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ALKBH1 alkB homolog 1, histone H2A dioxygenase [ Homo sapiens (human) ]

Gene ID: 8846, updated on 9-Dec-2024

Summary

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Official Symbol
ALKBH1provided by HGNC
Official Full Name
alkB homolog 1, histone H2A dioxygenaseprovided by HGNC
Primary source
HGNC:HGNC:17911
See related
Ensembl:ENSG00000100601 MIM:605345; AllianceGenome:HGNC:17911
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ABH; ABH1; alkB; hABH; ALKBH
Summary
This gene encodes a homolog to the E. coli alkB gene product. The E. coli alkB protein is part of the adaptive response mechanism of DNA alkylation damage repair. It is involved in damage reversal by oxidative demethylation of 1-methyladenine and 3-methylcytosine. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 4.0), thyroid (RPKM 3.4) and 25 other tissues See more
Orthologs
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Genomic context

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See ALKBH1 in Genome Data Viewer
Location:
14q24.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77672404..77708023, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71881741..71917378, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78138747..78174366, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene serine palmitoyltransferase long chain base subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8805 Neighboring gene RNA, 7SL, cytoplasmic 587, pseudogene Neighboring gene MPRA-validated peak2208 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78072555-78073054 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78073869-78074370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78074371-78074870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8808 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:78082775-78083307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78128831-78129662 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 11 Neighboring gene MPRA-validated peak2209 silencer Neighboring gene MPRA-validated peak2210 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78151521-78152022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78152023-78152522 Neighboring gene ribosomal protein L21 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8810 Neighboring gene zinc finger MYND-type containing 19 pseudogene 1 Neighboring gene SRA stem-loop interacting RNA binding protein Neighboring gene SNW domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78226689-78227463 Neighboring gene SLIRP overlapping transcript 1

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. Characterization of human AlkB homolog 1 produced in mammalian cells and demonstration of mitochondrial dysfunction in ALKBH1-deficient cells. Müller TA, et al. Biochem Biophys Res Commun, 2018 Jan 1. PMID 29097205, Free PMC Article
  2. Evaluating the Potential for ABO-incompatible Islet Transplantation: Expression of ABH Antigens on Human Pancreata, Isolated Islets, and Embryonic Stem Cell-derived Islets. Verhoeff K, et al. Transplantation, 2023 Apr 1. PMID 36228319
  3. ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. Kawarada L, et al. Nucleic Acids Res, 2017 Jul 7. PMID 28472312, Free PMC Article
  4. DNA demethylase ALKBH1 promotes adipogenic differentiation via regulation of HIF-1 signaling. Liu Y, et al. J Biol Chem, 2022 Jan. PMID 34922943, Free PMC Article
  5. Homology modeling and function prediction of hABH1, involving in repair of alkylation damaged DNA. Shankaracharya, et al. Interdiscip Sci, 2011 Sep. PMID 21956739

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The N[6]-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis by disrupting NRF1 binding capacity.
    Title: The N(6)-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis by disrupting NRF1 binding capacity.
  2. DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma.
    Title: DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma.
  3. ALKBH1 contributes to renal cell carcinoma progression by reducing N6-methyladenine of GPR137.
    Title: ALKBH1 contributes to renal cell carcinoma progression by reducing N6-methyladenine of GPR137.
  4. Evaluating the Potential for ABO-incompatible Islet Transplantation: Expression of ABH Antigens on Human Pancreata, Isolated Islets, and Embryonic Stem Cell-derived Islets.
    Title: Evaluating the Potential for ABO-incompatible Islet Transplantation: Expression of ABH Antigens on Human Pancreata, Isolated Islets, and Embryonic Stem Cell-derived Islets.
  5. DNA demethylase ALKBH1 promotes adipogenic differentiation via regulation of HIF-1 signaling.
    Title: DNA demethylase ALKBH1 promotes adipogenic differentiation via regulation of HIF-1 signaling.
  6. Demethyltransferase AlkBH1 substrate diversity and relationship to human diseases.
    Title: Demethyltransferase AlkBH1 substrate diversity and relationship to human diseases.
  7. ALKBH1-demethylated DNA N6-methyladenine modification triggers vascular calcification via osteogenic reprogramming in chronic kidney disease.
    Title: ALKBH1-demethylated DNA N6-methyladenine modification triggers vascular calcification via osteogenic reprogramming in chronic kidney disease.
  8. ALKBH1 promotes lung cancer by regulating m6A RNA demethylation.
    Title: ALKBH1 promotes lung cancer by regulating m6A RNA demethylation.
  9. A positive feedback loop between AlkB homolog 5 and miR-193a-3p promotes growth and metastasis in esophageal squamous cell carcinoma.
    Title: A positive feedback loop between AlkB homolog 5 and miR-193a-3p promotes growth and metastasis in esophageal squamous cell carcinoma.
  10. Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1.
    Title: Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1.
Submit: New GeneRIF Correction See all GeneRIFs (30)

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

EBI GWAS Catalog

Description
Genome-wide association study of prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA N6-methyladenine demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables broad specificity oxidative DNA demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables broad specificity oxidative DNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables chemoattractant activity IEA
Inferred from Electronic Annotation
more info
  
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ferrous iron binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ferrous iron binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables oxidative RNA demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables oxidative RNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in developmental growth IEA
Inferred from Electronic Annotation
more info
  
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron projection development IEA
Inferred from Electronic Annotation
more info
  
involved_in oxidative RNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in oxidative RNA demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in placenta development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression, epigenetic IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of translational elongation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of translational initiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of translational initiation by tRNA modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA wobble cytosine modification IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in euchromatin IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion HTP PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
nucleic acid dioxygenase ALKBH1
Names
DNA 6mA demethylase
DNA N6-methyl adenine demethylase ALKBH1
DNA demethylase ALKBH1
DNA lyase ABH1
DNA oxidative demethylase ALKBH1
alkB, alkylation repair homolog 1
alkylated DNA repair protein alkB homolog 1
alkylation repair, alkB homolog
alpha-ketoglutarate-dependent dioxygenase ABH1
mRNA N(3)-methylcytidine demethylase
tRNA N1-methyl adenine demethylase
NP_006011.2
XP_047287804.1
XP_054232852.1

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_006020.3 → NP_006011.2  nucleic acid dioxygenase ALKBH1

    See identical proteins and their annotated locations for NP_006011.2

    Status: REVIEWED

    Source sequence(s)
    AC008044, BC015024, BC025787
    Consensus CDS
    CCDS32127.1
    UniProtKB/Swiss-Prot
    Q13686, Q8TAU1, Q9ULA7
    UniProtKB/TrEMBL
    Q5XKL0
    Related
    ENSP00000216489.3, ENST00000216489.8
    Conserved Domains (1) summary
    TIGR00568
    Location:119 → 289
    alkb; DNA alkylation damage repair protein AlkB

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    77672404..77708023 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431848.1 → XP_047287804.1  nucleic acid dioxygenase ALKBH1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71881741..71917378 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376877.1 → XP_054232852.1  nucleic acid dioxygenase ALKBH1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001039506.1: Suppressed sequence

    Description
    NM_001039506.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13686.2 GenPept UniProtKB/Swiss-Prot:Q13686

Gene LinkOut

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Chemical Information
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