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    Gmds GDP-mannose 4, 6-dehydratase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 291095, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Gmdsprovided by RGD
    Official Full Name
    GDP-mannose 4, 6-dehydrataseprovided by RGD
    Primary source
    RGD:1311008
    See related
    EnsemblRapid:ENSRNOG00000017605 AllianceGenome:RGD:1311008
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable GDP-mannose 4,6-dehydratase activity; NADP+ binding activity; and identical protein binding activity. Predicted to be involved in 'de novo' GDP-L-fucose biosynthetic process and Notch signaling pathway. Predicted to be active in cytoplasm. 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, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 45.3), Brain (RPKM 43.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Gmds in Genome Data Viewer
    Location:
    17p12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (32304029..32830708)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (32095315..32621975)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (33408722..33938086)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S27a, pseudogene 20 Neighboring gene myosin light chain kinase family, member 4 Neighboring gene uncharacterized LOC108348555 Neighboring gene uncharacterized LOC134482705 Neighboring gene forkhead box C1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells. Ohyama C, et al. J Biol Chem, 1998 Jun 5. PMID 9603974
    2. Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. Gharahkhani P, et al. Nat Genet, 2014 Oct. PMID 25173105, Free PMC Article
    3. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. Sullivan FX, et al. J Biol Chem, 1998 Apr 3. PMID 9525924
    4. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). Gonzalez-Begne M, et al. J Proteome Res, 2009 Mar. PMID 19199708, Free PMC Article
    5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Fragoza R, et al. Nat Commun, 2019 Sep 12. PMID 31515488, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC125154

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables GDP-mannose 4,6-dehydratase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables NADP+ binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables NADP+ binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in GDP-mannose metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in Notch signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    GDP-mannose 4,6 dehydratase
    NP_001034695.1
    XP_038951422.1
    XP_038951423.1
    XP_038951424.1
    XP_063132253.1

    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_001039606.1 → NP_001034695.1  GDP-mannose 4,6 dehydratase

      See identical proteins and their annotated locations for NP_001034695.1

      Status: PROVISIONAL

      Source sequence(s)
      BC104708
      UniProtKB/TrEMBL
      F7FFK9, Q3MHS7
      Related
      ENSRNOP00000023691.4, ENSRNOT00000023691.7
      Conserved Domains (2) summary
      TIGR01472
      Location:24 → 366
      gmd; GDP-mannose 4,6-dehydratase
      pfam16363
      Location:27 → 358
      GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      32304029..32830708
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063276183.1 → XP_063132253.1  GDP-mannose 4,6 dehydratase isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZPV8

    2. XM_039095494.2 → XP_038951422.1  GDP-mannose 4,6 dehydratase isoform X2

      Conserved Domains (1) summary
      cl21454
      Location:24 → 300
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    3. XM_039095495.2 → XP_038951423.1  GDP-mannose 4,6 dehydratase isoform X3

      Conserved Domains (1) summary
      cl21454
      Location:1 → 287
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    4. XM_039095496.2 → XP_038951424.1  GDP-mannose 4,6 dehydratase isoform X4

      Conserved Domains (1) summary
      cl21454
      Location:1 → 259
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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