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

    Gene ID: 22289, updated on 25-Sep-2018

    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 Vega:OTTMUSG00000016960
    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
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 6.2), thymus adult (RPKM 6.1) and 28 other tissues See more
    Orthologs

    Genomic context

    See Kdm6a in Genome Data Viewer
    Location:
    X A1.2-A1.3; X 13.45 cM
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) X NC_000086.7 (18162364..18279936)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (17739793..17856484)

    Chromosome X - NC_000086.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41891 Neighboring gene myeloma-overexpressed gene 2 protein homolog pseudogene Neighboring gene dual specificity phosphatase 21 Neighboring gene up-regulated during skeletal muscle growth protein 5 pseudogene Neighboring gene RIKEN cDNA 4930578C19 gene

    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 FunctionsWhat's a GeneRIF?

    Variation

    Alleles

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

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    RNA polymerase II proximal promoter sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA polymerase II proximal promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone demethylase activity (H3-K27 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone demethylase activity (H3-K27 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cardiovascular system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic organ development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone H3-K27 demethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mesodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural tube development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    notochord morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    respiratory system process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    somite rostral/caudal axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    MLL3/4 complex ISO
    Inferred from Sequence Orthology
    more info
     
    histone methyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    lysine-specific demethylase 6A
    Names
    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

    NCBI Reference Sequences (RefSeq)

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

      See identical proteins and their annotated locations for NP_001297373.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the penultimate exon, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AJ002730, AK164248, AK164941, AL732451, AL773547, BC075703
      Consensus CDS
      CCDS81102.1
      UniProtKB/Swiss-Prot
      O70546
      UniProtKB/TrEMBL
      Q3TNW2, Q3TPN3
      Related
      ENSMUSP00000045862.6, OTTMUSP00000018424, ENSMUST00000044484.12, OTTMUST00000041127
      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_009483.2NP_033509.1  lysine-specific demethylase 6A isoform 1

      See identical proteins and their annotated locations for NP_033509.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AK164248, AL732451, AL773547, BC053433
      Consensus CDS
      CCDS30037.1
      UniProtKB/Swiss-Prot
      O70546
      UniProtKB/TrEMBL
      Q3TPN3
      Related
      ENSMUSP00000061539.8, OTTMUSP00000018503, ENSMUST00000052368.8, OTTMUST00000041259
      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: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000086.7 Reference GRCm38.p4 C57BL/6J

      Range
      18162364..18279936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527594.3XP_006527657.1  lysine-specific demethylase 6A isoform X1

      Conserved Domains (6) summary
      pfam02373
      Location:11851293
      JmjC; JmjC domain, hydroxylase
      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]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    2. XM_006527595.3XP_006527658.1  lysine-specific demethylase 6A isoform X2

      Conserved Domains (6) summary
      pfam02373
      Location:11851293
      JmjC; JmjC domain, hydroxylase
      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]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    3. XM_006527596.3XP_006527659.1  lysine-specific demethylase 6A isoform X4

      Conserved Domains (6) summary
      pfam02373
      Location:11401248
      JmjC; JmjC domain, hydroxylase
      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]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    4. XM_006527597.3XP_006527660.1  lysine-specific demethylase 6A isoform X5

      Conserved Domains (6) summary
      pfam02373
      Location:11401248
      JmjC; JmjC domain, hydroxylase
      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]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    5. XM_006527599.3XP_006527662.1  lysine-specific demethylase 6A isoform X6

      Conserved Domains (7) summary
      pfam02373
      Location:10881196
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10541118
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:319380
      TPR_11; TPR repeat
      pfam13424
      Location:207284
      TPR_12; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    6. XM_006527600.3XP_006527663.1  lysine-specific demethylase 6A isoform X7

      Conserved Domains (7) summary
      pfam02373
      Location:10881196
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:10541118
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:287314
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:132165
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:319380
      TPR_11; TPR repeat
      pfam13424
      Location:207284
      TPR_12; Tetratricopeptide repeat
      pfam13431
      Location:274305
      TPR_17; Tetratricopeptide repeat
    7. XM_017318461.1XP_017173950.1  lysine-specific demethylase 6A isoform X3

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