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Alkbh4 alkB homolog 4, lysine demethylase [ Mus musculus (house mouse) ]

Gene ID: 72041, updated on 28-Oct-2024

Summary

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Official Symbol
Alkbh4provided by MGI
Official Full Name
alkB homolog 4, lysine demethylaseprovided by MGI
Primary source
MGI:MGI:1919291
See related
Ensembl:ENSMUSG00000039754 AllianceGenome:MGI:1919291
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
Abj4; 2010004B12Rik
Summary
Enables broad specificity oxidative DNA demethylase activity. Involved in positive regulation of gene expression, epigenetic. Predicted to be located in cytoplasm and nucleolus. Predicted to be active in contractile ring and midbody. Orthologous to human ALKBH4 (alkB homolog 4, lysine demethylase). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Ubiquitous expression in thymus adult (RPKM 10.0), duodenum adult (RPKM 7.1) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Alkbh4 in Genome Data Viewer
Location:
5 G2; 5 75.82 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (136164999..136170654)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (136136145..136141800)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E856 Neighboring gene polymerase (RNA) II (DNA directed) polypeptide J Neighboring gene leucine-rich repeats and WD repeat domain containing 1 Neighboring gene STARR-positive B cell enhancer ABC_E6388 Neighboring gene ORAI calcium release-activated calcium modulator 2 Neighboring gene STARR-positive B cell enhancer ABC_E3629 Neighboring gene Prkr interacting protein 1 (IL11 inducible)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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

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Related articles in PubMed

  1. ALKBH4 depletion in mice leads to spermatogenic defects. Nilsen A, et al. PLoS One, 2014. PMID 25153837, Free PMC Article
  2. ALKBH4-dependent demethylation of actin regulates actomyosin dynamics. Li MM, et al. Nat Commun, 2013. PMID 23673617, Free PMC Article
  3. An Adversarial DNA N(6)-Methyladenine-Sensor Network Preserves Polycomb Silencing. Kweon SM, et al. Mol Cell, 2019 Jun 20. PMID 30982744, Free PMC Article
  4. Repair of methylation damage in DNA and RNA by mammalian AlkB homologues. Lee DH, et al. J Biol Chem, 2005 Nov 25. PMID 16174769
  5. The genetic program of hematopoietic stem cells. Phillips RL, et al. Science, 2000 Jun 2. PMID 10834841

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

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Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
NOT enables 2-oxoglutarate-dependent dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 2-oxoglutarate-dependent dioxygenase activity ISO
Inferred from Sequence Orthology
more info
  
enables DNA N6-methyladenine demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables actin binding ISO
Inferred from Sequence Orthology
more info
  
enables actin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables broad specificity oxidative DNA demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in actomyosin structure organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actomyosin structure organization ISO
Inferred from Sequence Orthology
more info
  
involved_in actomyosin structure organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cleavage furrow ingression ISO
Inferred from Sequence Orthology
more info
  
involved_in cleavage furrow ingression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in demethylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression, epigenetic IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in contractile ring IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in contractile ring ISO
Inferred from Sequence Orthology
more info
  
located_in contractile ring ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in midbody IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in midbody ISO
Inferred from Sequence Orthology
more info
  
located_in midbody ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
alpha-ketoglutarate-dependent dioxygenase alkB homolog 4
Names
DNA N6-methyl adenine demethylase ALKBH4
alkB, alkylation repair homolog 4
alkylated DNA repair protein alkB homolog 4
lysine-specific demethylase ALKBH4
probable alpha-ketoglutarate-dependent dioxygenase ABH4
NP_001334421.1
NP_001346343.1
NP_001346344.1
NP_001346345.1
NP_001346346.1
NP_082346.1
XP_006504568.1
XP_030110679.1

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_001347492.1 → NP_001334421.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3.
    Source sequence(s)
    AC087420
    Consensus CDS
    CCDS84973.1
    UniProtKB/Swiss-Prot
    Q8R1Y9, Q9D8F1
    Related
    ENSMUSP00000040403.4, ENSMUST00000041100.4

  2. NM_001359414.1 → NP_001346343.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AC087420, BY101560

  3. NM_001359415.1 → NP_001346344.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (2) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 3. Variants 2, 4, and 5 all encode the same isoform (2).
    Source sequence(s)
    AC087420, CA546379
    Consensus CDS
    CCDS19753.1

  4. NM_001359416.1 → NP_001346345.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (2) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 3. Variants 2, 4, and 5 all encode the same isoform (2).
    Source sequence(s)
    AC087420
    Consensus CDS
    CCDS19753.1

  5. NM_001359417.1 → NP_001346346.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (4) is shorter at the N-terminus compared to isoform 3.
    Source sequence(s)
    AC087420, BU698033

  6. NM_028070.1 → NP_082346.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform 2

    See identical proteins and their annotated locations for NP_082346.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (2) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 3. Variants 2, 4, and 5 all encode the same isoform (2).
    Source sequence(s)
    BC022729
    Consensus CDS
    CCDS19753.1
    UniProtKB/Swiss-Prot
    Q9D8F1
    Related
    ENSMUSP00000098134.3, ENSMUST00000100568.3

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_000071.7 Reference GRCm39 C57BL/6J

    Range
    136164999..136170654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006504505.4 → XP_006504568.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform X1

    See identical proteins and their annotated locations for XP_006504568.1

    UniProtKB/Swiss-Prot
    Q9D8F1

  2. XM_030254819.2 → XP_030110679.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform X1

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9D8F1.1 GenPept UniProtKB/Swiss-Prot:Q9D8F1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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