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    SHMT1 serine hydroxymethyltransferase 1 [ Sus scrofa (pig) ]

    Gene ID: 397181, updated on 17-Aug-2024

    Summary

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    Official Symbol
    SHMT1provided by VGNC
    Official Full Name
    serine hydroxymethyltransferase 1provided by VGNC
    Primary source
    VGNC:VGNC:92855
    See related
    Ensembl:ENSSSCG00000036208
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Sus scrofa
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus
    Also known as
    SHMT
    Expression
    Biased expression in liver (RPKM 60.7), mixtures (RPKM 24.9) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See SHMT1 in Genome Data Viewer
    Location:
    chromosome: 12
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    106 current Sscrofa11.1 (GCF_000003025.6) 12 NC_010454.4 (60414421..60435451)
    105 previous assembly Sscrofa10.2 (GCF_000003025.5) Unplaced Scaffold NW_003539013.1 (24994..34374)

    Chromosome 12 - NC_010454.4Genomic Context describing neighboring genes Neighboring gene phosphoribosyl pyrophosphate synthetase associated protein 2 Neighboring gene uncharacterized LOC106508506 Neighboring gene SMCR8-C9orf72 complex subunit Neighboring gene DNA topoisomerase III alpha Neighboring gene mitochondrial elongation factor 2 Neighboring gene FLII actin remodeling protein Neighboring gene LLGL scribble cell polarity complex component 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome data used for gene annotation Transcriptome data used for gene annotation
    • Description: Nine kinds of tissues and a mixture of multiple tissues were sequenced for genome annotation
    • BioProject: PRJNA311523
    • Publication: PMID 27646534
    • Analysis date: Thu Dec 14 17:10:49 2017

    Bibliography

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    Related articles in PubMed

    1. Effects of breed, parity, and folic Acid supplement on the expression of folate metabolism genes in endometrial and embryonic tissues from sows in early pregnancy. Vallée M, et al. Biol Reprod, 2002 Oct. PMID 12297544
    2. PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Uenishi H, et al. Nucleic Acids Res, 2007 Jan. PMID 17145712, Free PMC Article
    3. PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Uenishi H, et al. Nucleic Acids Res, 2004 Jan 1. PMID 14681463, Free PMC Article
    4. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    5. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables cobalt ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables glycine hydroxymethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables mRNA 5'-UTR binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables mRNA regulatory element binding translation repressor activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables serine binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-serine catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in folic acid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in glycine biosynthetic process from serine IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in protein homotetramerization IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in purine nucleobase biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    serine hydroxymethyltransferase, cytosolic
    Names
    serine hydroxymethyltransferase 2 (mitochondrial)

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Sus scrofa Annotation Release 106 details...Open this link in a new tab

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

    Reference Sscrofa11.1 Primary Assembly

    Genomic

    1. NC_010454.4 Reference Sscrofa11.1 Primary Assembly

      Range
      60414421..60435451
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021067992.1 → XP_020923651.1  serine hydroxymethyltransferase, cytosolic

      UniProtKB/TrEMBL
      A0A286ZN35, A0A4X1SYS9, A0A8D0Q5D9
      Related
      ENSSSCP00000050013.1, ENSSSCT00000056927.3
      Conserved Domains (1) summary
      PLN03226
      Location:24 → 481
      PLN03226; serine hydroxymethyltransferase; Provisional

    2. XM_021067993.1 → XP_020923652.1  serine hydroxymethyltransferase, cytosolic

      UniProtKB/TrEMBL
      A0A286ZN35, A0A4X1SYS9, A0A8D0Q5D9
      Conserved Domains (1) summary
      PLN03226
      Location:24 → 481
      PLN03226; serine hydroxymethyltransferase; Provisional

    3. XM_021067989.1 → XP_020923648.1  serine hydroxymethyltransferase, cytosolic

      UniProtKB/TrEMBL
      A0A286ZN35, A0A4X1SYS9, A0A8D0Q5D9
      Conserved Domains (1) summary
      PLN03226
      Location:24 → 481
      PLN03226; serine hydroxymethyltransferase; Provisional

    4. XM_021067990.1 → XP_020923649.1  serine hydroxymethyltransferase, cytosolic

      UniProtKB/TrEMBL
      A0A286ZN35, A0A4X1SYS9, A0A8D0Q5D9
      Conserved Domains (1) summary
      PLN03226
      Location:24 → 481
      PLN03226; serine hydroxymethyltransferase; Provisional

    RNA

    1. XR_002337401.1 RNA Sequence

    2. XR_002337402.1 RNA Sequence

    3. XR_002337404.1 RNA Sequence

      Related
      ENSSSCT00000063631.3

    4. XR_002337398.1 RNA Sequence

    5. XR_002337399.1 RNA Sequence

    6. XR_002337400.1 RNA Sequence

    7. XR_002337397.1 RNA Sequence

    8. XR_002337403.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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