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

Gene ID: 393461, updated on 14-Nov-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 several processes, including central nervous system development; regulation of Notch signaling pathway; and retina layer formation. Predicted to be active in cytoplasm. Is expressed in several structures, including EVL; corneal epithelium; epidermis; 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, Nov 2024]
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
  • 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. Metabolic labeling of fucosylated glycans in developing zebrafish. Dehnert KW, et al. ACS Chem Biol, 2011 Jun 17. PMID 21425872, Free PMC Article
  4. Protein fucosylation is required for Notch dependent vascular integrity in zebrafish. Fowler G, et al. Dev Biol, 2021 Dec. PMID 34400136
  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 (16) 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
  
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 

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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