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    Alkbh3 alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362169, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Alkbh3provided by RGD
    Official Full Name
    alkB homolog 3, alpha-ketoglutarate-dependent dioxygenaseprovided by RGD
    Primary source
    RGD:1359731
    See related
    EnsemblRapid:ENSRNOG00000021678 AllianceGenome:RGD:1359731
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA demethylase activity; ferrous iron binding activity; and mRNA N1-methyladenosine dioxygenase activity. Predicted to be involved in DNA alkylation repair; cell population proliferation; and negative regulation of cytoplasmic translation. Predicted to be located in cytosol. Predicted to be active in mitochondrion and nucleoplasm. Orthologous to human ALKBH3 (alkB homolog 3, alpha-ketoglutarate dependent dioxygenase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 461.0), Muscle (RPKM 383.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Alkbh3 in Genome Data Viewer
    Location:
    3q31
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (100394942..100429466, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (79939515..79972820, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (82874242..82907467, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene ATP synthase membrane subunit c locus 1, pseudogene 3 Neighboring gene similar to human chromosome 11 open reading frame 96 Neighboring gene hydroxysteroid (17-beta) dehydrogenase 12 Neighboring gene translocase of inner mitochondrial membrane 23, pseudogene 8 Neighboring gene transfer RNA alanine (anticodon AGC)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Li X, et al. Nat Chem Biol, 2016 May. PMID 26863410
    2. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. Sundheim O, et al. EMBO J, 2006 Jul 26. PMID 16858410, Free PMC Article
    3. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Dominissini D, et al. Nature, 2016 Feb 25. PMID 26863196, Free PMC Article
    4. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Dango S, et al. Mol Cell, 2011 Nov 4. PMID 22055184, Free PMC Article
    5. Repair of methylation damage in DNA and RNA by mammalian AlkB homologues. Lee DH, et al. J Biol Chem, 2005 Nov 25. PMID 16174769

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables broad specificity oxidative DNA demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables broad specificity oxidative DNA demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables cytosine C-5 DNA demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT enables endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT enables exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ferrous iron binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ferrous iron binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables mRNA N1-methyladenosine dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA N1-methyladenosine dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables oxidative RNA demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA alkylation repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA alkylation repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of cytoplasmic translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
    Names
    alkB, alkylation repair homolog 3
    alkylated DNA repair protein alkB homolog 3
    alkylation repair-like protein 3
    NP_001014202.1
    XP_006234647.1
    XP_038961360.1
    XP_038961361.1
    XP_063140221.1

    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_001014180.1 → NP_001014202.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

      See identical proteins and their annotated locations for NP_001014202.1

      Status: PROVISIONAL

      Source sequence(s)
      BC083756
      UniProtKB/Swiss-Prot
      Q5XIC8
      UniProtKB/TrEMBL
      A0A8I6AIA0, A6HNK1
      Related
      ENSRNOP00000093084.1, ENSRNOT00000112362.2
      Conserved Domains (1) summary
      cl21496
      Location:90 → 275
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      100394942..100429466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105433.2 → XP_038961361.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X3

      UniProtKB/TrEMBL
      A6HNK3
      Conserved Domains (1) summary
      cl21496
      Location:17 → 157
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    2. XM_006234585.5 → XP_006234647.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_006234647.1

      UniProtKB/Swiss-Prot
      Q5XIC8
      UniProtKB/TrEMBL
      A0A8I6AIA0, A6HNK1
      Conserved Domains (1) summary
      cl21496
      Location:90 → 275
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    3. XM_039105432.2 → XP_038961360.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X2

      UniProtKB/TrEMBL
      A0A158URU1
      Conserved Domains (1) summary
      cl21496
      Location:90 → 228
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    4. XM_063284151.1 → XP_063140221.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5XIC8.1 GenPept UniProtKB/Swiss-Prot:Q5XIC8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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