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

    Gene ID: 99982, updated on 3-Oct-2021

    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
    Ao; LS; Aof2; Kdm1; Lsd1; AA408884; mKIAA0601; D4Ertd478e; 1810043O07Rik
    Expression
    Ubiquitous expression in CNS E14 (RPKM 42.5), whole brain E14.5 (RPKM 40.5) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    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 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-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 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 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    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
     
    acts_upstream_of_or_within regulation of cellular protein localization ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    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 
    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 
    located_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)

    NEW Try the new Transcript table

    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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