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    Kdm6a lysine (K)-specific demethylase 6A [ Mus musculus (house mouse) ]

    Gene ID: 22289, updated on 9-Dec-2024

    Summary

    Official Symbol
    Kdm6aprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 6Aprovided by MGI
    Primary source
    MGI:MGI:1095419
    See related
    Ensembl:ENSMUSG00000037369 AllianceGenome:MGI:1095419
    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
    Utx
    Summary
    Enables DNA binding activity; histone H3K27me2/H3K27me3 demethylase activity; and identical protein binding activity. Involved in chromatin remodeling. Acts upstream of or within several processes, including chordate embryonic development; embryonic morphogenesis; and respiratory system process. Located in nucleus. Part of histone methyltransferase complex. Is expressed in several structures, including alimentary system; early conceptus; gonad; liver; and spleen. Used to study chronic myelomonocytic leukemia. Human ortholog(s) of this gene implicated in several diseases, including Kabuki syndrome; bladder urothelial carcinoma; gastrointestinal system cancer (multiple); lung carcinoma (multiple); and triple-receptor negative breast cancer. Orthologous to human KDM6A (lysine demethylase 6A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 6.2), thymus adult (RPKM 6.1) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Kdm6a in Genome Data Viewer
    Location:
    X A1.2- A1.3; X 13.45 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (18027101..18147061)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (18160862..18279936)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 41891 Neighboring gene STARR-seq mESC enhancer starr_46839 Neighboring gene dual specificity phosphatase 21 Neighboring gene COP9 signalosome complex subunit 9 pseudogene Neighboring gene STARR-seq mESC enhancer starr_46840 Neighboring gene STARR-seq mESC enhancer starr_46841 Neighboring gene STARR-seq mESC enhancer starr_46842 Neighboring gene STARR-seq mESC enhancer starr_46843 Neighboring gene STARR-seq mESC enhancer starr_46844 Neighboring gene nuclear encoded rRNA 5S 5 Neighboring gene up-regulated during skeletal muscle growth protein 5 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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to angiotensin IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to endothelin IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to vitamin D IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to vitamin D ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within circulatory system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within embryonic organ development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within heart morphogenesis 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 mesodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neural tube development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within notochord morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell size IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell size ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein modification process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein modification process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within respiratory system process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within somite rostral/caudal axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of MLL3/4 complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of histone methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    lysine-specific demethylase 6A
    Names
    [histone H3]-trimethyl-L-lysine(27) demethylase 6A
    histone demethylase UTX
    ubiquitously transcribed TPR protein on the X chromosome
    ubiquitously transcribed X chromosome tetratricopeptide repeat protein
    ubiquitously transcribed tetratricopeptide repeat gene, X chromosome
    NP_001297373.1
    NP_001390300.1
    NP_001390301.1
    NP_001390302.1
    NP_001390303.1
    NP_001390304.1
    NP_001390305.1
    NP_001390306.1
    NP_001390307.1
    NP_001390308.1
    NP_001390309.1
    NP_001390310.1
    NP_033509.1
    XP_006527657.1
    XP_006527659.1
    XP_017173950.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001310444.2NP_001297373.1  lysine-specific demethylase 6A isoform 2

      See identical proteins and their annotated locations for NP_001297373.1

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
      Consensus CDS
      CCDS81102.1
      UniProtKB/Swiss-Prot
      A2AID2, O70546, Q6DI80, Q7TSG4
      Related
      ENSMUSP00000045862.7, ENSMUST00000044484.13
      Conserved Domains (6) summary
      pfam02373
      Location:11331241
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10991163
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:108401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    2. NM_001403371.1NP_001390300.1  lysine-specific demethylase 6A isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    3. NM_001403372.1NP_001390301.1  lysine-specific demethylase 6A isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    4. NM_001403373.1NP_001390302.1  lysine-specific demethylase 6A isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    5. NM_001403374.1NP_001390303.1  lysine-specific demethylase 6A isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    6. NM_001403375.1NP_001390304.1  lysine-specific demethylase 6A isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    7. NM_001403376.1NP_001390305.1  lysine-specific demethylase 6A isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    8. NM_001403377.1NP_001390306.1  lysine-specific demethylase 6A isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    9. NM_001403378.1NP_001390307.1  lysine-specific demethylase 6A isoform 10

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    10. NM_001403379.1NP_001390308.1  lysine-specific demethylase 6A isoform 11

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    11. NM_001403380.1NP_001390309.1  lysine-specific demethylase 6A isoform 12

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    12. NM_001403381.1NP_001390310.1  lysine-specific demethylase 6A isoform 13

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
    13. NM_009483.3NP_033509.1  lysine-specific demethylase 6A isoform 1

      See identical proteins and their annotated locations for NP_033509.1

      Status: VALIDATED

      Source sequence(s)
      AL732451, AL773547
      Consensus CDS
      CCDS30037.1
      UniProtKB/Swiss-Prot
      O70546
      UniProtKB/TrEMBL
      Q3TPN3
      Related
      ENSMUSP00000061539.9, ENSMUST00000052368.9
      Conserved Domains (6) summary
      pfam02373
      Location:11331241
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10991163
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:108401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      18027101..18147061
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527594.4XP_006527657.1  lysine-specific demethylase 6A isoform X1

      Conserved Domains (4) summary
      smart00558
      Location:11511215
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:108401
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:11851293
      JmjC; JmjC domain, hydroxylase
    2. XM_006527596.4XP_006527659.1  lysine-specific demethylase 6A isoform X4

      Conserved Domains (5) summary
      smart00558
      Location:11061170
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:108403
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam05109
      Location:533872
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam02373
      Location:11401248
      JmjC; JmjC domain, hydroxylase
    3. XM_017318461.2XP_017173950.1  lysine-specific demethylase 6A isoform X3

      Conserved Domains (5) summary
      smart00558
      Location:11181182
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:77368
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285316
      TPR; TPR repeat [structural motif]
      pfam05109
      Location:545884
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam02373
      Location:11521260
      JmjC; JmjC domain, hydroxylase