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    alkbh3 alkB homolog 3, alpha-ketoglutarate dependent dioxygenase [ Danio rerio (zebrafish) ]

    Gene ID: 792266, updated on 9-Dec-2024

    Summary

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    Official Symbol
    alkbh3provided by ZNC
    Official Full Name
    alkB homolog 3, alpha-ketoglutarate dependent dioxygenaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040801-254
    See related
    Ensembl:ENSDARG00000045606 AllianceGenome:ZFIN:ZDB-GENE-040801-254
    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
    zgc:91935; im:6900103
    Summary
    Predicted to enable mRNA N1-methyladenosine dioxygenase activity. Acts upstream of or within cilium assembly. Predicted to be active in mitochondrion and nucleoplasm. Is expressed in brain. Orthologous to human ALKBH3 (alkB homolog 3, alpha-ketoglutarate dependent dioxygenase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See alkbh3 in Genome Data Viewer
    Location:
    chromosome: 25
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 25 NC_007136.7 (30233686..30298347)
    105 previous assembly GRCz10 (GCF_000002035.5) 25 NC_007136.6 (29790669..29856653)

    Chromosome 25 - NC_007136.7Genomic Context describing neighboring genes Neighboring gene si:ch211-147k10.6 Neighboring gene microRNA mir-129-4 Neighboring gene hydroxysteroid (17-beta) dehydrogenase 12a Neighboring gene si:ch1073-281m9.1 Neighboring gene TopBP1-interacting, checkpoint, and replication regulator

    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. ALKBH3-dependent m(1)A demethylation of Aurora A mRNA inhibits ciliogenesis. Kuang W, et al. Cell Discov, 2022 Mar 11. PMID 35277482, Free PMC Article
    2. Alkbh4 and Atrn Act Maternally to Regulate Zebrafish Epiboly. Sun Q, et al. Int J Biol Sci, 2017. PMID 28924386, 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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    Homology

    Clone Names

    • MGC91935

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA N1-methyladenosine dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA alkylation repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cilium assembly IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
    Names
    alkB, alkylation repair homolog 3
    NP_001003511.2
    XP_005163201.1
    XP_005163203.1
    XP_009296382.1

    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_001003511.2 → NP_001003511.2  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

      Status: VALIDATED

      Source sequence(s)
      CR376745
      UniProtKB/TrEMBL
      A0A8M1N1B3, F1QRD8
      Related
      ENSDARP00000067056.4, ENSDART00000067057.6
      Conserved Domains (1) summary
      pfam13532
      Location:81 → 267
      2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily

    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_007136.7 Reference GRCz11 Primary Assembly

      Range
      30233686..30298347
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009298107.4 → XP_009296382.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_009296382.1

      UniProtKB/TrEMBL
      A0A8M1N1B3, F1QRD8
      Conserved Domains (1) summary
      pfam13532
      Location:81 → 267
      2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily

    2. XM_005163144.5 → XP_005163201.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_005163201.1

      UniProtKB/TrEMBL
      A0A8M1N1B3, F1QRD8
      Related
      ENSDARP00000149194.1, ENSDART00000192558.1
      Conserved Domains (1) summary
      pfam13532
      Location:81 → 267
      2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily

    3. XM_005163146.4 → XP_005163203.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M2BAA9
      Conserved Domains (1) summary
      cl21496
      Location:81 → 212
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily
    Nucleotide Protein
    Heading Accession and Version

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