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

Gene ID: 23028, updated on 14-Jun-2018
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
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

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • 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...
Products Interactant Other Gene Complex Source Pubs Description

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 histone ubiquitination 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
 
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

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
  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 (5) summary
    pfam01593
    Location:288831
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:177264
    SWIRM; SWIRM domain
    pfam13450
    Location:283341
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
    cl17182
    Location:421529
    NAT_SF; N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate
    cl21568
    Location:375471
    SurA_N_3; SurA N-terminal domain
  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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