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

    Gene ID: 72041, updated on 9-Dec-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, Dec 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
    • 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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