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Alkbh1 alkB homolog 1, histone H2A dioxygenase [ Mus musculus (house mouse) ]

Gene ID: 211064, updated on 18-Apr-2024

Summary

Official Symbol
Alkbh1provided by MGI
Official Full Name
alkB homolog 1, histone H2A dioxygenaseprovided by MGI
Primary source
MGI:MGI:2384034
See related
Ensembl:ENSMUSG00000079036 AllianceGenome:MGI:2384034
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Abh; alkB; hABH; Alkbh; 2700073G19Rik
Summary
Enables chemoattractant activity and oxidative DNA demethylase activity. Involved in DNA demethylation and tRNA demethylation. Acts upstream of or within several processes, including generation of neurons; negative regulation of neuron apoptotic process; and placenta development. Located in euchromatin. Is expressed in several structures, including branchial arch; central nervous system; gonad; hemolymphoid system gland; and limb bud. Orthologous to human ALKBH1 (alkB homolog 1, histone H2A dioxygenase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 17.2), CNS E11.5 (RPKM 14.3) and 28 other tissues See more
Orthologs
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Genomic context

Location:
12 D2; 12 41.65 cM
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (87474847..87490609, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (87428077..87443839, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene serine palmitoyltransferase, long chain base subunit 2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:88729340-88729523 Neighboring gene predicted gene, 33444 Neighboring gene STARR-seq mESC enhancer starr_32884 Neighboring gene STARR-seq mESC enhancer starr_32886 Neighboring gene STARR-seq mESC enhancer starr_32888 Neighboring gene 60S ribosomal protein L21-like Neighboring gene STARR-seq mESC enhancer starr_32889 Neighboring gene microRNA 3068 Neighboring gene SRA stem-loop interacting RNA binding protein Neighboring gene neural regeneration protein Neighboring gene SNW domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_32890 Neighboring gene RNA exonuclease 1 homolog pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Targeted (6)  1 citation
  • Endonuclease-mediated (3) 

General gene information

Markers

Gene Ontology Provided by MGI

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

General protein information

Preferred Names
nucleic acid dioxygenase ALKBH1
Names
Alkylated DNA repair protein alkB homolog 1
DNA 6mA demethylase
DNA N6-methyl adenine demethylase ALKBH1
DNA demethylase ALKBH1
DNA lyase ABH1
DNA oxidative demethylase ALKBH1
alkB, alkylation repair homolog 1
alpha-ketoglutarate-dependent dioxygenase ABH1
mRNA N(3)-methylcytidine demethylase
tRNA N1-methyl adenine demethylase
NP_001096035.1

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_001102565.1NP_001096035.1  nucleic acid dioxygenase ALKBH1

    See identical proteins and their annotated locations for NP_001096035.1

    Status: VALIDATED

    Source sequence(s)
    AK144828, BC094381
    Consensus CDS
    CCDS49120.1
    UniProtKB/Swiss-Prot
    P0CB42
    Related
    ENSMUSP00000124565.2, ENSMUST00000162961.8
    Conserved Domains (1) summary
    cl21496
    Location:119289
    2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    87474847..87490609 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)