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    KDM1A lysine demethylase 1A [ Homo sapiens (human) ]

    Gene ID: 23028, updated on 20-Feb-2024

    Summary

    Official Symbol
    KDM1Aprovided by HGNC
    Official Full Name
    lysine demethylase 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:29079
    See related
    Ensembl:ENSG00000004487 MIM:609132; AllianceGenome:HGNC:29079
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AOF2; CPRF; KDM1; LSD1; BHC110
    Summary
    This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
    Expression
    Broad expression in testis (RPKM 45.8), endometrium (RPKM 15.8) and 25 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:
    1p36.12
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (23019468..23083689)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (22845130..22909357)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (23345961..23410182)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23287810-23287985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23290925-23291425 Neighboring gene lactamase beta like 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:23336854-23338053 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:23345765-23346452 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:23346453-23347138 Neighboring gene testis expressed 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 356 Neighboring gene microRNA 3115 Neighboring gene leucine zipper protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23459884-23460190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23466860-23467360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23467361-23467861 Neighboring gene RNA, U6 small nuclear 514, pseudogene Neighboring gene RNA, U6 small nuclear 135, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat LSD1/KDM1 demethylates HIV-1 Tat at position K51 in vitro and in cells PubMed
    tat LSD1 interacts with CTIP2 and co-localizes with HIV-1 Tat. LSD1 is required for CTIP2 recruitment at the HIV-1 proximal promoter to repress HIV-1 replication and transcription PubMed
    tat LSD1/KDM1 and CoREST proteins are recruited to the HIV-1 LTR in response to HIV-1 Tat and formation of the LSD1/KDM1/CoREST complex functions as a co-activator of HIV-1 transcription PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0601

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables FAD-dependent H3K4me/H3K4me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables MRF binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables flavin adenine dinucleotide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables flavin adenine dinucleotide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K9 demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables histone demethylase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables histone demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables nuclear androgen receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear receptor coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables oxidoreductase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables oxidoreductase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables p53 binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables promoter-specific chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT enables telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables telomeric repeat-containing RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA repair-dependent chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to UV IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to gamma radiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in guanine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of DNA binding IC
    Inferred by Curator
    more info
    PubMed 
    involved_in negative regulation of DNA damage response, signal transduction by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in 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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell size IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of neural precursor cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of protein ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of stem cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein demethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA methylation-dependent heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of androgen receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to fungicide IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of DNA repair complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    lysine-specific histone demethylase 1A
    Names
    BRAF35-HDAC complex protein BHC110
    FAD-binding protein BRAF35-HDAC complex, 110 kDa subunit
    [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A
    amine oxidase (flavin containing) domain 2
    flavin-containing amine oxidase domain-containing protein 2
    lysine (K)-specific demethylase 1A
    lysine-specific histone demethylase 1
    NP_001009999.1
    NP_001350583.1
    NP_001397691.1
    NP_001397692.1
    NP_055828.2
    XP_005245843.1
    XP_006710536.1
    XP_016856205.1
    XP_047305633.1
    XP_054191226.1
    XP_054191227.1
    XP_054191228.1
    XP_054191229.1
    XP_054191230.1

    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.

    Genomic

    1. NG_047129.1 RefSeqGene

      Range
      5026..69247
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001009999.3NP_001009999.1  lysine-specific histone demethylase 1A isoform a

      See identical proteins and their annotated locations for NP_001009999.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC025362, BC040194, BC048134, BG717076
      Consensus CDS
      CCDS53278.1
      UniProtKB/TrEMBL
      A0A8I5QKM3
      Related
      ENSP00000383042.5, ENST00000400181.9
      Conserved Domains (4) summary
      pfam01593
      Location:308849
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:197284
      SWIRM; SWIRM domain
      pfam13450
      Location:303361
      NAD_binding_8; NAD(P)-binding Rossmann-like domain
      cl21568
      Location:391495
      SurA_N_3; SurA N-terminal domain
    2. NM_001363654.2NP_001350583.1  lysine-specific histone demethylase 1A isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons and uses an alternate in-frame splice for a 3' exon, compared to variant 1. The encoded protein (isoform c) is shorter than isoform a.
      Source sequence(s)
      AL031428
      Consensus CDS
      CCDS85939.1
      UniProtKB/TrEMBL
      A0A8I5QJJ5, R4GMQ1
      Related
      ENSP00000473297.2, ENST00000465864.2
      Conserved Domains (2) summary
      cl27535
      Location:183831
      Amino_oxidase; Flavin containing amine oxidoreductase
      cl27975
      Location:2398
      EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
    3. NM_001410762.1NP_001397691.1  lysine-specific histone demethylase 1A isoform d

      Status: REVIEWED

      Source sequence(s)
      AL031428
      Consensus CDS
      CCDS90880.1
      UniProtKB/TrEMBL
      A0A8I5KXU4, A0A8I5QKM3
      Related
      ENSP00000509257.1, ENST00000685102.1
    4. NM_001410763.1NP_001397692.1  lysine-specific histone demethylase 1A isoform e

      Status: REVIEWED

      Source sequence(s)
      AL031428
      Consensus CDS
      CCDS90881.1
      UniProtKB/TrEMBL
      A0A8I5KSH0, A0A8I5KVZ4
      Related
      ENSP00000509679.1, ENST00000691682.1
    5. NM_015013.4NP_055828.2  lysine-specific histone demethylase 1A isoform b

      See identical proteins and their annotated locations for NP_055828.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1. The encoded protein (isoform b) is shorter than isoform a.
      Source sequence(s)
      AB011173, BC025362, BG717076
      Consensus CDS
      CCDS30627.1
      UniProtKB/Swiss-Prot
      A8MWP9, O60341, Q5TH94, Q5TH95, Q86VT7, Q8IXK4, Q8NDP6, Q8TAZ3, Q96AW4
      UniProtKB/TrEMBL
      A0A8I5QJJ5
      Related
      ENSP00000349049.3, ENST00000356634.7
      Conserved Domains (2) summary
      PLN02328
      Location:183825
      PLN02328; lysine-specific histone demethylase 1 homolog
      PHA03378
      Location:2398
      PHA03378; EBNA-3B; Provisional

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      23019468..23083689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006710473.4XP_006710536.1  lysine-specific histone demethylase 1A isoform X2

      UniProtKB/TrEMBL
      A0A8I5KV76
      Conserved Domains (4) summary
      smart00150
      Location:430532
      SPEC; Spectrin repeats
      pfam01593
      Location:308809
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:197284
      SWIRM; SWIRM domain
      pfam13450
      Location:303361
      NAD_binding_8; NAD(P)-binding Rossmann-like domain
    2. XM_017000716.2XP_016856205.1  lysine-specific histone demethylase 1A isoform X3

      UniProtKB/TrEMBL
      A0A8I5KV76
      Related
      ENSP00000509252.1, ENST00000691404.1
    3. XM_005245786.3XP_005245843.1  lysine-specific histone demethylase 1A isoform X1

      See identical proteins and their annotated locations for XP_005245843.1

      UniProtKB/TrEMBL
      A0A8I5QKM3
      Related
      ENSP00000508820.1, ENST00000690627.1
      Conserved Domains (2) summary
      PLN02328
      Location:203845
      PLN02328; lysine-specific histone demethylase 1 homolog
      PHA03378
      Location:2398
      PHA03378; EBNA-3B; Provisional
    4. XM_047449677.1XP_047305633.1  lysine-specific histone demethylase 1A isoform X4

      UniProtKB/TrEMBL
      A0A8I5KVZ4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      22845130..22909357
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335252.1XP_054191227.1  lysine-specific histone demethylase 1A isoform X2

      UniProtKB/TrEMBL
      A0A8I5KV76
    2. XM_054335253.1XP_054191228.1  lysine-specific histone demethylase 1A isoform X3

      UniProtKB/TrEMBL
      A0A8I5KV76
    3. XM_054335251.1XP_054191226.1  lysine-specific histone demethylase 1A isoform X1

      UniProtKB/TrEMBL
      A0A8I5QKM3
    4. XM_054335254.1XP_054191229.1  lysine-specific histone demethylase 1A isoform X4

      UniProtKB/TrEMBL
      A0A8I5KVZ4
    5. XM_054335255.1XP_054191230.1  lysine-specific histone demethylase 1A isoform X5

      UniProtKB/TrEMBL
      A8K2R3