Kdm1a lysine (K)-specific demethylase 1A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm1aprovided by MGI
Official Full Name: lysine (K)-specific demethylase 1Aprovided by MGI
Primary source: MGI:MGI:1196256
See related: Ensembl:ENSMUSG00000036940 AllianceGenome:MGI:1196256
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: Aof2; Kdm1; Lsd1; mKIAA0601; D4Ertd478e; 1810043O07Rik
Summary: Enables several functions, including DNA-binding transcription factor binding activity; histone H3 demethylase activity; and transcription coregulator activity. Involved in several processes, including positive regulation of cell population proliferation; regulation of myeloid cell differentiation; and regulation of transcription by RNA polymerase II. Acts upstream of or within DNA repair-dependent chromatin remodeling; negative regulation of neurogenesis; and nervous system development. Located in chromatin and nucleus. Is expressed in several structures, including articular cartilage; brain; reproductive system; retina; and urinary system. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Ubiquitous expression in CNS E14 (RPKM 42.5), whole brain E14.5 (RPKM 40.5) and 28 other tissues See more
Orthologs: all
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Genomic context

Location:: 4 D3; 4 68.8 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (136277844..136330127, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (136550533..136602787, complement)

Chromosome 4 - NC_000070.7 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?

The scaffolding function of LSD1 controls DNA methylation in mouse ESCs.
Title: The scaffolding function of LSD1 controls DNA methylation in mouse ESCs.
Restoration of TFPI2 by LSD1 inhibition suppresses tumor progression and potentiates antitumor immunity in breast cancer.
Title: Restoration of TFPI2 by LSD1 inhibition suppresses tumor progression and potentiates antitumor immunity in breast cancer.
Downregulation of lysine-specific histone demethylase 1A (KDM1A/LSD1) in medial prefrontal cortex facilitates chronic stress-induced pain and emotional dysfunction in female mice.
Title: Downregulation of lysine-specific histone demethylase 1A (KDM1A/LSD1) in medial prefrontal cortex facilitates chronic stress-induced pain and emotional dysfunction in female mice.
LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model.
Title: LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model.
Histone demethylase KDM1A promotes hepatic steatosis and inflammation by increasing chromatin accessibility in NAFLD.
Title: Histone demethylase KDM1A promotes hepatic steatosis and inflammation by increasing chromatin accessibility in NAFLD.
Inhibition of the lysine demethylase LSD1 modulates the balance between inflammatory and antiviral responses against coronaviruses.
Title: Inhibition of the lysine demethylase LSD1 modulates the balance between inflammatory and antiviral responses against coronaviruses.
Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.
Title: Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.
Lsd1 safeguards T-cell development via suppressing endogenous retroelements and interferon responses.
Title: Lsd1 safeguards T-cell development via suppressing endogenous retroelements and interferon responses.
Lnc_000048 Promotes Histone H3K4 Methylation of MAP2K2 to Reduce Plaque Stability by Recruiting KDM1A in Carotid Atherosclerosis.
Title: Lnc_000048 Promotes Histone H3K4 Methylation of MAP2K2 to Reduce Plaque Stability by Recruiting KDM1A in Carotid Atherosclerosis.
Crucial Role of Lysine-Specific Histone Demethylase 1 in RANKL-Mediated Osteoclast Differentiation.
Title: Crucial Role of Lysine-Specific Histone Demethylase 1 in RANKL-Mediated Osteoclast Differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (135)

Variation

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Alleles

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

Endonuclease-mediated (3)
Gene trapped (3)
Targeted (16) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AA408884 (e-PCR)
- UniSTS:159310

D4Ertd478e (e-PCR), detects polymorphism
- UniSTS:167397

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables MRF binding	IEA Inferred from Electronic Annotation more info
enables MRF binding	IPI Inferred from Physical Interaction more info	PubMed
enables MRF binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info	PubMed
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables flavin adenine dinucleotide binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IEA Inferred from Electronic Annotation more info
enables flavin adenine dinucleotide binding	ISO Inferred from Sequence Orthology more info
enables flavin adenine dinucleotide binding	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K4 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4 demethylase activity	ISO Inferred from Sequence Orthology more info	PubMed
enables histone H3K4 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K9 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me2/H3K9me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H4K20 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K20 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables lncRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear androgen receptor binding	ISO Inferred from Sequence Orthology more info
enables nuclear androgen receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	ISO Inferred from Sequence Orthology more info
enables oxidoreductase activity	ISS Inferred from Sequence or Structural Similarity more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein demethylase activity	ISO Inferred from Sequence Orthology more info
enables telomeric repeat-containing RNA binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair-dependent chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA repair-dependent chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to UV	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within cellular response to gamma radiation	ISO Inferred from Sequence Orthology more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in epigenetic regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in granulocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in guanine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA damage response, signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neurogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription initiation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription initiation-coupled chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection extension	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuron projection extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron projection morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pituitary gland development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cold-induced thermogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of megakaryocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of multicellular organismal process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info	PubMed
involved_in positive regulation of stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	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 regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info	PubMed
involved_in regulation of neurogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of neurogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of primitive erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of protein localization	ISO Inferred from Sequence Orthology more info	PubMed
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of DNA repair complex	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IEA Inferred from Electronic Annotation more info
is_active_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
part_of histone methyltransferase complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info	PubMed
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific histone demethylase 1A

Names: BRAF35-HDAC complex protein BHC110; amine oxidase (flavin containing) domain 2; flavin-containing amine oxidase domain-containing protein 2; flavin-containingso amine oxidase domain-containing protein 2; lysine (K)-specific demethylase 1; lysine-specific histone demethylase 1

NP_001334150.1

EC 1.14.11.65

EC 1.14.99.66

NP_001343496.1

EC 1.14.11.65

EC 1.14.99.66

NP_598633.2

EC 1.14.11.65

EC 1.14.99.66

XP_006539392.1

EC 1.14.11.65

EC 1.14.99.66

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_001347221.1 → NP_001334150.1 lysine-specific histone demethylase 1A isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL671173

Consensus CDS

CCDS84806.1

Related

ENSMUSP00000101473.2, ENSMUST00000105847.8
NM_001356567.1 → NP_001343496.1 lysine-specific histone demethylase 1A isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon but also contains an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AW494983, BC059885, BM949344, CJ134496

Conserved Domains (2) summary

cl27535
Location:184 → 830

Amino_oxidase; Flavin containing amine oxidoreductase

cl27975
Location:39 → 99

EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
NM_133872.2 → NP_598633.2 lysine-specific histone demethylase 1A isoform 2

See identical proteins and their annotated locations for NP_598633.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AK129170, AW494983, BC059885, CJ134496

Consensus CDS

CCDS51331.1

UniProtKB/Swiss-Prot

A3KG93, A3KG94, F6Z4I3, Q6PB53, Q6ZQ88, Q8VEA1

Related

ENSMUSP00000111977.3, ENSMUST00000116273.9

Conserved Domains (4) summary

smart00150
Location:411 → 513

SPEC; Spectrin repeats

pfam01593
Location:289 → 826

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:178 → 265

SWIRM; SWIRM domain

pfam13450
Location:284 → 342

NAD_binding_8; NAD(P)-binding Rossmann-like domain

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_000070.7 Reference GRCm39 C57BL/6J

Range

136277844..136330127 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006539329.5 → XP_006539392.1 lysine-specific histone demethylase 1A isoform X1

Conserved Domains (2) summary

PLN02328
Location:204 → 850

PLN02328; lysine-specific histone demethylase 1 homolog

PHA03378
Location:39 → 99

PHA03378; EBNA-3B; Provisional