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    ggps1 geranylgeranyl diphosphate synthase 1 [ Danio rerio (zebrafish) ]

    Gene ID: 336798, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ggps1provided by ZNC
    Official Full Name
    geranylgeranyl diphosphate synthase 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-8742
    See related
    Ensembl:ENSDARG00000023627 AllianceGenome:ZFIN:ZDB-GENE-030131-8742
    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
    qm; fb05f09; zgc:56514; wu:fb05f09; zgc:101591
    Summary
    Predicted to enable farnesyltranstransferase activity. Predicted to be involved in isoprenoid biosynthetic process. Orthologous to human GGPS1 (geranylgeranyl diphosphate synthase 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ggps1 in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (49727333..49769372)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (49436611..49478694)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene translocase of outer mitochondrial membrane 20 Neighboring gene small nucleolar RNA SNORA14 Neighboring gene AT-rich interaction domain 4B Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2 Neighboring gene uncharacterized LOC137487446 Neighboring gene G protein subunit gamma 4

    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables farnesyltranstransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in isoprenoid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within isoprenoid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    geranylgeranyl pyrophosphate synthase
    NP_001278689.1
    NP_001278690.1
    XP_017214197.1

    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_001291760.1 → NP_001278689.1  geranylgeranyl pyrophosphate synthase isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      CU639409, CU914439, FP017283
      UniProtKB/TrEMBL
      A0A0R4ILW8, A0A8M6Z9I5
      Related
      ENSDARP00000134732.1, ENSDART00000168799.3
      Conserved Domains (1) summary
      pfam00348
      Location:59 → 297
      polyprenyl_synt; Polyprenyl synthetase

    2. NM_001291761.1 → NP_001278690.1  geranylgeranyl pyrophosphate synthase isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      CU639409, CU914439
      UniProtKB/TrEMBL
      A0A8M1P649, F1R4B6
      Related
      ENSDARP00000037908.4, ENSDART00000037559.6
      Conserved Domains (1) summary
      pfam00348
      Location:23 → 231
      polyprenyl_synt; Polyprenyl synthetase

    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_007124.7 Reference GRCz11 Primary Assembly

      Range
      49727333..49769372
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017358708.3 → XP_017214197.1  geranylgeranyl pyrophosphate synthase isoform X1

      UniProtKB/TrEMBL
      A0A0R4ILW8, A0A8M6Z9I5
      Conserved Domains (1) summary
      pfam00348
      Location:59 → 297
      polyprenyl_synt; Polyprenyl synthetase

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_200035.1: Suppressed sequence

      Description
      NM_200035.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version

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