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    kdm6al lysine (K)-specific demethylase 6A, like [ Danio rerio (zebrafish) ]

    Gene ID: 569207, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm6alprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 6A, likeprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070112-2002
    See related
    Ensembl:ENSDARG00000059794 AllianceGenome:ZFIN:ZDB-GENE-070112-2002
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    uty; utxl1; zgc:158313
    Summary
    Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; chromatin DNA binding activity; and histone H3K27me2/H3K27me3 demethylase activity. Acts upstream of or within several processes, including anterior/posterior pattern specification; germ cell migration; and heart development. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. Is expressed in blood island and telencephalon. 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) and UTY (ubiquitously transcribed tetratricopeptide repeat containing, Y-linked). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm6al in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (59854203..59895080)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (59921966..59962868)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene calcium/calmodulin-dependent serine protein kinase b Neighboring gene DEAD-box helicase 3 X-linked b Neighboring gene G-protein coupled bile acid receptor 1 Neighboring gene angio-associated, migratory cell protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Haploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate. Lindgren AM, et al. Hum Genet, 2013 May. PMID 23354975, Free PMC Article
    2. Kabuki syndrome genes KMT2D and KDM6A: functional analyses demonstrate critical roles in craniofacial, heart and brain development. Van Laarhoven PM, et al. Hum Mol Genet, 2015 Aug 1. PMID 25972376, Free PMC Article
    3. The histone demethylase UTX regulates stem cell migration and hematopoiesis. Thieme S, et al. Blood, 2013 Mar 28. PMID 23365460
    4. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. Gagnon JA, et al. PLoS One, 2014. PMID 24873830, Free PMC Article
    5. Histone demethylases Kdm6ba and Kdm6bb redundantly promote cardiomyocyte proliferation during zebrafish heart ventricle maturation. Akerberg AA, et al. Dev Biol, 2017 Jun 1. PMID 28372944, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables histone H3K27me2/H3K27me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior pattern specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within germ cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine (K)-specific demethylase 6A, like
    Names
    ubiquitously transcribed tetratricopeptide repeat, X chromosome like 1
    utx1
    NP_001073662.1
    XP_005168853.1

    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_001080193.1 → NP_001073662.1  lysine (K)-specific demethylase 6A, like

      See identical proteins and their annotated locations for NP_001073662.1

      Status: PROVISIONAL

      Source sequence(s)
      BC129198
      UniProtKB/TrEMBL
      A0A8M1NBH9, A1L1S9
      Related
      ENSDARP00000077934.4, ENSDART00000083499.6
      Conserved Domains (6) summary
      pfam02373
      Location:1042 → 1150
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1008 → 1072
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      COG0457
      Location:106 → 402
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:285 → 312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130 → 163
      TPR_1; Tetratricopeptide repeat
      pfam13431
      Location:272 → 303
      TPR_17; Tetratricopeptide repeat

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007117.7 Reference GRCz11 Primary Assembly

      Range
      59854203..59895080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005168796.5 → XP_005168853.1  lysine (K)-specific demethylase 6A, like isoform X1

      UniProtKB/TrEMBL
      A0A8M2BG42
      Conserved Domains (6) summary
      pfam02373
      Location:1087 → 1195
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1053 → 1117
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:285 → 312
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:130 → 163
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:129 → 194
      TPR_11; TPR repeat
      pfam13431
      Location:272 → 303
      TPR_17; Tetratricopeptide repeat
    Nucleotide Protein Strain
    Heading Accession and Version

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