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

Gene ID: 221120, updated on 10-Dec-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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See ALKBH3 in Genome Data Viewer
Location:
11p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (43880831..43920274)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (44036210..44075625)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA. Kanazhevskaya LY, et al. Int J Mol Sci, 2024 Jan 17. PMID 38256217, Free PMC Article
  2. ALKBH3 contributes to survival and angiogenesis of human urothelial carcinoma cells through NADPH oxidase and tweak/Fn14/VEGF signals. Shimada K, et al. Clin Cancer Res, 2012 Oct 1. PMID 22850567
  3. Clinical significance and therapeutic potential of prostate cancer antigen-1/ALKBH3 in human renal cell carcinoma. Hotta K, et al. Oncol Rep, 2015 Aug. PMID 26035443
  4. anti-tumor effect of AlkB homolog 3 knockdown in hormone- independent prostate cancer cells. Koike K, et al. Curr Cancer Drug Targets, 2012 Sep. PMID 22515525
  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 (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PUS7-dependent pseudouridylation of ALKBH3 mRNA inhibits gastric cancer progression.
    Title: PUS7-dependent pseudouridylation of ALKBH3 mRNA inhibits gastric cancer progression.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
    Title: Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (29)

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)

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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cytoplasmic translation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
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_2024_08

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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