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

Gene ID: 792266, updated on 18-Sep-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 dioxygenase activity. Predicted to act upstream of or within DNA dealkylation involved in DNA repair and oxidative single-stranded DNA demethylation. Predicted to be active in nucleus. Orthologous to human ALKBH3 (alkB homolog 3, alpha-ketoglutarate dependent dioxygenase). [provided by Alliance of Genome Resources, Apr 2022]
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 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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