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ALKBH3 alkB homolog 3, alpha-ketoglutarate dependent dioxygenase [ Homo sapiens (human) ]

Gene ID: 221120, updated on 11-Apr-2024

Summary

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Official Symbol
ALKBH3provided by HGNC
Official Full Name
alkB homolog 3, alpha-ketoglutarate dependent dioxygenaseprovided by HGNC
Primary source
HGNC:HGNC:30141
See related
Ensembl:ENSG00000166199 MIM:610603; AllianceGenome:HGNC:30141
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ABH3; PCA1; DEPC1; hABH3; DEPC-1
Summary
The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 (MIM 610602) and ALKBH3 are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in testis (RPKM 6.9), prostate (RPKM 6.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (43880831..43920274)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (44036210..44075625)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (43902381..43941824)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hydroxysteroid 17-beta dehydrogenase 12 Neighboring gene uncharacterized LOC107984328 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:43852011-43853210 Neighboring gene uncharacterized LOC105376644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4646 Neighboring gene SEC14 like 1 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:43941776-43942975 Neighboring gene ALKBH3 antisense RNA 1 Neighboring gene uncharacterized LOC124902663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43949635-43950136 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:43955407-43955585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:43964814-43965643 Neighboring gene 1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like Neighboring gene chromosome 11 open reading frame 96

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase. Xie S, et al. Angew Chem Int Ed Engl, 2021 Sep 1. PMID 34081827
  2. Epigenetic loss of m1A RNA demethylase ALKBH3 in Hodgkin lymphoma targets collagen, conferring poor clinical outcome. Esteve-Puig R, et al. Blood, 2021 Feb 18. PMID 32915956, Free PMC Article
  3. ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy. Pilžys T, et al. Sci Rep, 2019 Sep 13. PMID 31519943, Free PMC Article
  4. CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer. Stefansson OA, et al. BMC Cancer, 2017 Jul 5. PMID 28679371, Free PMC Article
  5. AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells. Ueda Y, et al. Sci Rep, 2017 Feb 13. PMID 28205560, Free PMC Article

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.
    Title: Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.
  2. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA.
    Title: The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA.
  3. The Molecular Basis of Human ALKBH3 Mediated RNA N[1] -methyladenosine (m[1] A) Demethylation.
    Title: The Molecular Basis of Human ALKBH3 Mediated RNA N(1) -methyladenosine (m(1) A) Demethylation.
  4. LncRNA ALKBH3-AS1 enhances ALKBH3 mRNA stability to promote hepatocellular carcinoma cell proliferation and invasion.
    Title: LncRNA ALKBH3-AS1 enhances ALKBH3 mRNA stability to promote hepatocellular carcinoma cell proliferation and invasion.
  5. Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
    Title: Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
  6. ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA.
    Title: ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA.
  7. Epigenetic loss of m1A RNA demethylase ALKBH3 in Hodgkin lymphoma targets collagen, conferring poor clinical outcome.
    Title: Epigenetic loss of m1A RNA demethylase ALKBH3 in Hodgkin lymphoma targets collagen, conferring poor clinical outcome.
  8. ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy.
    Title: ALKBH overexpression in head and neck cancer: potential target for novel anticancer therapy.
  9. Evidence that RAD51C-ALKBH3 interaction stimulates ALKBH3-mediated repair of methyl-adduct located within 3'-tailed DNA, which serves as a substrate for the RAD51 recombinase. The lack of RAD51C-ALKBH3 interaction affects ALKBH3 function in vitro and in vivo.
    Title: Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase.
  10. Data show that the three DNA repair enzymes ALKBH2, ALKBH3, and AlkB are not only able to repair DNA adducts, but also can edit the epigenetic modification and generate the corresponding oxidative derivatives.
    Title: DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro.
Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of alkB, alkylation repair homolog 3 (E. coli, ALKBH3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ43614, MGC118790, MGC118792, MGC118793

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-ascorbic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables broad specificity oxidative DNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables broad specificity oxidative DNA demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables ferrous iron binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA N1-methyladenosine dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables oxidative RNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA alkylation repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus 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 homolog 3, alpha-ketoglutaratedependent dioxygenase
alkB, alkylation repair homolog 3
alkylated DNA repair protein alkB homolog 3
prostate cancer antigen-1
NP_631917.1

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_139178.4 → NP_631917.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

    See identical proteins and their annotated locations for NP_631917.1

    Status: VALIDATED

    Source sequence(s)
    AC087521
    Consensus CDS
    CCDS7906.1
    UniProtKB/Swiss-Prot
    A6NDJ1, Q3SYI0, Q6NX57, Q96BU8, Q96Q83
    Related
    ENSP00000302232.4, ENST00000302708.9
    Conserved Domains (1) summary
    cl21496
    Location:90 → 275
    2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    43880831..43920274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    44036210..44075625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96Q83.1 GenPept UniProtKB/Swiss-Prot:Q96Q83

Gene LinkOut

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

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