ALKBH3 (alkB homolog 3, alpha-ketoglutarate dependent dioxygenase)

Gene

• Entrez ID: 221120
• Gene name: AlkB homolog 3, alpha-ketoglutarate dependent dioxygenase
• Gene symbol: ALKBH3
• Synonyms (NCBI Gene): ABH3, DEPC-1, DEPC1, PCA1, hABH3
• Chromosome: 11
• Chromosome location: 11p11.2
• 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-methy

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT714528	hsa-miR-942-5p	HITS-CLIP	19536157
MIRT714527	hsa-miR-3928-5p	HITS-CLIP	19536157
MIRT714526	hsa-miR-6806-3p	HITS-CLIP	19536157
MIRT714525	hsa-miR-6873-3p	HITS-CLIP	19536157
MIRT714524	hsa-miR-127-5p	HITS-CLIP	19536157
MIRT714523	hsa-miR-4768-5p	HITS-CLIP	19536157
MIRT714522	hsa-miR-6833-3p	HITS-CLIP	19536157
MIRT714528	hsa-miR-942-5p	HITS-CLIP	19536157
MIRT714527	hsa-miR-3928-5p	HITS-CLIP	19536157
MIRT714526	hsa-miR-6806-3p	HITS-CLIP	19536157
MIRT714525	hsa-miR-6873-3p	HITS-CLIP	19536157
MIRT714524	hsa-miR-127-5p	HITS-CLIP	19536157
MIRT714523	hsa-miR-4768-5p	HITS-CLIP	19536157
MIRT714522	hsa-miR-6833-3p	HITS-CLIP	19536157
MIRT778749	hsa-miR-4470	CLIP-seq
MIRT778750	hsa-miR-495	CLIP-seq
MIRT2473272	hsa-miR-1226	CLIP-seq
MIRT2473273	hsa-miR-1260	CLIP-seq
MIRT2473274	hsa-miR-1260b	CLIP-seq
MIRT2473275	hsa-miR-1273g	CLIP-seq
MIRT2473276	hsa-miR-15a	CLIP-seq
MIRT2473277	hsa-miR-15b	CLIP-seq
MIRT2473278	hsa-miR-16	CLIP-seq
MIRT2473279	hsa-miR-188-3p	CLIP-seq
MIRT2473280	hsa-miR-195	CLIP-seq
MIRT2473281	hsa-miR-219-1-3p	CLIP-seq
MIRT2473282	hsa-miR-29a	CLIP-seq
MIRT2473283	hsa-miR-29b	CLIP-seq
MIRT2473284	hsa-miR-29c	CLIP-seq
MIRT2473285	hsa-miR-3064-3p	CLIP-seq
MIRT2473286	hsa-miR-3065-3p	CLIP-seq
MIRT2473287	hsa-miR-3117-3p	CLIP-seq
MIRT2473288	hsa-miR-3119	CLIP-seq
MIRT2473289	hsa-miR-3128	CLIP-seq
MIRT2473290	hsa-miR-3145-5p	CLIP-seq
MIRT2473291	hsa-miR-3152-5p	CLIP-seq
MIRT2473292	hsa-miR-3156-3p	CLIP-seq
MIRT2473293	hsa-miR-3160-3p	CLIP-seq
MIRT2473294	hsa-miR-3162-5p	CLIP-seq
MIRT2473295	hsa-miR-3169	CLIP-seq
MIRT2473296	hsa-miR-320e	CLIP-seq
MIRT2473297	hsa-miR-3682-3p	CLIP-seq
MIRT2473298	hsa-miR-3684	CLIP-seq
MIRT2473299	hsa-miR-376c	CLIP-seq
MIRT2473300	hsa-miR-411	CLIP-seq
MIRT2473301	hsa-miR-424	CLIP-seq
MIRT778749	hsa-miR-4470	CLIP-seq
MIRT2473302	hsa-miR-4487	CLIP-seq
MIRT2473303	hsa-miR-4524	CLIP-seq
MIRT2473304	hsa-miR-4729	CLIP-seq
MIRT2473305	hsa-miR-4744	CLIP-seq
MIRT2473306	hsa-miR-4759	CLIP-seq
MIRT2473307	hsa-miR-4774-3p	CLIP-seq
MIRT2473308	hsa-miR-4775	CLIP-seq
MIRT2473309	hsa-miR-497	CLIP-seq
MIRT2473310	hsa-miR-503	CLIP-seq
MIRT2473311	hsa-miR-556-3p	CLIP-seq
MIRT2473312	hsa-miR-558	CLIP-seq
MIRT2473313	hsa-miR-571	CLIP-seq
MIRT2473314	hsa-miR-579	CLIP-seq
MIRT2473315	hsa-miR-633	CLIP-seq
MIRT2473316	hsa-miR-646	CLIP-seq
MIRT2473317	hsa-miR-936	CLIP-seq
MIRT2473273	hsa-miR-1260	CLIP-seq
MIRT2473274	hsa-miR-1260b	CLIP-seq
MIRT2473275	hsa-miR-1273g	CLIP-seq
MIRT2473279	hsa-miR-188-3p	CLIP-seq
MIRT2473281	hsa-miR-219-1-3p	CLIP-seq
MIRT2473285	hsa-miR-3064-3p	CLIP-seq
MIRT2473288	hsa-miR-3119	CLIP-seq
MIRT2473291	hsa-miR-3152-5p	CLIP-seq
MIRT2473292	hsa-miR-3156-3p	CLIP-seq
MIRT2473293	hsa-miR-3160-3p	CLIP-seq
MIRT2473294	hsa-miR-3162-5p	CLIP-seq
MIRT2473297	hsa-miR-3682-3p	CLIP-seq
MIRT2473298	hsa-miR-3684	CLIP-seq
MIRT2473299	hsa-miR-376c	CLIP-seq
MIRT2473300	hsa-miR-411	CLIP-seq
MIRT2473302	hsa-miR-4487	CLIP-seq
MIRT2473304	hsa-miR-4729	CLIP-seq
MIRT2473305	hsa-miR-4744	CLIP-seq
MIRT2473307	hsa-miR-4774-3p	CLIP-seq
MIRT2473308	hsa-miR-4775	CLIP-seq
MIRT2473311	hsa-miR-556-3p	CLIP-seq
MIRT2473312	hsa-miR-558	CLIP-seq
MIRT2473313	hsa-miR-571	CLIP-seq
MIRT2473314	hsa-miR-579	CLIP-seq
MIRT2473315	hsa-miR-633	CLIP-seq
MIRT2473317	hsa-miR-936	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	22055184, 25416956, 29892012, 31515488, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IBA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005829	Component	Cytosol	IDA
GO:0006281	Process	DNA repair	IBA
GO:0006281	Process	DNA repair	IEA
GO:0006307	Process	DNA alkylation repair	IDA	20714506, 22055184
GO:0006307	Process	DNA alkylation repair	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0008198	Function	Ferrous iron binding	IDA	16858410
GO:0008283	Process	Cell population proliferation	IMP	22055184
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0035515	Function	Oxidative RNA demethylase activity	IDA	16174769
GO:0035515	Function	Oxidative RNA demethylase activity	IEA
GO:0035516	Function	Broad specificity oxidative DNA demethylase activity	IDA	12486230, 16174769, 16858410, 20714506
GO:0035516	Function	Broad specificity oxidative DNA demethylase activity	IEA
GO:0035516	Function	Broad specificity oxidative DNA demethylase activity	IMP	22055184
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:1990930	Function	MRNA N1-methyladenosine dioxygenase activity	IDA	26863196, 26863410
GO:1990930	Function	MRNA N1-methyladenosine dioxygenase activity	IEA
GO:2000766	Process	Negative regulation of cytoplasmic translation	IDA	26863196

Other IDs

• MIM: 610603
• HGNC: 30141
• e!Ensembl: ENSG00000166199

Protein

• UniProt ID: Q96Q83
• Protein name: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (EC 1.14.11.33) (EC 1.14.11.54) (Alkylated DNA repair protein alkB homolog 3) (hABH3) (DEPC-1) (Prostate cancer antigen 1)
• Protein 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-methy
• PDB: 2IUW, 8JNK, 8JNR, 9NCZ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13532	2OG-FeII_Oxy_2	89 → 275	2OG-Fe(II) oxygenase superfamily	Domain

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. Detected in heart, pancreas, skeletal muscle, thymus, testis, ovary, spleen, prostate, small intestine, peripheral blood leukocytes, urinary bladder and colon. {ECO:0000269|PubMed:12486230, ECO:0000269|PubMed:16174769, ECO:
• Sequence:

  MEEKRRRARVQGAWAAPVKSQAIAQPATTAKSHLHQKPGQTWKNKEHHLSDREFVFKEPQ
  QVVRRAPEPRVIDREGVYEISLSPTGVSRVCLYPGFVDVKEADWILEQLCQDVPWKQRTG
  IREDITYQQPRLTAWYGELPYTYSRITMEPNPHWHPVLRTLKNRIEENTGHTFNSLLCNL
  YRNEKDSVDWHSDDEPSLGRCPIIASLSFGATRTFEMRKKPPPEENGDYTYVERVKIPLD
  HGTLLIMEGATQADWQHRVPKEYHSREPRVNLTFRTVYPDPRGAPW

• Sequence length: 286

Pathways

Reactome:

ALKBH3 mediated reversal of alkylation damage

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	21285982		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	21285982		★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	BEFREE	24693973		★☆☆☆☆ Found in Text Mining only
Benign Prostatic Hyperplasia	Benign Prostatic Hyperplasia	BEFREE	16033822, 22515525		★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	22850567		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	19290481		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	28679371		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	28679371	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	17970783, 22850567		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36098205	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	22850567		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	21285982		★☆☆☆☆ Found in Text Mining only
Encephalitis	Encephalitis	BEFREE	29485697		★☆☆☆☆ Found in Text Mining only
Hairy Cell Leukemia	Hairy Cell Leukemia	BEFREE	3871642		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29415318		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	28679371		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	21285982, 28479246		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	22826605		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	16033822, 17970783, 21285982, 22515525, 26967262		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	22850567		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	17970783, 21285982, 22055184, 22826605, 28679371, 30041948, 30342176, 30541109		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	28679371		★☆☆☆☆ Found in Text Mining only
Monoclonal Gammopathy of Undetermined Significance	Monoclonal Gammapathies	BEFREE	1830500		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	1830500		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21285982, 26967262, 29415318, 3871642		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	21285982		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	19852088	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	22826605		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	16033822, 17970783, 21285982, 22515525, 26967262		★☆☆☆☆ Found in Text Mining only
Prostatic Intraepithelial Neoplasia	Prostatic intraepithelial neoplasia	Pubtator	17968469	Associate	★☆☆☆☆ Found in Text Mining only
Prostatic Intraepithelial Neoplasias	Prostatic Neoplasms	BEFREE	16033822		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	LHGDN	17968469		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	17968469	Associate	★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	31519943	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	31519943		★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	21642358	Associate	★☆☆☆☆ Found in Text Mining only
Urothelial Carcinoma	Urothelial Carcinoma	BEFREE	22850567		★☆☆☆☆ Found in Text Mining only