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

Gene ID: 569207, updated on 17-Aug-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 H3-tri/di-methyl-lysine-27 demethylase activity. Acts upstream of or within animal organ development; anterior/posterior pattern specification; and germ cell migration. Predicted to be part of MLL3/4 complex. Is expressed in blood island. 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, Apr 2022]
Orthologs
all
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Genomic context

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Location:
chromosome: 6
Exon count:
30
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (59851523..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 uncharacterized LOC101883235 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 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 (17) 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K27me2/H3K27me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
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 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of MLL3/4 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    59851523..59895080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005168796.4 → 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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