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    ogfod1 2-oxoglutarate and iron-dependent oxygenase domain containing 1 [ Danio rerio (zebrafish) ]

    Gene ID: 324573, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ogfod1provided by ZNC
    Official Full Name
    2-oxoglutarate and iron-dependent oxygenase domain containing 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-3294
    See related
    Ensembl:ENSDARG00000036061 AllianceGenome:ZFIN:ZDB-GENE-030131-3294
    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
    D63; zgc:66379; wu:fc33b08
    Summary
    Predicted to enable peptidyl-proline dioxygenase activity. Predicted to be involved in regulation of translational termination. Predicted to be active in cytoplasm. Orthologous to human OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain containing 1). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ogfod1 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (29096194..29109490)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (28825044..28838340)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene VRK serine/threonine kinase 3 Neighboring gene ACD shelterin complex subunit and telomerase recruitment factor Neighboring gene F-box and leucine-rich repeat protein 8 Neighboring gene tnfrsf1a-associated via death domain

    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. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    3. 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
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. 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 2-oxoglutarate-dependent dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidyl-proline dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of translational termination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    prolyl 3-hydroxylase OGFOD1
    NP_955983.2

    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_199689.3 → NP_955983.2  prolyl 3-hydroxylase OGFOD1

      Status: VALIDATED

      Source sequence(s)
      CR848675, EH542776, EH558754
      UniProtKB/TrEMBL
      A0A8M1PED0, F1QTC6
      Related
      ENSDARP00000052348.7, ENSDART00000052349.8
      Conserved Domains (2) summary
      smart00702
      Location:73 → 239
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
      pfam10637
      Location:262 → 518
      Ofd1_CTDD; Oxoglutarate and iron-dependent oxygenase degradation C-term

    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_007118.7 Reference GRCz11 Primary Assembly

      Range
      29096194..29109490
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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