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

Gene ID: 99982, updated on 18-Jan-2022

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
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; AA408884; mKIAA0601; D4Ertd478e; 1810043O07Rik
Summary
Enables several functions, including DNA-binding transcription factor binding activity; histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity; and promoter-specific chromatin binding activity. Involved in several processes, including negative regulation of macromolecule metabolic process; positive regulation of cell population proliferation; and regulation of myeloid cell differentiation. Acts upstream of or within histone H3-K4 demethylation; nervous system development; and positive regulation of transcription by RNA polymerase II. Located in chromatin and nucleus. Is expressed in several structures, including brain; inner cell mass; reproductive system; retina; and urinary system. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Nov 2021]
Expression
Ubiquitous expression in CNS E14 (RPKM 42.5), whole brain E14.5 (RPKM 40.5) and 28 other tissues See more
Orthologs
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Genomic context

See Kdm1a in Genome Data Viewer
Location:
4 D3; 4 68.8 cM
Exon count:
21
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (136106448..136158638, complement)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 31295 Neighboring gene 5-hydroxytryptamine (serotonin) receptor 1D Neighboring gene leucine zipper protein 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene Neighboring gene testis expressed 46 Neighboring gene lactamase, beta-like 1

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

Homology

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 MRF binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables MRF binding ISO
Inferred from Sequence Orthology
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 IPI
Inferred from Physical Interaction
more info
PubMed 
enables androgen receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
PubMed 
enables demethylase activity ISO
Inferred from Sequence Orthology
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
PubMed 
enables flavin adenine dinucleotide binding ISO
Inferred from Sequence Orthology
more info
 
enables histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3-methyl-lysine-4 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3-methyl-lysine-9 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables lncRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor coactivator activity ISO
Inferred from Sequence Orthology
more info
 
enables oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables oxidoreductase activity ISO
Inferred from Sequence Orthology
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 telomeric repeat-containing RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
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 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in granulocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within histone H3-K4 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within histone H3-K4 demethylation ISO
Inferred from Sequence Orthology
more info
PubMed 
involved_in histone H3-K4 demethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone H3-K9 demethylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
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 DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of histone H3-K9 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 protein binding ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
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, DNA-templated 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 
acts_upstream_of_or_within pituitary gland development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cold-induced thermogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of erythrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of histone ubiquitination ISO
Inferred from Sequence Orthology
more info
PubMed 
involved_in positive regulation of megakaryocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
involved_in protein demethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA methylation-dependent heterochromatin assembly ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
PubMed 
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, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of DNA repair complex ISO
Inferred from Sequence Orthology
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
PubMed 

General protein information

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
lysine (K)-specific demethylase 1
lysine-specific histone demethylase 1
NP_001334150.1
NP_001343496.1
NP_598633.2
XP_006539392.1

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_001347221.1NP_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
    UniProtKB/TrEMBL
    A3KG93
    Related
    ENSMUSP00000101473.2, ENSMUST00000105847.8
  2. NM_001356567.1NP_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:184830
    Amino_oxidase; Flavin containing amine oxidoreductase
    cl27975
    Location:3999
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
  3. NM_133872.2NP_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
    Q6ZQ88
    Related
    ENSMUSP00000111977.3, ENSMUST00000116273.9
    Conserved Domains (4) summary
    smart00150
    Location:411513
    SPEC; Spectrin repeats
    pfam01593
    Location:289826
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:178265
    SWIRM; SWIRM domain
    pfam13450
    Location:284342
    NAD_binding_8; NAD(P)-binding Rossmann-like domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    136277844..136330127 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    PLN02328
    Location:204850
    PLN02328; lysine-specific histone demethylase 1 homolog
    PHA03378
    Location:3999
    PHA03378; EBNA-3B; Provisional
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