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

Gene ID: 362169, updated on 4-Jan-2025

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, Jan 2025]
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
  • 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 ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
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

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