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Aliases for ALKBH3 Gene

Aliases for ALKBH3 Gene

  • AlkB Homolog 3, Alpha-Ketoglutaratedependent Dioxygenase 2 3 5
  • Alkylated DNA Repair Protein AlkB Homolog 3 3 4
  • DEPC-1 3 4
  • DEPC1 3 4
  • HABH3 3 4
  • ABH3 3 4
  • AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase 3
  • Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 3 3
  • AlkB, Alkylation Repair Homolog 3 (E. Coli) 2
  • AlkB, Alkylation Repair Homolog 3 3
  • Prostate Cancer Antigen-1 3
  • Prostate Cancer Antigen 1 4
  • EC 1.14.11.54 4
  • EC 1.14.11 56
  • PCA1 3

External Ids for ALKBH3 Gene

Previous GeneCards Identifiers for ALKBH3 Gene

  • GC11P043859
  • GC11P043611

Summaries for ALKBH3 Gene

Entrez Gene Summary for ALKBH3 Gene

  • 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]

GeneCards Summary for ALKBH3 Gene

ALKBH3 (AlkB Homolog 3, Alpha-Ketoglutaratedependent Dioxygenase) is a Protein Coding gene. Diseases associated with ALKBH3 include Prostate Cancer. Among its related pathways are DNA Damage Reversal and DNA Double-Strand Break Repair. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and L-ascorbic acid binding. An important paralog of this gene is ALKBH2.

UniProtKB/Swiss-Prot for ALKBH3 Gene

  • Dioxygenase that mediates demethylation of DNA and RNA containing 1-methyladenosine (m1A) (PubMed:12486230, PubMed:12594517, PubMed:16174769, PubMed:26863196, PubMed:26863410). Repairs alkylated DNA containing 1-methyladenosine (m1A) and 3-methylcytosine (m3C) by oxidative demethylation (PubMed:12486230, PubMed:12594517, PubMed:16174769). Has a strong preference for single-stranded DNA (PubMed:12486230, PubMed:12594517, PubMed:16174769). Able to process alkylated m3C within double-stranded regions via its interaction with ASCC3, which promotes DNA unwinding to generate single-stranded substrate needed for ALKBH3 (PubMed:22055184). Also acts on RNA (PubMed:12594517, PubMed:16174769, PubMed:26863196, PubMed:26863410, PubMed:16858410). Demethylates N(1)-methyladenosine (m1A) RNA, an epigenetic internal modification of messenger RNAs (mRNAs) highly enriched within 5-untranslated regions (UTRs) and in the vicinity of start codons (PubMed:26863196, PubMed:26863410). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:22055184, PubMed:16858410).

Additional gene information for ALKBH3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALKBH3 Gene

Genomics for ALKBH3 Gene

GeneHancer (GH) Regulatory Elements for ALKBH3 Gene

Promoters and enhancers for ALKBH3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I043880 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 570.5 +0.2 161 1.6 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 SLC30A9 ALKBH3 LOC105376644 SEC14L1P1 EXT2 ENSG00000254409 RN7SKP287
GH11I044560 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 22.9 +685.3 685319 10.5 HDGF PKNOX1 SIN3A GLI4 IRF4 YY1 ZNF121 GLIS2 ZNF143 ATF7 CD82 ALKBH3 SEC14L1P1 ENSG00000254693 ENSG00000255092 EXT2
GH11I043904 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 27.9 +25.1 25061 2.6 RFX1 JUN TSC22D4 NR2F2 RBAK POLR2A ZNF24 RCOR1 CHD2 ALKBH3 LOC105376644 PPIAP41 API5 TTC17 SEC14L1P1 ALKBH3-AS1
GH11I043941 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 14.4 +62.8 62780 4.9 ATF1 SIN3A ZNF48 YY1 GLIS2 ZNF143 FOS RUNX3 RXRA REST C11orf96 SEC14L1P1 ALKBH3 EXT2 ENSG00000254907 TTC17 ACCS ALKBH3-AS1 ENSG00000254409 LOC105376644
GH11I043357 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.5 -521.4 -521391 3 HDGF PKNOX1 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF766 E2F8 TTC17 ENSG00000254907 SEC14L1P1 ALKBH3 ACCS EXT2 API5 ENSG00000255340
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ALKBH3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ALKBH3 gene promoter:

Genomic Locations for ALKBH3 Gene

Genomic Locations for ALKBH3 Gene
chr11:43,880,807-43,920,275
(GRCh38/hg38)
Size:
39,469 bases
Orientation:
Plus strand
chr11:43,902,357-43,941,825
(GRCh37/hg19)

Genomic View for ALKBH3 Gene

Genes around ALKBH3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALKBH3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALKBH3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALKBH3 Gene

Proteins for ALKBH3 Gene

  • Protein details for ALKBH3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96Q83-ALKB3_HUMAN
    Recommended name:
    Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
    Protein Accession:
    Q96Q83
    Secondary Accessions:
    • A6NDJ1
    • Q3SYI0
    • Q6NX57
    • Q96BU8

    Protein attributes for ALKBH3 Gene

    Size:
    286 amino acids
    Molecular mass:
    33375 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with the ASC-1 complex, notably composed of ASCC3 (PubMed:22055184).
    SequenceCaution:
    • Sequence=AAH15155.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ALKBH3 Gene

    Alternative splice isoforms for ALKBH3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ALKBH3 Gene

Selected DME Specific Peptides for ALKBH3 Gene

Q96Q83:
  • FEMRKKPPPE
  • NLTFRTVYPDPRGA

Post-translational modifications for ALKBH3 Gene

No Post-translational modifications

Other Protein References for ALKBH3 Gene

Domains & Families for ALKBH3 Gene

Gene Families for ALKBH3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for ALKBH3 Gene

Suggested Antigen Peptide Sequences for ALKBH3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96Q83

UniProtKB/Swiss-Prot:

ALKB3_HUMAN :
  • Belongs to the alkB family.
Family:
  • Belongs to the alkB family.
genes like me logo Genes that share domains with ALKBH3: view

Function for ALKBH3 Gene

Molecular function for ALKBH3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
N(1)-methyladenine in mRNA + 2-oxoglutarate + O(2) = adenine in mRNA + formaldehyde + succinate + CO(2).
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by ascorbate.
UniProtKB/Swiss-Prot Function:
Dioxygenase that mediates demethylation of DNA and RNA containing 1-methyladenosine (m1A) (PubMed:12486230, PubMed:12594517, PubMed:16174769, PubMed:26863196, PubMed:26863410). Repairs alkylated DNA containing 1-methyladenosine (m1A) and 3-methylcytosine (m3C) by oxidative demethylation (PubMed:12486230, PubMed:12594517, PubMed:16174769). Has a strong preference for single-stranded DNA (PubMed:12486230, PubMed:12594517, PubMed:16174769). Able to process alkylated m3C within double-stranded regions via its interaction with ASCC3, which promotes DNA unwinding to generate single-stranded substrate needed for ALKBH3 (PubMed:22055184). Also acts on RNA (PubMed:12594517, PubMed:16174769, PubMed:26863196, PubMed:26863410, PubMed:16858410). Demethylates N(1)-methyladenosine (m1A) RNA, an epigenetic internal modification of messenger RNAs (mRNAs) highly enriched within 5-untranslated regions (UTRs) and in the vicinity of start codons (PubMed:26863196, PubMed:26863410). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:22055184, PubMed:16858410).

Enzyme Numbers (IUBMB) for ALKBH3 Gene

Phenotypes From GWAS Catalog for ALKBH3 Gene

Gene Ontology (GO) - Molecular Function for ALKBH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22055184
GO:0008198 ferrous iron binding IDA 16858410
GO:0016491 oxidoreductase activity IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA --
GO:0031418 L-ascorbic acid binding IEA --
genes like me logo Genes that share ontologies with ALKBH3: view
genes like me logo Genes that share phenotypes with ALKBH3: view

Animal Models for ALKBH3 Gene

MGI Knock Outs for ALKBH3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ALKBH3 Gene

Localization for ALKBH3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALKBH3 Gene

Nucleus. Cytoplasm. Note=Predominantly localizes to the nucleus. {ECO:0000269 PubMed:12486230, ECO:0000269 PubMed:12594517, ECO:0000269 PubMed:17979886}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ALKBH3 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Mitochondria (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ALKBH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with ALKBH3: view

Pathways & Interactions for ALKBH3 Gene

genes like me logo Genes that share pathways with ALKBH3: view

Gene Ontology (GO) - Biological Process for ALKBH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA,IDA 16858410
GO:0006307 DNA dealkylation involved in DNA repair IEA,TAS --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0008283 cell proliferation IMP 22055184
GO:0035552 oxidative single-stranded DNA demethylation IMP,IEA 22055184
genes like me logo Genes that share ontologies with ALKBH3: view

No data available for SIGNOR curated interactions for ALKBH3 Gene

Drugs & Compounds for ALKBH3 Gene

(2) Drugs for ALKBH3 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target 581,581
2-Ketobutyric acid Experimental Pharma 0

(1) Additional Compounds for ALKBH3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
15438-31-0
genes like me logo Genes that share compounds with ALKBH3: view

Transcripts for ALKBH3 Gene

Unigene Clusters for ALKBH3 Gene

AlkB, alkylation repair homolog 3 (E. coli):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALKBH3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b · 12c
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - - -
SP5: - -
SP6: - - - - -
SP7: - - -
SP8:

Relevant External Links for ALKBH3 Gene

GeneLoc Exon Structure for
ALKBH3
ECgene alternative splicing isoforms for
ALKBH3

Expression for ALKBH3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ALKBH3 Gene

Protein differential expression in normal tissues from HIPED for ALKBH3 Gene

This gene is overexpressed in Serum (61.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ALKBH3 Gene



NURSA nuclear receptor signaling pathways regulating expression of ALKBH3 Gene:

ALKBH3

SOURCE GeneReport for Unigene cluster for ALKBH3 Gene:

Hs.720708

mRNA Expression by UniProt/SwissProt for ALKBH3 Gene:

Q96Q83-ALKB3_HUMAN
Tissue specificity: Ubiquitous. Detected in heart, pancreas, skeletal muscle, thymus, testis, ovary, spleen, prostate, small intestine, peripheral blood leukocytes, urinary bladder and colon.

Evidence on tissue expression from TISSUES for ALKBH3 Gene

  • Nervous system(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with ALKBH3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ALKBH3 Gene

Orthologs for ALKBH3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALKBH3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALKBH3 33 34
  • 99.65 (n)
cow
(Bos Taurus)
Mammalia ALKBH3 33 34
  • 89.39 (n)
dog
(Canis familiaris)
Mammalia ALKBH3 33 34
  • 88.85 (n)
rat
(Rattus norvegicus)
Mammalia Alkbh3 33
  • 85.03 (n)
mouse
(Mus musculus)
Mammalia Alkbh3 33 16 34
  • 84.8 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 79 (a)
OneToMany
-- 34
  • 52 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia ALKBH3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALKBH3 33 34
  • 67.85 (n)
lizard
(Anolis carolinensis)
Reptilia ALKBH3 34
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia alkbh3 33
  • 64.37 (n)
zebrafish
(Danio rerio)
Actinopterygii alkbh3 33 34
  • 58.06 (n)
Dr.14529 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 41 (a)
OneToMany
Species where no ortholog for ALKBH3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for ALKBH3 Gene

ENSEMBL:
Gene Tree for ALKBH3 (if available)
TreeFam:
Gene Tree for ALKBH3 (if available)

Paralogs for ALKBH3 Gene

Paralogs for ALKBH3 Gene

genes like me logo Genes that share paralogs with ALKBH3: view

Variants for ALKBH3 Gene

Sequence variations from dbSNP and Humsavar for ALKBH3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000116828 -- 43,891,231(+) A/G intron_variant
rs1000186486 -- 43,919,366(+) C/G intron_variant
rs1000266609 -- 43,916,552(+) G/T intron_variant
rs1000326399 -- 43,909,425(+) C/A/T intron_variant
rs1000432239 -- 43,902,823(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ALKBH3 Gene

Variant ID Type Subtype PubMed ID
dgv630n106 CNV deletion 24896259
esv2028436 CNV deletion 18987734
esv2616474 CNV deletion 19546169
esv2663316 CNV deletion 23128226
esv2744413 CNV deletion 23290073
esv3434768 CNV insertion 20981092
esv3547674 CNV deletion 23714750
esv3626155 CNV loss 21293372
esv6093 CNV loss 19470904
nsv1076691 CNV deletion 25765185
nsv467867 CNV gain 19166990
nsv554171 CNV gain 21841781
nsv832138 CNV gain 17160897
nsv957189 CNV deletion 24416366

Variation tolerance for ALKBH3 Gene

Residual Variation Intolerance Score: 57.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.06; 80.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ALKBH3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALKBH3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALKBH3 Gene

Disorders for ALKBH3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ALKBH3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
prostate cancer
  • prostate cancer, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ALKBH3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ALKBH3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ALKBH3 Gene

Publications for ALKBH3 Gene

  1. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. (PMID: 22055184) Dango S … Shi Y (Molecular cell 2011) 2 3 4 58
  2. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. (PMID: 26863196) Dominissini D … He C (Nature 2016) 3 4 58
  3. Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. (PMID: 26863410) Li X … Yi C (Nature chemical biology 2016) 3 4 58
  4. Prostate cancer antigen-1 as a potential novel marker for prostate cancer. (PMID: 17968469) Liu BQ … Liu RL (Asian journal of andrology 2007) 3 22 58
  5. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. (PMID: 16858410) Sundheim O … Slupphaug G (The EMBO journal 2006) 3 4 58

Products for ALKBH3 Gene

Sources for ALKBH3 Gene

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