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

Summary

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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
Title: Programmable RNA N(1) -Methyladenosine Demethylation by a Cas13d-Directed Demethylase.
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.
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.
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.
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.
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

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH48832 (e-PCR)
- UniSTS:13576

RH16415 (e-PCR)
- UniSTS:28473

NoName (e-PCR)
- UniSTS:483001

SGC33963 (e-PCR)
- UniSTS:78304

ha2500 (e-PCR)
- UniSTS:515556

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 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
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

Go to the top of the page Help

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

EC 1.14.11.33

EC 1.14.11.54

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.