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ALKBH4 alkB homolog 4, lysine demethylase [ Homo sapiens (human) ]

Gene ID: 54784, updated on 11-Apr-2024

Summary

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Official Symbol
ALKBH4provided by HGNC
Official Full Name
alkB homolog 4, lysine demethylaseprovided by HGNC
Primary source
HGNC:HGNC:21900
See related
Ensembl:ENSG00000160993 MIM:613302; AllianceGenome:HGNC:21900
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ABH4
Summary
Enables 2-oxoglutarate-dependent dioxygenase activity and actin binding activity. Involved in actomyosin structure organization; cleavage furrow ingression; and protein demethylation. Located in contractile ring and midbody. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 3.1), spleen (RPKM 3.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7q22.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (102456238..102464863, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (103773867..103782492, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (102096685..102105310, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100289561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18502 Neighboring gene LOC100289561-PRKRIP1 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18503 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:102036787-102037328 Neighboring gene PRKR interacting protein 1 Neighboring gene uncharacterized LOC105375433 Neighboring gene microRNA 548o Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26431 Neighboring gene NANOG hESC enhancer GRCh37_chr7:102061269-102061799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:102066011-102066914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26433 Neighboring gene Sharpr-MPRA regulatory region 9959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18505 Neighboring gene ORAI calcium release-activated calcium modulator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:102086939-102087486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:102095159-102095659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:102105053-102105702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:102105832-102106358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:102106359-102106884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26437 Neighboring gene microRNA 5090 Neighboring gene leucine rich repeats and WD repeat domain containing 1 Neighboring gene microRNA 4467

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Quantitative proteomics revealed new functions of ALKBH4. Yu K, et al. Proteomics, 2022 Apr. PMID 34951099, Free PMC Article
  2. ALKBH4 promotes tumourigenesis with a poor prognosis in non-small-cell lung cancer. Jingushi K, et al. Sci Rep, 2021 Apr 21. PMID 33883577, Free PMC Article
  3. Expression and sub-cellular localization of human ABH family molecules. Tsujikawa K, et al. J Cell Mol Med, 2007 Sep-Oct. PMID 17979886, Free PMC Article
  4. Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4. Bjørnstad LG, et al. Biochem J, 2011 Mar 15. PMID 21166655, Free PMC Article
  5. ALKBH4-dependent demethylation of actin regulates actomyosin dynamics. Li MM, et al. Nat Commun, 2013. PMID 23673617, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ALKBH4 is a novel enzyme that promotes translation through modified uridine regulation.
    Title: ALKBH4 is a novel enzyme that promotes translation through modified uridine regulation.
  2. Quantitative proteomics revealed new functions of ALKBH4.
    Title: Quantitative proteomics revealed new functions of ALKBH4.
  3. ALKBH4 promotes tumourigenesis with a poor prognosis in non-small-cell lung cancer.
    Title: ALKBH4 promotes tumourigenesis with a poor prognosis in non-small-cell lung cancer.
  4. ALKBH4-dependent actin demethylation regulates actomyosin function by promoting actin-non-muscle myosin II interaction.
    Title: ALKBH4-dependent demethylation of actin regulates actomyosin dynamics.
  5. The regions mediating binding to ALKBH4 comprised domains previously reported to be involved in interaction with DNA or chromatin.
    Title: Human ALKBH4 interacts with proteins associated with transcription.
  6. ALKBH4 represents an active Fe(II)/2OG-dependent decarboxylase and suggest that the cysteine cluster is involved in processes other than Fe co-ordination.
    Title: Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20013

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA N6-methyladenine demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables actin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables broad specificity oxidative DNA demethylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein demethylase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in actomyosin structure organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actomyosin structure organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cleavage furrow ingression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in demethylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression, epigenetic IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression, epigenetic ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein demethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in contractile ring IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in contractile ring IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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 homolog 4, lysine demthylase
alkB, alkylation repair homolog 4
alkylated DNA repair protein alkB homolog 4
lysine-specific demethylase ALKBH4
probable alpha-ketoglutarate-dependent dioxygenase ABH4
NP_060091.1
XP_005250521.1
XP_054214492.1

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_017621.4 → NP_060091.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4

    See identical proteins and their annotated locations for NP_060091.1

    Status: VALIDATED

    Source sequence(s)
    BC017096, BX353099
    Consensus CDS
    CCDS5723.1
    UniProtKB/Swiss-Prot
    Q53H92, Q9H6A4, Q9NXW9
    Related
    ENSP00000292566.3, ENST00000292566.4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    102456238..102464863 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005250464.4 → XP_005250521.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform X1

    See identical proteins and their annotated locations for XP_005250521.1

    UniProtKB/Swiss-Prot
    Q9NXW9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    103773867..103782492 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358517.1 → XP_054214492.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXW9.1 GenPept UniProtKB/Swiss-Prot:Q9NXW9

Gene LinkOut

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