17420066 (4)
    tumors 0 2 9422575 (1), 9757129 (1)
    lymphoma 0 1 12604405 (1)

    Genetic Association Database (GAD): SHMT1
    Human Genome Epidemiology (HuGE) Navigator: SHMT1 (75 documents)

    Export disorders for SHMT1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SHMT1 gene, integrated from 10 sources (see all 171):
    (articles sorted by number of sources associating them with SHMT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Is mutated serine hydroxymethyltransferase (SHMT) involved in the etiology of neural tube defects? (PubMed id 11386852)1, 4, 7, 9 Heil S.G....Blom H.J. (Mol. Genet. Metab. 2001)
    2. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PubMed id 8505317)1, 2, 3, 9 Garrow T.A.... Shane B. (J. Biol. Chem. 1993)
    3. No association between cSHMT genotypes and the risk of breast cancer in the Nurses' Health Study. (PubMed id 19707223)1, 4, 9 Bentley A.R....Cassano P.A. (Eur J Clin Nutr 2010)
    4. Polymorphisms of cytosolic serine hydroxymethyltransferase and risk of lung cancer: a case-control analysis. (PubMed id 17420066)1, 4, 9 Wang L....Wei Q. (Lung Cancer 2007)
    5. The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. (PubMed id 9753690)1, 2, 9 Renwick S.B.... Baumann U. (Structure 1998)
    6. Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan. (PubMed id 17896178)1, 4, 9 Cheng C.W....Shen C.Y. (Breast Cancer Res. Treat. 2008)
    7. Polymorphisms in cytoplasmic serine hydroxymethyltransferase and methylenetetrahydrofolate reductase affect the risk of cardiovascular disease in men. (PubMed id 16046727)1, 4, 9 Lim U....Cassano P.A. (J. Nutr. 2005)
    8. Mimosine attenuates serine hydroxymethyltransferase transcription by chelating zinc. Implications for inhibition of DNA replication. (PubMed id 15531579)1, 7, 9 Perry C....Stover P.J. (J. Biol. Chem. 2005)
    9. Polymorphisms in the one-carbon metabolic pathway, plasma folate levels and colorectal cancer in a prospective study. (PubMed id 15122597)1, 4, 9 Chen J....Ma J. (Int. J. Cancer 2004)
    10. Dietary intake of B-vitamins, polymorphisms in thymidylate synthase and serine hydroxymethyltransferase 1, and colorectal adenoma risk: a Dutch case-control study. (PubMed id 17113224)1, 4, 9 van den Donk M....Kampman E. (Cancer Lett. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6470 HGNC: 10850 AceView: SHMT1 Ensembl:ENSG00000176974 euGenes: HUgn6470
    ECgene: SHMT1 Kegg: 6470 H-InvDB: SHMT1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SHMT1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SHMT1 gene:
    Search GeneIP for patents involving SHMT1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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