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SHMT2 Gene

protein-coding   GIFtS: 62
GCID: GC12P057623

Serine Hydroxymethyltransferase 2 (Mitochondrial)


(Previous symbol: SHMT)
  See SHMT2-related disease
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 2 (Mitochondrial)1 2     Epididymis Secretory Sperm Binding Protein Li 51e2
SHMT1 2 3     GLY A+2
Glycine Hydroxymethyltransferase2 3     Glycine Auxotroph A, Human Complement For Hamster2
Serine Methylase2 3     Serine Aldolase2
EC 2.1.2.13 8     Serine Hydroxymethylase2
GLYA2 5     Serine Hydroxymethyltransferase, Mitochondrial2
HEL-S-51e2     Threonine Aldolase2

External Ids:    HGNC: 108521   Entrez Gene: 64722   Ensembl: ENSG000001821997   OMIM: 1384505   UniProtKB: P348973   

Export aliases for SHMT2 gene to outside databases

Previous GC identifers: GC12U990093 GC12P057340 GC12P055909 GC12P055886 GC12P054662


(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 SHMT2 Gene:
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)

GeneCards Summary for SHMT2 Gene:
SHMT2 (serine hydroxymethyltransferase 2 (mitochondrial)) is a protein-coding gene. Diseases associated with SHMT2 include pyridoxine deficiency. GO annotations related to this gene include pyridoxal phosphate binding and identical protein binding. An important paralog of this gene is SHMT1.

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897
Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil
accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the SHMT2 gene promoter:
         E2F-3a   E2F-1   Sp1   E2F-2   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSHMT2 promoter sequence
   Search Chromatin IP Primers for SHMT2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SHMT2


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

Entrez Gene cytogenetic band: 12q12-q14   Ensembl cytogenetic band:  12q13.3   HGNC cytogenetic band: 12q12-q14

SHMT2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHMT2 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P057623:  view genomic region     (about GC identifiers)

Start:
57,623,110 bp from pter      End:
57,628,718 bp from pter
Size:
5,609 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SHMT2

(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: GLYM_HUMAN, P34897 (See protein sequence)
Recommended Name: Serine hydroxymethyltransferase, mitochondrial precursor  
Size: 504 amino acids; 55993 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 SHMT2:
3OU5 (3D)    
Secondary accessions: B7Z9F1 E7EQ19 E7EU43 O00740 Q8N1A5
Alternative splicing: 3 isoforms:  P34897-1   P34897-2   P34897-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SHMT2: NX_P34897

Explore proteomics data for SHMT2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys95, Lys200, Lys409, Lys469, Lys474
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for SHMT2 (P34897) (see all 22)
     VTTTTHK  LIASENF  LVSGGTD  GGTDNHL 


    See SHMT2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_001159828.1  NP_001159829.1  NP_001159830.1  NP_001159831.1  NP_005403.2  

    ENSEMBL proteins: 
     ENSP00000333667   ENSP00000451169   ENSP00000452315   ENSP00000450930   ENSP00000452035  
     ENSP00000450594   ENSP00000451630   ENSP00000450610   ENSP00000406881   ENSP00000450927  
     ENSP00000450452   ENSP00000452161   ENSP00000450893   ENSP00000452045   ENSP00000452419  
     ENSP00000451968   ENSP00000452404   ENSP00000413770   ENSP00000451872   ENSP00000452339  
     ENSP00000451371   ENSP00000452163   ENSP00000451495   ENSP00000450490   ENSP00000377413  

    SHMT2 Human Recombinant Protein Products:

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    Novus Biologicals SHMT2 Proteins
    Novus Biologicals SHMT2 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SHMT2

     
    Search eBioscience for Proteins for SHMT2 

    SHMT2 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    LSBio Antibodies in human, mouse, rat for SHMT2

    SHMT2 Assay Products:

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    Cloud-Clone Corp. ELISAs for SHMT2
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    Search eBioscience for ELISAs for SHMT2 


    (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 P34897

    ProtoNet protein and cluster: P34897

    1 Blocks protein domain: IPB001085 Glycine hydroxymethyltransferase

    UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897
    Similarity: Belongs to the SHMT family


    Find genes that share domains with SHMT2           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: GLYM_HUMAN, P34897
    Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil
    accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA
    Catalytic activity: 5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine

         Genatlas biochemistry entry for SHMT2:
    serine hydroxy-methyltransferase,pyridoxal dependent,mitochondrial,catalyzing 5-10 methylene THF
    synthesis,"one-carbone" metabolism,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 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA18063578
    GO:0004372glycine hydroxymethyltransferase activity IDA17482557
    GO:0008168methyltransferase activity ----
    GO:0008732L-allo-threonine aldolase activity IEA--
    GO:0016597amino acid binding IEA--
         
    Find genes that share ontologies with SHMT2           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SHMT2
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SHMT2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SHMT2
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SHMT2

    miRNA
    Products:
        
    miRTarBase miRNAs that target SHMT2:
    hsa-mir-92a-3p (MIRT049169), hsa-let-7a-5p (MIRT052431), hsa-mir-193b-3p (MIRT006985), hsa-mir-423-3p (MIRT042617), hsa-mir-186-5p (MIRT045122), hsa-mir-124-3p (MIRT022849), hsa-mir-615-3p (MIRT040137), hsa-mir-940 (MIRT036608)

    Block miRNA regulation of human, mouse, rat SHMT2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SHMT2 (see all 25):
    hsa-miR-579 hsa-miR-485-5p hsa-miR-495 hsa-miR-657 hsa-miR-4299 hsa-miR-4314 hsa-miR-183* hsa-miR-1184
    SwitchGear 3'UTR luciferase reporter plasmidSHMT2 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SHMT2
    Predesigned siRNA for gene silencing in human, mouse, rat SHMT2

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for SHMT2

    Clone
    Products:
         
    OriGene clones in human, mouse for SHMT2 (see all 26)
    OriGene ORF clones in mouse, rat for SHMT2
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 5): SHMT2 (NM_005412)
    Sino Biological Human cDNA Clone for SHMT2
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SHMT2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SHMT2
    Addgene plasmids for SHMT2 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for SHMT2
    Browse ESI BIO Cell Lines and PureStem Progenitors for SHMT2 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHMT2


    (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
    GLYM_HUMAN, P34897: Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion inner membrane
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    cytoskeleton4
    chloroplast2
    peroxisome2
    cytosol1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA--
    GO:0005743mitochondrial inner membrane IDA--
    GO:0005758mitochondrial intermembrane space IEA--
    GO:0005759mitochondrial matrix IDA11516159
    GO:0015630microtubule cytoskeleton IDA--

    Find genes that share ontologies with SHMT2           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 SHMT2 About   (see all 8)  
    See pathways by source

    SuperPathContained pathways About
    1One carbon pool by folate
    One carbon pool by folate0.53
    Trans-sulfuration and one carbon metabolism0.43
    One Carbon Metabolism0.53
    dTMP de novo biosynthesis (mitochondrial)0.00
    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
    4Carbon metabolism
    Carbon metabolism0.38
    Biosynthesis of amino acids0.38
    5Metabolism
    Metabolic pathways0.38


    Find genes that share SuperPaths with SHMT2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SHMT2
        Glucose / Energy Metabolism

    Selected BioSystems Pathways for SHMT2 (see all 10)
        One Carbon Metabolism
    folate transformations
    folate polyglutamylation
    dTMP de novo biosynthesis (mitochondrial)
    glycine biosynthesis I



    Selected Kegg Pathways  (Kegg details for SHMT2) (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: GLYM_HUMAN, P34897
    Pathway: One-carbon metabolism; tetrahydrofolate interconversion

        Pathway & Disease-focused RT2 Profiler PCR Array including SHMT2: 

              Amino Acid Metabolism II in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for SHMT2

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

    Selected Interacting proteins for SHMT2 (P348972, 3 ENSP000003336674) via UniProtKB, MINT, STRING, and/or I2D (see all 433)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRMT10CQ7L0Y32, 3, ENSP000003123564MINT-8079030 I2D: score=1 STRING: ENSP00000312356
    EEF1A1P681042, 3MINT-8076236 I2D: score=1 
    KARSQ150462, 3MINT-8079030 I2D: score=1 
    CSNK2BP678703, ENSP000003650254I2D: score=2 STRING: ENSP00000365025
    ENSG00000206406P678703I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006544glycine metabolic process ----
    GO:0006545glycine biosynthetic process ----
    GO:0006563L-serine metabolic process ----
    GO:0006564L-serine biosynthetic process IEA--
    GO:0006730one-carbon metabolic process IDA11516159

    Find genes that share ontologies with SHMT2           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 SHMT2 (GLYM)

    6 HMDB Compounds for SHMT2    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--

    3 DrugBank Compounds for SHMT2    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17664250 16876889 17142057 16980404 17355947
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor15865438 11877399 17482557 17651438 16980404
    Tetrahydrofolic acid5,6,7,8-tetrahydrofolate (see all 3)135-16-0targetcofactor9449840 17142057 11386852 17651438 11737206

    Selected Novoseek inferred chemical compound relationships for SHMT2 gene (see all 12)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    4-deoxypyridoxine 88.7 1 7526359 (1)
    tetrahydrofolate 86.8 3 8786078 (1), 19815026 (1), 15170323 (1)
    pyridoxal 5-phosphate 79.8 14 12913008 (3), 10387080 (3), 19158217 (1), 8405393 (1) (see all 5)
    5,10-methenyltetrahydrofolate 78.4 1 15170323 (1)
    serine 73.2 44 18029478 (2), 8435385 (2), 2127307 (2), 11189372 (2) (see all 26)
    vitamin b6 57.8 5 19158217 (2), 7526359 (1)
    leucovorin 45.7 4 15170323 (2), 15888445 (1)
    folate 44.6 5 15170323 (2), 16137637 (1), 10656824 (1)
    aspartate 33.8 3 10493937 (1), 10656824 (1), 8405393 (1)
    lysine 15.9 1 10387080 (1)



    Find genes that share compounds with SHMT2           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 SHMT2 gene (5 alternative transcripts): 
    NM_001166356.1  NM_001166357.1  NM_001166358.1  NM_001166359.1  NM_005412.5  

    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 36):
    ENST00000328923(uc001snf.2 uc009zpk.2 uc001sng.2 uc001sni.2 uc010srh.2)
    ENST00000556825(uc001snh.2 uc010srg.2 uc010srj.2) ENST00000557740
    ENST00000554600 ENST00000553324 ENST00000554467 ENST00000557487 ENST00000553950
    ENST00000555634 ENST00000556689 ENST00000557269 ENST00000555563 ENST00000557433
    ENST00000414700 ENST00000557348 ENST00000557703 ENST00000553529 ENST00000554310

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SHMT2 (see all 25):
    hsa-miR-579 hsa-miR-485-5p hsa-miR-495 hsa-miR-657 hsa-miR-4299 hsa-miR-4314 hsa-miR-183* hsa-miR-1184
    SwitchGear 3'UTR luciferase reporter plasmidSHMT2 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SHMT2
    Predesigned siRNA for gene silencing in human, mouse, rat SHMT2
    Clone
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    OriGene clones in human, mouse for SHMT2 (see all 26)
    OriGene ORF clones in mouse, rat for SHMT2
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 5): SHMT2 (NM_005412)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SHMT2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SHMT2
    Addgene plasmids for SHMT2 
    Primer
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    OriGene qPCR primer pairs and template standards for SHMT2
    OriGene qSTAR qPCR primer pairs in human, mouse for SHMT2
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SHMT2
      QuantiTect SYBR Green Assays in human, mouse, rat SHMT2
      QuantiFast Probe-based Assays in human, mouse, rat SHMT2

    Selected AceView cDNA sequences (see all 1296):

    CB240828 BE294128 BQ683990 BM457584 BI823409 BQ061618 CR613033 AI138694 
    AW246735 BQ706965 BU627081 BM677703 AW264652 AL560314 BM717816 CA306154 
    BM920284 AW069245 BP872305 BQ709963 CF132149 W73771 AI554740 BU167619 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SHMT2 (see all 38)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ·
    SP1:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -               
    SP2:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -               
    SP3:                                                                                      -     -     -     -     -     -     -     -     -     -               
    SP4:                                                                                      -     -     -     -     -     -     -     -     -     -               
    SP5:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -           -   

    ExUns: 5d · 5e ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ^ 10a · 10b · 10c · 10d ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^
    SP1:                          -                                                                 -                             -                                 
    SP2:                          -                                                                 -                             -     -                           
    SP3:  -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -                             -                                 
    SP4:                          -                                                                 -                             -                                 
    SP5:  -     -     -     -     -                                                                 -                             -                                 

    ExUns: 14a · 14b · 14c · 14d · 14e ^ 15 ^ 16a · 16b · 16c ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c
    SP1:                                -                                                                                 
    SP2:                                -                                                                                 
    SP3:                                -                                                                                 
    SP4:                                                                                                                  
    SP5:                                                                                                                  


    ECgene alternative splicing isoforms for SHMT2

    (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)
    About This Section

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    SHMT2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATCACAGTGT
    SHMT2 Expression
    About this image


    SHMT2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 13) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Mandibular Condyle
     
     Eye (Sensory Organs)
             Mature Horizontal Cells Inner Nuclear Layer
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    SHMT2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SHMT2 Protein Expression
        Pathway & Disease-focused RT2 Profiler PCR Array including SHMT2: 
              Amino Acid Metabolism II in human mouse rat

    Primer
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    (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 SHMT2 gene from Selected species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shmt21 , 5 serine hydroxymethyltransferase 2 (mitochondrial)1, 5 87.87(n)1
    94.04(a)1
      10 (74.51 cM)5
    1080371  NM_028230.41  NP_082506.11 
     1275171235 
    lizard
    (Anolis carolinensis)
    Reptilia SHMT26
    serine hydroxymethyltransferase 2 (mitochondrial)
    81(a)
    1 ↔ 1
    GL343212.1(1740134-1769844)
    African clawed frog
    (Xenopus laevis)
    Amphibia BX853756.12   -- 76.63(n)    BX853756.1 
    zebrafish
    (Danio rerio)
    Actinopterygii shmt21 serine hydroxymethyltransferase 2 (mitochondrial) 71.75(n)
    78.05(a)
      100144628  NM_001123374.1  NP_001116846.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG30113 glycine hydroxymethyltransferase 60(a)   5C7   --
    worm
    (Caenorhabditis elegans)
    Secernentea mel-323   -- 57(a)   III(6512024-6514577)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SHM1(YBR263W)4
    SHM11
    Mitochondrial serine hydroxymethyltransferase, converts more4
    SHM11
    53.84(n)1
    55.26(a)1
      2(736264-737736)4
    8525651, 4  NP_009822.41  NP_009822.24 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SHM11 SHM1 59.99(n)
    62.56(a)
      829949  NM_119954.3  NP_195506.1 
    rice
    (Oryza sativa)
    Liliopsida Os.121482 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.3(n)    AK100404.1 


    ENSEMBL Gene Tree for SHMT2 (if available)
    TreeFam Gene Tree for SHMT2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SHMT2 gene
    SHMT12  
    3 SIMAP similar genes for SHMT2 using alignment to 17 protein entries:     GLYM_HUMAN (see all proteins):
    DKFZp686P09201    SHMT1    SHMT

    Find genes that share paralogs with SHMT2           About GenesLikeMe



    (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)
    About This Section

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    Selected SNPs for SHMT2 (see all 212)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1149576411,2
    F--57455437(+) GCTACA/GGTAAA 3 -- us2k11Minor allele frequency- G:0.02WA 118
    rs1156493881,2
    F--57455830(+) ACTCCC/TACTGC 5 -- us2k11Minor allele frequency- T:0.02WA 118
    rs1919335691,2
    --57455989(+) TCTACC/TAAAAA 5 -- us2k10--------
    rs1512444511,2
    --57456013(+) CTGGAC/TGTGGT 5 -- us2k10--------
    rs767585081,2
    C,F--57456093(+) GGTTGC/TAGTGA 7 -- us2k12Minor allele frequency- T:0.50WA CSA 4
    rs1132638341,2
    C--57456165(+) AAAAC-/AAAAAA 9 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1445105751,2
    C--57456218(+) AGTGCA/GGTGGC 9 -- us2k10--------
    rs1180435231,2
    F--57456322(+) TAGGTA/GATTTA 9 -- us2k11Minor allele frequency- G:0.01EA 120
    rs128261781,2
    C,F--57456345(+) ttgtaG/Tagata 9 -- us2k1 tfbs34Minor allele frequency- T:0.10NA 126
    rs1831367041,2
    --57456377(+) GCTGGC/TTTAGA 9 -- us2k10--------

    HapMap Linkage Disequilibrium report for SHMT2 (57623110 - 57628718 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SHMT2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv899116CNV Loss21882294
    dgv96n21CNV Loss19592680
    nsv519293CNV Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SHMT2
    DNA2.0 Custom Variant and Variant Library Synthesis for SHMT2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 138450    OMIM disorders: --

    1 disease for SHMT2:    
    About MalaCards
    pyridoxine deficiency


    Find genes that share disorders with SHMT2           About GenesLikeMe

    Genetic Association Database (GAD): SHMT2
    Human Genome Epidemiology (HuGE) Navigator: SHMT2 (9 documents)

    Export disorders for SHMT2 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 SHMT2 gene, integrated from 10 sources (see all 98):
    (articles sorted by number of sources associating them with SHMT2)
        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 Heil S.G....Blom H.J. (Mol. Genet. Metab. 2001)
    2. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. (PubMed id 8999870)1, 2, 3 Stover P.J.... Shane B. (J. Biol. Chem. 1997)
    3. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PubMed id 8505317)1, 2, 9 Garrow T.A.... Shane B. (J. Biol. Chem. 1993)
    4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    6. Oral facial clefts and gene polymorphisms in metabolism of folate/one-carbon and vitamin A: a pathway-wide association study. (PubMed id 19048631)1, 4 Boyles A.L....Lie R.T. (Genet. Epidemiol. 2009)
    7. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PubMed id 19086053)1, 4 GratacA^s M....Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009)
    8. MALDI-TOF MS genotyping of polymorphisms related to 1-carbon metabolism using common and mass-modified terminators. (PubMed id 18988749)1, 4 Meyer K....Ueland P.M. (Clin. Chem. 2009)
    9. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. (PubMed id 18636124)1, 4 Skibola C.F....Smith M.T. (PLoS ONE 2008)
    10. The layered structure of human mitochondrial DNA nucleoids. (PubMed id 18063578)1, 2 Bogenhagen D.F.... Burke S. (J. Biol. Chem. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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: 6472 HGNC: 10852 AceView: SHMT2andNXPH4 Ensembl:ENSG00000182199 euGenes: HUgn6472
    ECgene: SHMT2 Kegg: 6472 H-InvDB: SHMT2

    (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)
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    NameDescription
    PharmGKB entry for SHMT2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for SHMT2 gene:
    Search GeneIP for patents involving SHMT2

    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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