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

Gene ID: 22289, updated on 1-Jul-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 H3-tri/di-methyl-lysine-27 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 histone H3-K27 demethylation. Located in nucleus. Part of histone methyltransferase complex. Is expressed in several structures, including early conceptus; gonad; liver; lung; 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, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 6.2), thymus adult (RPKM 6.1) and 28 other tissues See more
Orthologs
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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 dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
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 oxidoreductase activity 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 vitamin D ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
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 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 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 ISO
Inferred from Sequence Orthology
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)

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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_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