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

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: human all
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Genomic context

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_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Kdm6a-CNN1 axis orchestrates epigenetic control of trauma-induced spinal cord microvascular endothelial cell senescence to balance neuroinflammation for improved neurological repair.
Title: Kdm6a-CNN1 axis orchestrates epigenetic control of trauma-induced spinal cord microvascular endothelial cell senescence to balance neuroinflammation for improved neurological repair.
Cutting Edge: Hypoxia Sensing by the Histone Demethylase UTX (KDM6A) Limits Colitogenic CD4+ T Cells in Mucosal Inflammation.
Title: Cutting Edge: Hypoxia Sensing by the Histone Demethylase UTX (KDM6A) Limits Colitogenic CD4+ T Cells in Mucosal Inflammation.
Extracellular vesicles from UTX-knockout endothelial cells boost neural stem cell differentiation in spinal cord injury.
Title: Extracellular vesicles from UTX-knockout endothelial cells boost neural stem cell differentiation in spinal cord injury.
KDM6A/UTX promotes spermatogenic gene expression across generations and is not required for male fertilitydagger.
Title: KDM6A/UTX promotes spermatogenic gene expression across generations and is not required for male fertility†.
Inhibition of UTX/KDM6A improves recovery of spinal cord injury by attenuating BSCB permeability and macrophage infiltration through the MLCK/p-MLC pathway.
Title: Inhibition of UTX/KDM6A improves recovery of spinal cord injury by attenuating BSCB permeability and macrophage infiltration through the MLCK/p-MLC pathway.
Altered expression, but small contribution, of the histone demethylase KDM6A in obstructive uropathy in mice.
Title: Altered expression, but small contribution, of the histone demethylase KDM6A in obstructive uropathy in mice.
The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
Title: The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
KDM6A epigenetically regulates subtype plasticity in small cell lung cancer.
Title: KDM6A epigenetically regulates subtype plasticity in small cell lung cancer.
UTX inactivation in germinal center B cells promotes the development of multiple myeloma with extramedullary disease.
Title: UTX inactivation in germinal center B cells promotes the development of multiple myeloma with extramedullary disease.
X Chromosome Factor Kdm6a Enhances Cognition Independent of Its Demethylase Function in the Aging XY Male Brain.
Title: X Chromosome Factor Kdm6a Enhances Cognition Independent of Its Demethylase Function in the Aging XY Male Brain.

Submit: New GeneRIF Correction See all GeneRIFs (90)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Gene trapped (1)
Targeted (22) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Utx (e-PCR), detects polymorphism
- UniSTS:265483

Utx (e-PCR), detects polymorphism
- UniSTS:265484

G34976 (e-PCR)
- UniSTS:28513

Utx (e-PCR), detects polymorphism
- UniSTS:256414

G49474 (e-PCR)
- UniSTS:109216

DXErtd770e (e-PCR), detects polymorphism
- UniSTS:167636

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

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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

EC 1.14.11.68

NP_001390300.1

EC 1.14.11.68

NP_001390301.1

EC 1.14.11.68

NP_001390302.1

EC 1.14.11.68

NP_001390303.1

EC 1.14.11.68

NP_001390304.1

EC 1.14.11.68

NP_001390305.1

EC 1.14.11.68

NP_001390306.1

EC 1.14.11.68

NP_001390307.1

EC 1.14.11.68

NP_001390308.1

EC 1.14.11.68

NP_001390309.1

EC 1.14.11.68

NP_001390310.1

EC 1.14.11.68

NP_033509.1

EC 1.14.11.68

XP_006527657.1

EC 1.14.11.68

XP_006527659.1

EC 1.14.11.68

XP_017173950.1

EC 1.14.11.68

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)

NM_001310444.2 → NP_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:1133 → 1241

JmjC; JmjC domain, hydroxylase

smart00558
Location:1099 → 1163

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

COG0457
Location:108 → 401

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:287 → 314

TPR; TPR repeat [structural motif]

pfam00515
Location:132 → 165

TPR_1; Tetratricopeptide repeat

pfam13431
Location:274 → 305

TPR_17; Tetratricopeptide repeat
NM_001403371.1 → NP_001390300.1 lysine-specific demethylase 6A isoform 3

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403372.1 → NP_001390301.1 lysine-specific demethylase 6A isoform 4

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403373.1 → NP_001390302.1 lysine-specific demethylase 6A isoform 5

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403374.1 → NP_001390303.1 lysine-specific demethylase 6A isoform 6

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403375.1 → NP_001390304.1 lysine-specific demethylase 6A isoform 7

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403376.1 → NP_001390305.1 lysine-specific demethylase 6A isoform 8

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403377.1 → NP_001390306.1 lysine-specific demethylase 6A isoform 9

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403378.1 → NP_001390307.1 lysine-specific demethylase 6A isoform 10

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403379.1 → NP_001390308.1 lysine-specific demethylase 6A isoform 11

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403380.1 → NP_001390309.1 lysine-specific demethylase 6A isoform 12

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_001403381.1 → NP_001390310.1 lysine-specific demethylase 6A isoform 13

Status: VALIDATED

Source sequence(s)

AL732451, AL773547
NM_009483.3 → NP_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:1133 → 1241

JmjC; JmjC domain, hydroxylase

smart00558
Location:1099 → 1163

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

COG0457
Location:108 → 401

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:287 → 314

TPR; TPR repeat [structural motif]

pfam00515
Location:132 → 165

TPR_1; Tetratricopeptide repeat

pfam13431
Location:274 → 305

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

NC_000086.8 Reference GRCm39 C57BL/6J

Range

18027101..18147061

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (4) summary

smart00558
Location:1151 → 1215

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

COG0457
Location:108 → 401

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:287 → 314

TPR; TPR repeat [structural motif]

pfam02373
Location:1185 → 1293

JmjC; JmjC domain, hydroxylase
XM_006527596.4 → XP_006527659.1 lysine-specific demethylase 6A isoform X4

Conserved Domains (5) summary

smart00558
Location:1106 → 1170

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

COG0457
Location:108 → 403

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:287 → 314

TPR; TPR repeat [structural motif]

pfam05109
Location:533 → 872

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam02373
Location:1140 → 1248

JmjC; JmjC domain, hydroxylase
XM_017318461.2 → XP_017173950.1 lysine-specific demethylase 6A isoform X3

Conserved Domains (5) summary

smart00558
Location:1118 → 1182

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

COG0457
Location:77 → 368

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:285 → 316

TPR; TPR repeat [structural motif]

pfam05109
Location:545 → 884

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

pfam02373
Location:1152 → 1260

JmjC; JmjC domain, hydroxylase