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shmt1 serine hydroxymethyltransferase 1 (soluble) [ Danio rerio (zebrafish) ]

Gene ID: 394021, updated on 4-Jan-2025

Summary

Official Symbol
shmt1provided by ZNC
Official Full Name
serine hydroxymethyltransferase 1 (soluble)provided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-1558
See related
Ensembl:ENSDARG00000052816 AllianceGenome:ZFIN:ZDB-GENE-040426-1558
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:66171; zgc:77524
Summary
Enables glycine hydroxymethyltransferase activity. Predicted to be involved in glycine biosynthetic process from serine and tetrahydrofolate metabolic process. Predicted to act upstream of or within methylation and one-carbon metabolic process. Located in cytosol and nucleus. Is expressed in several structures, including digestive system; immature eye; midbrain; neural tube; and oocyte. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
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Genomic context

See shmt1 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (40260974..40276034, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (40119113..40136184, complement)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase III alpha Neighboring gene Smith-Magenis syndrome chromosome region, candidate 8a Neighboring gene pdgfa associated protein 1b Neighboring gene BUD31 homolog

Genomic regions, transcripts, and products

Expression

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Pathways from PubChem

General gene information

Clone Names

  • MGC66171

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables glycine hydroxymethyltransferase activity  
enables glycine hydroxymethyltransferase activity PubMed 
enables glycine hydroxymethyltransferase activity  
enables glycine hydroxymethyltransferase activity PubMed 
enables methyltransferase activity  
enables pyridoxal phosphate binding  
enables pyridoxal phosphate binding  
enables transferase activity  
Component Evidence Code Pubs
is_active_in cytoplasm  
located_in cytoplasm PubMed 
located_in cytosol PubMed 
is_active_in mitochondrion  
is_active_in nucleus  
located_in nucleus PubMed 

General protein information

Preferred Names
serine hydroxymethyltransferase, cytosolic
Names
zSHMT-1
NP_957340.1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_201046.1NP_957340.1  serine hydroxymethyltransferase, cytosolic

    See identical proteins and their annotated locations for NP_957340.1

    Status: PROVISIONAL

    Source sequence(s)
    BC055527
    UniProtKB/TrEMBL
    Q7SXN1
    Related
    ENSDARP00000069223.4, ENSDART00000074737.6
    Conserved Domains (2) summary
    PLN03226
    Location:22478
    PLN03226; serine hydroxymethyltransferase; Provisional
    pfam00464
    Location:23422
    SHMT; Serine hydroxymethyltransferase

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007114.7 Reference GRCz11 Primary Assembly

    Range
    40260974..40276034 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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