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

    Gene ID: 23028, updated on 9-Sep-2018

    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; Vega:OTTHUMG00000003220
    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

    Genomic context

    See KDM1A in Genome Data Viewer
    Location:
    1p36.12
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (23019443..23083691)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (23345937..23410184)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lactamase beta like 1 Neighboring gene testis expressed 46 Neighboring gene microRNA 3115 Neighboring gene leucine zipper protein 1 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat'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 BioSystems

    • Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3, organism-specific biosystem (from REACTOME)
      Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3, organism-specific biosystemPKN1, activated by phosphorylation at threonine T774, binds activated AR (androgen receptor) and promotes transcription from AR-regulated promoters. On one hand, phosphorylated PKN1 promotes the form...
    • Androgen receptor signaling pathway, organism-specific biosystem (from WikiPathways)
      Androgen receptor signaling pathway, organism-specific biosystemAndrogens, mainly testosterone and 5alpha-dihydrotestosterone (DHT) play significant role in the growth and development of the male reproductive organs. These steroid hormones bring about their biolo...
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Coregulation of Androgen receptor activity, organism-specific biosystem (from Pathway Interaction Database)
      Coregulation of Androgen receptor activity, organism-specific biosystem
      Coregulation of Androgen receptor activity
    • Factors involved in megakaryocyte development and platelet production, organism-specific biosystem (from REACTOME)
      Factors involved in megakaryocyte development and platelet production, organism-specific biosystemMegakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they underg...
    • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
      HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...
    • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
      HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
    • Hemostasis, organism-specific biosystem (from REACTOME)
      Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
    • Notch signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
      Notch signaling pathway, organism-specific biosystem
      Notch signaling pathway
    • Notch-mediated HES/HEY network, organism-specific biosystem (from Pathway Interaction Database)
      Notch-mediated HES/HEY network, organism-specific biosystem
      Notch-mediated HES/HEY network
    • RHO GTPase Effectors, organism-specific biosystem (from REACTOME)
      RHO GTPase Effectors, organism-specific biosystemRHO GTPases regulate cell behaviour by activating a number of downstream effectors that regulate cytoskeletal organization, intracellular trafficking and transcription (reviewed by Sahai and Marshall...
    • RHO GTPases activate PKNs, organism-specific biosystem (from REACTOME)
      RHO GTPases activate PKNs, organism-specific biosystemProtein kinases N (PKN), also known as protein kinase C-related kinases (PKR) feature a C-terminal serine/threonine kinase domain and three RHO-binding motifs at the N-terminus. RHO GTPases RHOA, RHO...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by Rho GTPases, organism-specific biosystem (from REACTOME)
      Signaling by Rho GTPases, organism-specific biosystemThe Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as bi...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0601

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    MRF binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    androgen receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    flavin adenine dinucleotide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    flavin adenine dinucleotide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylase activity TAS
    Traceable Author Statement
    more info
     
    histone demethylase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    histone demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    histone demethylase activity (H3-K4 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity (H3-K9 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity (H3-K9 specific) TAS
    Traceable Author Statement
    more info
     
    histone demethylase activity (H3-dimethyl-K4 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone demethylase activity (H3-dimethyl-K4 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear receptor transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    oxidoreductase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    oxidoreductase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    p53 binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    telomeric DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    telomeric repeat-containing RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription regulatory region DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    alternative mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
     
    blood coagulation TAS
    Traceable Author Statement
    more info
     
    cellular response to UV IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to gamma radiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
     
    guanine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K4 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H3-K9 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylation IEA
    Inferred from Electronic Annotation
    more info
     
    muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    negative regulation of DNA binding IC
    Inferred by Curator
    more info
    PubMed 
    negative regulation of DNA damage response, signal transduction by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron maturation IEA
    Inferred from Electronic Annotation
    more info
     
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell size IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    positive regulation of histone ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuroblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein demethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cellular protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to fungicide IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    DNA repair complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    nuclear chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor 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
    amine oxidase (flavin containing) domain 2
    flavin-containing amine oxidase domain-containing protein 2
    lysine (K)-specific demethylase 1A
    lysine-specific histone demethylase 1

    NCBI Reference Sequences (RefSeq)

    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
      5006..69249
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001009999.2NP_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, BQ006926
      Consensus CDS
      CCDS53278.1
      UniProtKB/Swiss-Prot
      O60341
      Related
      ENSP00000383042.4, OTTHUMP00000003256, ENST00000400181.8, OTTHUMT00000008881
      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_001363654.1NP_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
      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_015013.3NP_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, BQ006926
      Consensus CDS
      CCDS30627.1
      UniProtKB/Swiss-Prot
      O60341
      Related
      ENSP00000349049.3, OTTHUMP00000003255, ENST00000356634.7, OTTHUMT00000008880
      Conserved Domains (2) summary
      cl27535
      Location:183825
      Amino_oxidase; Flavin containing amine oxidoreductase
      cl27975
      Location:2398
      EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)

    RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      23019443..23083691
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006710474.3XP_006710537.1  lysine-specific histone demethylase 1A isoform X1

      Conserved Domains (5) summary
      pfam01593
      Location:308851
      Amino_oxidase; Flavin containing amine oxidoreductase
      pfam04433
      Location:197284
      SWIRM; SWIRM domain
      pfam13450
      Location:303361
      NAD_binding_8; NAD(P)-binding Rossmann-like domain
      cl17182
      Location:441549
      NAT_SF; N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate
      cl21568
      Location:395491
      SurA_N_3; SurA N-terminal domain
    2. XM_017000716.1XP_016856205.1  lysine-specific histone demethylase 1A isoform X5

    3. XM_005245786.2XP_005245843.1  lysine-specific histone demethylase 1A isoform X2

      See identical proteins and their annotated locations for XP_005245843.1

      Conserved Domains (4) summary
      pfam01593
      Location:308845
      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:395491
      SurA_N_3; SurA N-terminal domain
    4. XM_006710472.3XP_006710535.1  lysine-specific histone demethylase 1A isoform X3

      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)
    5. XM_017000717.1XP_016856206.1  lysine-specific histone demethylase 1A isoform X6

    6. XM_006710473.3XP_006710536.1  lysine-specific histone demethylase 1A isoform X4

      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
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