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Aliases for ALKBH5 Gene

Aliases for ALKBH5 Gene

  • AlkB Homolog 5, RNA Demethylase 2 3 5
  • Oxoglutarate And Iron-Dependent Oxygenase Domain Containing 2 3
  • Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 5 3 4
  • Alkylated DNA Repair Protein AlkB Homolog 5 3 4
  • AlkB Family Member 5, RNA Demethylase 2 3
  • OFOXD1 3 4
  • ABH5 3 4
  • Probable Alpha-Ketoglutarate-Dependent Dioxygenase ABH5 3
  • AlkB, Alkylation Repair Homolog 5 (E. Coli) 2
  • AlkB, Alkylation Repair Homolog 5 3
  • RNA Demethylase ALKBH5 3
  • EC 1.14.11.- 4
  • OFOXD 3

External Ids for ALKBH5 Gene

Previous HGNC Symbols for ALKBH5 Gene

  • OFOXD1

Previous GeneCards Identifiers for ALKBH5 Gene

  • GC17P018031
  • GC17P018086
  • GC17P017840

Summaries for ALKBH5 Gene

GeneCards Summary for ALKBH5 Gene

ALKBH5 (AlkB Homolog 5, RNA Demethylase) is a Protein Coding gene. Diseases associated with ALKBH5 include Retinitis Pigmentosa 71 and Retinitis Pigmentosa 43. Among its related pathways are DNA Damage Reversal and DNA Double-Strand Break Repair. Gene Ontology (GO) annotations related to this gene include oxidative RNA demethylase activity.

UniProtKB/Swiss-Prot for ALKBH5 Gene

  • Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes (PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Can also demethylate N(6)-methyladenosine in single-stranded DNA (in vitro) (PubMed:24616105). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:21264265, PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Demethylation of m6A mRNA affects mRNA processing and export (PubMed:23177736). Required for spermatogenesis (By similarity).

Additional gene information for ALKBH5 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALKBH5 Gene

Genomics for ALKBH5 Gene

GeneHancer (GH) Regulatory Elements for ALKBH5 Gene

Promoters and enhancers for ALKBH5 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
GH17I018181 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.8 +2.0 2002 8 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 CBX5 ALKBH5 PIR34966 ENSG00000266677 SMCR8 MYO15A MIEF2 FAM106A FOXO3B SHMT1 ZNF286B
GH17I017356 Enhancer 1.2 Ensembl ENCODE dbSUPER 6.1 -826.8 -826777 0.6 RB1 ARID4B RAD21 ZNF335 GLIS2 ARID2 ZNF143 MIXL1 ZNF654 NCOA1 ALKBH5 GC17P017341 RPL13P12
GH17I017748 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.9 -429.2 -429242 10.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF143 FOS ZNF286B ENSG00000264885 RAI1 USP32P2 LOC100419436 MPRIP-AS1 SMCR5 ENSG00000273018 FAM106A CCDC144B
GH17I017689 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.8 -487.7 -487688 12.1 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YBX1 DRC3 SREBF1 RAI1 ENSG00000264885 ZNF286B LOC100419436 DRG2 MIR33B FLCN MYO15A
GH17I018157 Promoter/Enhancer 1.3 Ensembl ENCODE 0.3 -25.0 -25007 1.8 HDGF PKNOX1 ATF1 NFIB SIN3A EGR1 SCRT2 ZNF143 KLF7 IKZF2 SHMT1 LOC105371568 ALKBH5 MYO15A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ALKBH5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ALKBH5 gene promoter:

Genomic Locations for ALKBH5 Gene

Genomic Locations for ALKBH5 Gene
chr17:18,183,078-18,209,954
(GRCh38/hg38)
Size:
26,877 bases
Orientation:
Plus strand
chr17:18,086,392-18,113,268
(GRCh37/hg19)

Genomic View for ALKBH5 Gene

Genes around ALKBH5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALKBH5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALKBH5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALKBH5 Gene

Proteins for ALKBH5 Gene

  • Protein details for ALKBH5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P6C2-ALKB5_HUMAN
    Recommended name:
    RNA demethylase ALKBH5
    Protein Accession:
    Q6P6C2
    Secondary Accessions:
    • B4DVJ4
    • D3DXC6
    • Q9NXD6

    Protein attributes for ALKBH5 Gene

    Size:
    394 amino acids
    Molecular mass:
    44256 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • Sequence=BAA91078.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ALKBH5 Gene

    Alternative splice isoforms for ALKBH5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ALKBH5 Gene

Post-translational modifications for ALKBH5 Gene

  • Ubiquitination at posLast=147147
  • Modification sites at PhosphoSitePlus

Other Protein References for ALKBH5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ALKBH5 Gene

Domains & Families for ALKBH5 Gene

Gene Families for ALKBH5 Gene

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

Protein Domains for ALKBH5 Gene

Suggested Antigen Peptide Sequences for ALKBH5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6P6C2

UniProtKB/Swiss-Prot:

ALKB5_HUMAN :
  • Belongs to the alkB family.
Family:
  • Belongs to the alkB family.
genes like me logo Genes that share domains with ALKBH5: view

Function for ALKBH5 Gene

Molecular function for ALKBH5 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
N(6)-methyladenosine in mRNA + 2-oxoglutarate + O(2) = adenosine in mRNA + formaldehyde + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes (PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Can also demethylate N(6)-methyladenosine in single-stranded DNA (in vitro) (PubMed:24616105). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:21264265, PubMed:23177736, PubMed:24778178, PubMed:24616105, PubMed:24489119). Demethylation of m6A mRNA affects mRNA processing and export (PubMed:23177736). Required for spermatogenesis (By similarity).
UniProtKB/Swiss-Prot Induction:
By hypoxia, directly activated by HIF1A. Expression is regulated by PRMT7.

Enzyme Numbers (IUBMB) for ALKBH5 Gene

Phenotypes From GWAS Catalog for ALKBH5 Gene

Gene Ontology (GO) - Molecular Function for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,HDA 22658674
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 IDA 21264265
GO:0035515 oxidative RNA demethylase activity TAS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ALKBH5: view
genes like me logo Genes that share phenotypes with ALKBH5: view

Animal Models for ALKBH5 Gene

MGI Knock Outs for ALKBH5:

miRNA for ALKBH5 Gene

miRTarBase miRNAs that target ALKBH5

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ALKBH5 Gene

Localization for ALKBH5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALKBH5 Gene

Nucleus speckle.

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 ALKBH5 gene
Compartment Confidence
nucleus 5
cytosol 5
golgi apparatus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 21264265
GO:0005654 nucleoplasm TAS --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IDA --
GO:0016607 nuclear speck IDA,IEA 23177736
genes like me logo Genes that share ontologies with ALKBH5: view

Pathways & Interactions for ALKBH5 Gene

genes like me logo Genes that share pathways with ALKBH5: view

Pathways by source for ALKBH5 Gene

Interacting Proteins for ALKBH5 Gene

Gene Ontology (GO) - Biological Process for ALKBH5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 21264265
GO:0006307 DNA dealkylation involved in DNA repair TAS --
GO:0006397 mRNA processing IEA,IMP 23177736
GO:0006406 mRNA export from nucleus IMP 23177736
GO:0007283 spermatogenesis ISS --
genes like me logo Genes that share ontologies with ALKBH5: view

No data available for SIGNOR curated interactions for ALKBH5 Gene

Drugs & Compounds for ALKBH5 Gene

No Compound Related Data Available

Transcripts for ALKBH5 Gene

mRNA/cDNA for ALKBH5 Gene

Unigene Clusters for ALKBH5 Gene

AlkB, alkylation repair homolog 5 (E. coli):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALKBH5 Gene

No ASD Table

Relevant External Links for ALKBH5 Gene

GeneLoc Exon Structure for
ALKBH5
ECgene alternative splicing isoforms for
ALKBH5

Expression for ALKBH5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ALKBH5 Gene

Protein differential expression in normal tissues from HIPED for ALKBH5 Gene

This gene is overexpressed in Breast (10.6), Peripheral blood mononuclear cells (7.4), Stomach (7.0), and CD8 Tcells (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ALKBH5 Gene



Protein tissue co-expression partners for ALKBH5 Gene

NURSA nuclear receptor signaling pathways regulating expression of ALKBH5 Gene:

ALKBH5

SOURCE GeneReport for Unigene cluster for ALKBH5 Gene:

Hs.744130

mRNA Expression by UniProt/SwissProt for ALKBH5 Gene:

Q6P6C2-ALKB5_HUMAN
Tissue specificity: Widely expressed, with highest expression in lung, followed by testis, pancreas, spleen and ovary.

Evidence on tissue expression from TISSUES for ALKBH5 Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Spleen(4.3)
  • Muscle(2.4)
  • Heart(2)
genes like me logo Genes that share expression patterns with ALKBH5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ALKBH5 Gene

Orthologs for ALKBH5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALKBH5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALKBH5 33 34
  • 99.83 (n)
dog
(Canis familiaris)
Mammalia ALKBH5 33 34
  • 94.84 (n)
cow
(Bos Taurus)
Mammalia ALKBH5 33 34
  • 92.39 (n)
oppossum
(Monodelphis domestica)
Mammalia ALKBH5 34
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Alkbh5 33 16 34
  • 91.46 (n)
rat
(Rattus norvegicus)
Mammalia Alkbh5 33
  • 91.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ALKBH5 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALKBH5 33 34
  • 78.08 (n)
lizard
(Anolis carolinensis)
Reptilia ALKBH5 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia alkbh5 33
  • 75.24 (n)
zebrafish
(Danio rerio)
Actinopterygii alkbh5 33 34
  • 71.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10218 34
  • 46 (a)
OneToOne
Species where no ortholog for ALKBH5 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 ALKBH5 Gene

ENSEMBL:
Gene Tree for ALKBH5 (if available)
TreeFam:
Gene Tree for ALKBH5 (if available)

Paralogs for ALKBH5 Gene

No data available for Paralogs for ALKBH5 Gene

Variants for ALKBH5 Gene

Sequence variations from dbSNP and Humsavar for ALKBH5 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000028473 -- 18,203,458(+) G/A intron_variant
rs1000091629 -- 18,203,974(+) C/A intron_variant
rs1000126381 -- 18,209,657(+) G/A 3_prime_UTR_variant
rs1000168103 -- 18,192,695(+) T/C intron_variant
rs1000297008 -- 18,188,650(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ALKBH5 Gene

Variant ID Type Subtype PubMed ID
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv510702 CNV deletion 20534489

Variation tolerance for ALKBH5 Gene

Residual Variation Intolerance Score: 11.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.29; 6.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ALKBH5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALKBH5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALKBH5 Gene

Disorders for ALKBH5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ALKBH5 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 71
  • rp71
retinitis pigmentosa 43
  • rp43
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ALKBH5

genes like me logo Genes that share disorders with ALKBH5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ALKBH5 Gene

Publications for ALKBH5 Gene

  1. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. (PMID: 24778178) Xu C … Min J (The Journal of biological chemistry 2014) 2 3 4 58
  2. Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. (PMID: 24489119) Aik W … McDonough MA (Nucleic acids research 2014) 3 4 58
  3. Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. (PMID: 24616105) Feng C … Chen Z (The Journal of biological chemistry 2014) 3 4 58
  4. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. (PMID: 23177736) Zheng G … He C (Molecular cell 2013) 3 4 58
  5. Human AlkB homologue 5 is a nuclear 2-oxoglutarate dependent oxygenase and a direct target of hypoxia-inducible factor 1α (HIF-1α). (PMID: 21264265) Thalhammer A … Pollard PJ (PloS one 2011) 3 4 58

Products for ALKBH5 Gene

Sources for ALKBH5 Gene

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