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

Gene ID: 336798, updated on 27-Mar-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 prenyltransferase activity. Predicted to be involved in isoprenoid biosynthetic process. Orthologous to human GGPS1 (geranylgeranyl diphosphate synthase 1). [provided by Alliance of Genome Resources, Apr 2022]
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:
5
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (49727287..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 AT-rich interaction domain 4B Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2 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 prenyltransferase 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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    49727287..49769372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017358708.2 → 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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