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    gmds GDP-mannose 4,6-dehydratase [ Danio rerio (zebrafish) ]

    Gene ID: 393461, updated on 12-Sep-2024

    Summary

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    Official Symbol
    gmdsprovided by ZNC
    Official Full Name
    GDP-mannose 4,6-dehydrataseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050419-45
    See related
    Ensembl:ENSDARG00000026629 AllianceGenome:ZFIN:ZDB-GENE-050419-45
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    srn; twd; dZ84G17.1; zgc:63772; si:ch211-231n5.3
    Summary
    Enables fucosyltransferase activity. Acts upstream of or within Notch signaling pathway; central nervous system development; and retina layer formation. Predicted to be active in cytoplasm. Is expressed in EVL; corneal epithelium; neuromast; and periderm. Used to study congenital disorder of glycosylation type IIc. Human ortholog(s) of this gene implicated in open-angle glaucoma. Orthologous to human GMDS (GDP-mannose 4,6-dehydratase). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See gmds in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (26709009..26822550, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (26809919..26923460, complement)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137488655 Neighboring gene forkhead box F2b Neighboring gene forkhead box C1b Neighboring gene uncharacterized LOC137488656 Neighboring gene myosin light chain kinase family, member 4b Neighboring gene serpin peptidase inhibitor, clade B (ovalbumin), member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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

    Bibliography

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    Related articles in PubMed

    1. Direct Visualization of Live Zebrafish Glycans via Single-Step Metabolic Labeling with Fluorophore-Tagged Nucleotide Sugars. Hong S, et al. Angew Chem Int Ed Engl, 2019 Oct 1. PMID 31295389, Free PMC Article
    2. Neural and synaptic defects in slytherin, a zebrafish model for human congenital disorders of glycosylation. Song Y, et al. PLoS One, 2010 Oct 29. PMID 21060795, Free PMC Article
    3. Protein fucosylation is required for Notch dependent vascular integrity in zebrafish. Fowler G, et al. Dev Biol, 2021 Dec. PMID 34400136
    4. Metabolic labeling of fucosylated glycans in developing zebrafish. Dehnert KW, et al. ACS Chem Biol, 2011 Jun 17. PMID 21425872, Free PMC Article
    5. Fatty liver disease induced by perfluorooctane sulfonate: Novel insight from transcriptome analysis. Fai Tse WK, et al. Chemosphere, 2016 Sep. PMID 27289203

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Protein fucosylation is required for Notch dependent vascular integrity in zebrafish.
      Title: Protein fucosylation is required for Notch dependent vascular integrity in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC63772

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables GDP-mannose 4,6-dehydratase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GDP-mannose 4,6-dehydratase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GDP-mannose 4,6-dehydratase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables NADP+ binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables fucosyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in 'de novo' GDP-L-fucose biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in 'de novo' GDP-L-fucose biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in 'de novo' GDP-L-fucose biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in GDP-mannose metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within GDP-mannose metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in GDP-mannose metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within Notch signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within blood vessel development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within blood vessel development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal motor nucleus of vagus nerve development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of Notch signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of vascular associated smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within retina layer formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vagus nerve development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    GDP-mannose 4,6 dehydratase
    Names
    towhead
    NP_001095945.1
    NP_956783.3

    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_001102475.2 → NP_001095945.1  GDP-mannose 4,6 dehydratase isoform 1

      See identical proteins and their annotated locations for NP_001095945.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the shorter protein (isoform 1).
      Source sequence(s)
      CK686273, EH445452, EH459452, EH524042
      UniProtKB/TrEMBL
      A7BI55, Q1LVF8
      Related
      ENSDARP00000046763.7, ENSDART00000046764.9
      Conserved Domains (2) summary
      TIGR01472
      Location:22 → 364
      gmd; GDP-mannose 4,6-dehydratase
      pfam16363
      Location:26 → 356
      GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase

    2. NM_200489.3 → NP_956783.3  GDP-mannose 4,6 dehydratase isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the coding region compared to variant 1. The resulting protein (isoform 2) is longer but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      CK686273, EH447791, EH459452, EH497761
      UniProtKB/TrEMBL
      A0A8M1PF97, F1QPT3
      Related
      ENSDARP00000094011.3, ENSDART00000103234.5
      Conserved Domains (2) summary
      TIGR01472
      Location:22 → 371
      gmd; GDP-mannose 4,6-dehydratase
      pfam16363
      Location:26 → 363
      GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase

    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_007131.7 Reference GRCz11 Primary Assembly

      Range
      26709009..26822550 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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