Free for academic non-profit institutions. Other users need a Commercial license

Aliases for ALKBH1 Gene

Aliases for ALKBH1 Gene

  • AlkB Homolog 1, Histone H2A Dioxygenase 2 3 5
  • Alpha-Ketoglutarate-Dependent Dioxygenase ABH1 3 4
  • Alkylated DNA Repair Protein AlkB Homolog 1 3 4
  • DNA N6-Methyl Adenine Demethylase 3 4
  • DNA Oxidative Demethylase ALKBH1 3 4
  • DNA 6mA Demethylase 3 4
  • DNA Lyase ABH1 3 4
  • EC 1.14.11.- 4 4
  • ALKBH 3 4
  • ABH1 3 4
  • ABH 3 4
  • AlkB, Alkylation Repair Homolog 1 (E. Coli) 2
  • AlkB, Alkylation Repair Homolog (E. Coli) 2
  • AlkB, Alkylation Repair Homolog 1 3
  • Alkylation Repair, AlkB Homolog 3
  • DNA Demethylase ALKBH1 3
  • EC 1.14.11.33 4
  • EC 4.2.99.18 4
  • AlkB 3
  • HABH 3

External Ids for ALKBH1 Gene

Previous HGNC Symbols for ALKBH1 Gene

  • ALKBH

Previous GeneCards Identifiers for ALKBH1 Gene

  • GC14M077208
  • GC14M078138
  • GC14M058306

Summaries for ALKBH1 Gene

Entrez Gene Summary for ALKBH1 Gene

  • 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]

GeneCards Summary for ALKBH1 Gene

ALKBH1 (AlkB Homolog 1, Histone H2A Dioxygenase) is a Protein Coding gene. Among its related pathways are Integrated Breast Cancer Pathway. GO annotations related to this gene include chemoattractant activity and DNA-(apurinic or apyrimidinic site) lyase activity.

UniProtKB/Swiss-Prot for ALKBH1 Gene

  • Dioxygenase that acts as a DNA demethylase (PubMed:18603530). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:18603530). Specifically demethylates DNA methylated on the 6th position of adenine (N(6)-methyladenosine) DNA. N(6)-methyladenosine (m6A) DNA is present at some L1 elements in embryonic stem cells and probably promotes their silencing (By similarity). Also able to repair alkylated single-stranded DNA and RNA containing 3-methylcytosine by oxidative demethylation, but with low activity (PubMed:18603530). Also has DNA lyase activity and introduces double-stranded breaks at abasic sites: cleaves both single-stranded DNA and double-stranded DNA at abasic sites, with the greatest activity towards double-stranded DNA with two abasic sites (PubMed:19959401). DNA lyase activity does not require alpha-ketoglutarate and iron and leads to the formation of an irreversible covalent protein-DNA adduct with the 5 DNA product (PubMed:19959401, PubMed:23577621). DNA lyase activity is not required during base excision repair and class switch recombination of the immunoglobulin heavy chain during B lymphocyte activation. May play a role in placental trophoblast lineage differentiation (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALKBH1 Gene

Genomics for ALKBH1 Gene

Regulatory Elements for ALKBH1 Gene

Enhancers for ALKBH1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around ALKBH1 on UCSC Golden Path with GeneCards custom track

Promoters for ALKBH1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around ALKBH1 on UCSC Golden Path with GeneCards custom track

Genomic Location for ALKBH1 Gene

Chromosome:
14
Start:
77,672,404 bp from pter
End:
77,708,032 bp from pter
Size:
35,629 bases
Orientation:
Minus strand

Genomic View for ALKBH1 Gene

Genes around ALKBH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALKBH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALKBH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALKBH1 Gene

Proteins for ALKBH1 Gene

  • Protein details for ALKBH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13686-ALKB1_HUMAN
    Recommended name:
    DNA demethylase ALKBH1
    Protein Accession:
    Q13686
    Secondary Accessions:
    • Q8TAU1
    • Q9ULA7

    Protein attributes for ALKBH1 Gene

    Size:
    389 amino acids
    Molecular mass:
    43832 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Monomer (PubMed:19959401). Interacts with DNAJB6 (By similarity).
    SequenceCaution:
    • Sequence=CAA63047.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

neXtProt entry for ALKBH1 Gene

Post-translational modifications for ALKBH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ALKBH1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for ALKBH1 Gene

Domains & Families for ALKBH1 Gene

Gene Families for ALKBH1 Gene

Protein Domains for ALKBH1 Gene

Suggested Antigen Peptide Sequences for ALKBH1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13686

UniProtKB/Swiss-Prot:

ALKB1_HUMAN :
  • Contains 1 Fe2OG dioxygenase domain.
  • Belongs to the alkB family.
Domain:
  • Contains 1 Fe2OG dioxygenase domain.
Family:
  • Belongs to the alkB family.
genes like me logo Genes that share domains with ALKBH1: view

Function for ALKBH1 Gene

Molecular function for ALKBH1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
The C-O-P bond 3 to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3-terminal unsaturated sugar and a product with a terminal 5-phosphate.
UniProtKB/Swiss-Prot CatalyticActivity:
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2).
UniProtKB/Swiss-Prot CatalyticActivity:
N(6)-methyladenine in DNA + 2-oxoglutarate + O(2) = adenine in DNA + formaldehyde + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Dioxygenase that acts as a DNA demethylase (PubMed:18603530). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:18603530). Specifically demethylates DNA methylated on the 6th position of adenine (N(6)-methyladenosine) DNA. N(6)-methyladenosine (m6A) DNA is present at some L1 elements in embryonic stem cells and probably promotes their silencing (By similarity). Also able to repair alkylated single-stranded DNA and RNA containing 3-methylcytosine by oxidative demethylation, but with low activity (PubMed:18603530). Also has DNA lyase activity and introduces double-stranded breaks at abasic sites: cleaves both single-stranded DNA and double-stranded DNA at abasic sites, with the greatest activity towards double-stranded DNA with two abasic sites (PubMed:19959401). DNA lyase activity does not require alpha-ketoglutarate and iron and leads to the formation of an irreversible covalent protein-DNA adduct with the 5 DNA product (PubMed:19959401, PubMed:23577621). DNA lyase activity is not required during base excision repair and class switch recombination of the immunoglobulin heavy chain during B lymphocyte activation. May play a role in placental trophoblast lineage differentiation (By similarity).

Enzyme Numbers (IUBMB) for ALKBH1 Gene

Gene Ontology (GO) - Molecular Function for ALKBH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity IDA 19959401
GO:0005515 protein binding IEA --
GO:0008198 ferrous iron binding IDA 18603530
GO:0042056 chemoattractant activity IEA --
GO:0070579 methylcytosine dioxygenase activity IDA 18603530
genes like me logo Genes that share ontologies with ALKBH1: view
genes like me logo Genes that share phenotypes with ALKBH1: view

Animal Models for ALKBH1 Gene

MGI Knock Outs for ALKBH1:

Animal Model Products

  • Taconic Biosciences Mouse Models for ALKBH1

CRISPR Products

miRNA for ALKBH1 Gene

miRTarBase miRNAs that target ALKBH1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ALKBH1 Gene

Localization for ALKBH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALKBH1 Gene

Nucleus. Mitochondrion. Note=Mainly localizes in euchromatin, largely excluded from heterochromatin and nucleoli (By similarity). {ECO:0000250 UniProtKB:P0CB42}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for ALKBH1 Gene COMPARTMENTS Subcellular localization image for ALKBH1 gene
Compartment Confidence
mitochondrion 5
nucleus 4
extracellular 2
cytosol 1
lysosome 1
peroxisome 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for ALKBH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005719 nuclear euchromatin IEA --
GO:0005739 mitochondrion IDA 18603530
genes like me logo Genes that share ontologies with ALKBH1: view

Pathways & Interactions for ALKBH1 Gene

genes like me logo Genes that share pathways with ALKBH1: view

Pathways by source for ALKBH1 Gene

1 BioSystems pathway for ALKBH1 Gene

Interacting Proteins for ALKBH1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000216489%0d%0a9606.ENSP00000262177%0d%0a9606.ENSP00000344818%0d%0a
Selected Interacting proteins: ENSP00000216489 Q13686-ALKB1_HUMAN for ALKBH1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for ALKBH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001764 neuron migration IEA --
GO:0001890 placenta development IEA --
GO:0006281 DNA repair IDA 18603530
GO:0006307 DNA dealkylation involved in DNA repair IDA 18603530
genes like me logo Genes that share ontologies with ALKBH1: view

No data available for SIGNOR curated interactions for ALKBH1 Gene

Drugs & Compounds for ALKBH1 Gene

(4) Drugs for ALKBH1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Formaldehyde Approved, Vet_approved Pharma 83
Oxygen Approved, Vet_approved Pharma 0
Succinic acid Approved Nutra Full agonist, Agonist 0

(8) Additional Compounds for ALKBH1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with ALKBH1: view

Transcripts for ALKBH1 Gene

mRNA/cDNA for ALKBH1 Gene

Unigene Clusters for ALKBH1 Gene

AlkB, alkylation repair homolog 1 (E. coli):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALKBH1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d
SP1:
SP2: -
SP3: - -
SP4: - -

Relevant External Links for ALKBH1 Gene

GeneLoc Exon Structure for
ALKBH1
ECgene alternative splicing isoforms for
ALKBH1

Expression for ALKBH1 Gene

mRNA expression in normal human tissues for ALKBH1 Gene

Protein differential expression in normal tissues from HIPED for ALKBH1 Gene

This gene is overexpressed in Pancreas (35.5) and Fetal testis (33.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ALKBH1 Gene



Protein tissue co-expression partners for ALKBH1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ALKBH1 Gene:

ALKBH1

SOURCE GeneReport for Unigene cluster for ALKBH1 Gene:

Hs.94542

mRNA Expression by UniProt/SwissProt for ALKBH1 Gene:

Q13686-ALKB1_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with ALKBH1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ALKBH1 Gene

Orthologs for ALKBH1 Gene

This gene was present in the common ancestor of animals.

Orthologs for ALKBH1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia ALKBH1 34
  • 87.55 (n)
  • 87.91 (a)
ALKBH1 35
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ALKBH1 34
  • 86.72 (n)
  • 87.4 (a)
ALKBH1 35
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Alkbh1 34
  • 84.49 (n)
  • 82.78 (a)
Alkbh1 16
Alkbh1 35
  • 83 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia ALKBH1 34
  • 99.74 (n)
  • 99.74 (a)
ALKBH1 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Alkbh1 34
  • 78.57 (n)
  • 78.06 (a)
oppossum
(Monodelphis domestica)
Mammalia ALKBH1 35
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ALKBH1 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALKBH1 34
  • 69.03 (n)
  • 70.49 (a)
ALKBH1 35
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ALKBH1 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia alkbh1 34
  • 57.52 (n)
  • 61.71 (a)
Str.16044 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.24969 34
zebrafish
(Danio rerio)
Actinopterygii alkbh1 34
  • 60.7 (n)
  • 59.7 (a)
alkbh1 35
  • 60 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1823 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000155 34
  • 50.87 (n)
  • 42.57 (a)
fruit fly
(Drosophila melanogaster)
Insecta AlkB 34
  • 46.26 (n)
  • 38.46 (a)
AlkB 35
  • 35 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y51H7C.5 34
  • 45.1 (n)
  • 34.95 (a)
Y51H7C.5 35
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10211 35
  • 39 (a)
OneToOne
Species where no ortholog for ALKBH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ALKBH1 Gene

ENSEMBL:
Gene Tree for ALKBH1 (if available)
TreeFam:
Gene Tree for ALKBH1 (if available)

Paralogs for ALKBH1 Gene

No data available for Paralogs for ALKBH1 Gene

Variants for ALKBH1 Gene

Sequence variations from dbSNP and Humsavar for ALKBH1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs17825440 - 77,694,788(+) TTAGA(C/T)ATGTG reference, missense
rs6494 - 77,674,012(-) GTTCT(A/G/T)TGGAG reference, missense
rs6493 -- 77,673,986(-) GCCAG(C/T)TACTT reference, synonymous-codon
rs7143265 -- 77,681,624(+) AGACA(C/T)AGCAG intron-variant
rs7143382 -- 77,690,843(+) gttgc(C/T)caggc intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ALKBH1 Gene

Variant ID Type Subtype PubMed ID
esv2759998 CNV gain 17122850
esv34940 CNV gain 17911159
esv3635010 CNV gain 21293372
esv3635012 CNV gain 21293372
nsv1053810 CNV gain 25217958
nsv520021 CNV gain 19592680
nsv521287 CNV gain 19592680
nsv9156 CNV loss 18304495
nsv976357 CNV duplication 23825009

Variation tolerance for ALKBH1 Gene

Residual Variation Intolerance Score: 69.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.76; 66.62% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ALKBH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALKBH1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALKBH1 Gene

Disorders for ALKBH1 Gene

Relevant External Links for ALKBH1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ALKBH1

No disorders were found for ALKBH1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ALKBH1 Gene

Publications for ALKBH1 Gene

  1. Molecular cloning and functional analysis of a human cDNA encoding an Escherichia coli AlkB homolog, a protein involved in DNA alkylation damage repair. (PMID: 8600462) Wei Y.F. … Shell B.K. (Nucleic Acids Res. 1996) 2 3 4 22 65
  2. ALKBH1 is a histone H2A dioxygenase involved in neural differentiation. (PMID: 22961808) Ougland R. … Larsen E. (Stem Cells 2012) 2 3 4 65
  3. Human AlkB homologue 1 (ABH1) exhibits DNA lyase activity at abasic sites. (PMID: 19959401) Muller T.A. … Hausinger R.P. (DNA Repair 2010) 3 4 22 65
  4. A covalent protein-DNA 5'-product adduct is generated following AP lyase activity of human ALKBH1 (AlkB homologue 1). (PMID: 23577621) MA1ller T.A. … Hausinger R.P. (Biochem. J. 2013) 3 4 65
  5. Human AlkB homolog 1 is a mitochondrial protein that demethylates 3- methylcytosine in DNA and RNA. (PMID: 18603530) Westbye M.P. … Krokan H.E. (J. Biol. Chem. 2008) 3 4 65

Products for ALKBH1 Gene

Sources for ALKBH1 Gene

Content