Free for academic non-profit institutions. Other users need a Commercial license

Aliases for KDM1A Gene

Aliases for KDM1A Gene

  • Lysine Demethylase 1A 2 3
  • Flavin-Containing Amine Oxidase Domain-Containing Protein 2 3 4
  • Amine Oxidase (Flavin Containing) Domain 2 2 3
  • Lysine (K)-Specific Demethylase 1A 3 5
  • BRAF35-HDAC Complex Protein BHC110 3 4
  • Lysine (K)-Specific Demethylase 1 2 3
  • AOF2 3 4
  • KDM1 3 4
  • LSD1 3 4
  • FAD-Binding Protein BRAF35-HDAC Complex, 110 KDa Subunit 3
  • Lysine-Specific Histone Demethylase 1 3
  • EC 1.-.-.- 4
  • KIAA0601 4
  • BHC110 3
  • CPRF 3

External Ids for KDM1A Gene

Previous HGNC Symbols for KDM1A Gene

  • AOF2
  • KDM1

Previous GeneCards Identifiers for KDM1A Gene

  • GC01P023220
  • GC01P023347
  • GC01P021590

Summaries for KDM1A Gene

Entrez Gene Summary for KDM1A Gene

  • 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]

GeneCards Summary for KDM1A Gene

KDM1A (Lysine Demethylase 1A) is a Protein Coding gene. Diseases associated with KDM1A include kbg syndrome. Among its related pathways are Chromatin Regulation / Acetylation and Notch Signaling Pathways. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and enzyme binding. An important paralog of this gene is KDM1B.

UniProtKB/Swiss-Prot for KDM1A Gene

  • Histone demethylase that demethylates both Lys-4 (H3K4me) and Lys-9 (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of Thr-6 of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated Lys-370 of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.

Tocris Summary for KDM1A Gene

No data available for Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM1A Gene

Genomics for KDM1A Gene

Regulatory Elements for KDM1A Gene

Enhancers for KDM1A Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around KDM1A on UCSC Golden Path with GeneCards custom track

Promoters for KDM1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM1A on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM1A Gene

Chromosome:
1
Start:
23,019,443 bp from pter
End:
23,083,691 bp from pter
Size:
64,249 bases
Orientation:
Plus strand

Genomic View for KDM1A Gene

Genes around KDM1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM1A Gene

Proteins for KDM1A Gene

  • Protein details for KDM1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60341-KDM1A_HUMAN
    Recommended name:
    Lysine-specific histone demethylase 1A
    Protein Accession:
    O60341
    Secondary Accessions:
    • A8MWP9
    • Q5TH94
    • Q5TH95
    • Q86VT7
    • Q8IXK4
    • Q8NDP6
    • Q8TAZ3
    • Q96AW4

    Protein attributes for KDM1A Gene

    Size:
    852 amino acids
    Molecular mass:
    92903 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Component of a RCOR/GFI/KDM1A/HDAC complex. Interacts directly with GFI1 and GFI1B. Interacts with INSM1 (By similarity). Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it from the proteasome while PHF21A/BHC80 inhibits the demethylase activity. Interacts with the androgen receptor (AR). Interacts with ASXL1. Interacts with SNAI1 (via SNAG domain).
    SequenceCaution:
    • Sequence=BAA25527.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM1A Gene

    Alternative splice isoforms for KDM1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM1A Gene

Proteomics data for KDM1A Gene at MOPED

Post-translational modifications for KDM1A Gene

  • Ubiquitination at Lys 280, Lys 322, Lys 355, Lys 374, Lys 492, Lys 647, Lys 732, and Lys 744
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM1A Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for KDM1A (LSD1)

No data available for DME Specific Peptides for KDM1A Gene

Domains & Families for KDM1A Gene

Gene Families for KDM1A Gene

Protein Domains for KDM1A Gene

Suggested Antigen Peptide Sequences for KDM1A Gene

Graphical View of Domain Structure for InterPro Entry

O60341

UniProtKB/Swiss-Prot:

KDM1A_HUMAN :
  • The SWIRM domain may act as an anchor site for a histone tail.
  • Belongs to the flavin monoamine oxidase family.
Domain:
  • The SWIRM domain may act as an anchor site for a histone tail.
  • Contains 1 SWIRM domain.
Family:
  • Belongs to the flavin monoamine oxidase family.
genes like me logo Genes that share domains with KDM1A: view

Function for KDM1A Gene

Molecular function for KDM1A Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.0 uM for H3 monomethyl-K4 {ECO:0000269 PubMed:16223729}; KM=4.2 uM for H3 dimethyl-K4 {ECO:0000269 PubMed:16223729}; KM=3.9 uM for H3 monomethyl-K4-monomethyl-K9 {ECO:0000269 PubMed:16223729}; KM=17.5 uM for monomethyl-K4-acetyl-K9 {ECO:0000269 PubMed:16223729};
UniProtKB/Swiss-Prot Function:
Histone demethylase that demethylates both Lys-4 (H3K4me) and Lys-9 (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of Thr-6 of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated Lys-370 of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.

Enzyme Numbers (IUBMB) for KDM1A Gene

Gene Ontology (GO) - Molecular Function for KDM1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002039 p53 binding IPI 17805299
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0032454 histone demethylase activity (H3-K9 specific) IDA 16079795
GO:0043426 MRF binding IEA,IDA 20833138
genes like me logo Genes that share ontologies with KDM1A: view
genes like me logo Genes that share phenotypes with KDM1A: view

Animal Models for KDM1A Gene

MGI Knock Outs for KDM1A:

Animal Model Products

  • Taconic Biosciences Mouse Models for KDM1A

CRISPR Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM1A Gene

Localization for KDM1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM1A Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM1A Gene COMPARTMENTS Subcellular localization image for KDM1A gene
Compartment Confidence
nucleus 5
cytosol 2
endoplasmic reticulum 1
extracellular 1
lysosome 1
mitochondrion 1
peroxisome 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for KDM1A Gene

Pathways & Interactions for KDM1A Gene

genes like me logo Genes that share pathways with KDM1A: view

Gene Ontology (GO) - Biological Process for KDM1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0001701 in utero embryonic development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006482 protein demethylation IMP 17805299
GO:0007596 blood coagulation TAS --
genes like me logo Genes that share ontologies with KDM1A: view

No data available for SIGNOR curated interactions for KDM1A Gene

Drugs & Compounds for KDM1A Gene

(8) Drugs for KDM1A Gene - From: ApexBio, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Tranylcypromine Approved Pharma inhibitor 21
FAD Approved Pharma 0
OG-L002 Pharma LSD1 inhibitor,potent and specific 0
GSK J4 HCl Pharma Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 0
NCL-1 Pharma 0

(5) Additional Compounds for KDM1A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(2) ApexBio Compounds for KDM1A Gene

Compound Action Cas Number
GSK J4 HCl Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 1373423-53-0
OG-L002 LSD1 inhibitor,potent and specific 1357302-64-7
genes like me logo Genes that share compounds with KDM1A: view

Drug Products

Transcripts for KDM1A Gene

Unigene Clusters for KDM1A Gene

Lysine (K)-specific demethylase 1A:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for KDM1A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b ^ 20 ^
SP1: - - - -
SP2: - - - - -
SP3: - - - -
SP4: - -
SP5:
SP6:

ExUns: 21
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for KDM1A Gene

GeneLoc Exon Structure for
KDM1A
ECgene alternative splicing isoforms for
KDM1A

Expression for KDM1A Gene

mRNA expression in normal human tissues for KDM1A Gene

Protein differential expression in normal tissues from HIPED for KDM1A Gene

This gene is overexpressed in Serum (32.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM1A Gene



SOURCE GeneReport for Unigene cluster for KDM1A Gene Hs.591518

mRNA Expression by UniProt/SwissProt for KDM1A Gene

O60341-KDM1A_HUMAN
Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expression patterns with KDM1A: view

Protein tissue co-expression partners for KDM1A Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for KDM1A Gene

Orthologs for KDM1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDM1A Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia KDM1A 35
  • 93.61 (n)
  • 99.41 (a)
KDM1A 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM1A 35
  • 94.13 (n)
  • 99.52 (a)
KDM1A 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm1a 35
  • 88.97 (n)
  • 96.83 (a)
Kdm1a 16
Kdm1a 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia KDM1A 35
  • 98.49 (n)
  • 98.36 (a)
KDM1A 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm1a 35
  • 90.37 (n)
  • 98.51 (a)
oppossum
(Monodelphis domestica)
Mammalia KDM1A 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia AOF2 36
  • 91 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM1A 35
  • 83.12 (n)
  • 98.19 (a)
KDM1A 36
  • 97 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM1A 36
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm1a 35
  • 75.5 (n)
  • 90.18 (a)
Str.3510 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.24726 35
zebrafish
(Danio rerio)
Actinopterygii kdm1a 35
  • 73.94 (n)
  • 88.36 (a)
wufc51a02 35
kdm1a 36
  • 88 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011661 35
  • 59.91 (n)
  • 65.09 (a)
fruit fly
(Drosophila melanogaster)
Insecta Su(var)3-3 35
  • 56.59 (n)
  • 56.37 (a)
Su(var)3-3 36
  • 49 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea spr-5 35
  • 43.04 (n)
  • 30.54 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons LDL2 35
  • 50.07 (n)
  • 44.07 (a)
rice
(Oryza sativa)
Liliopsida Os08g0143400 35
  • 49.2 (n)
  • 42.4 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU09120 35
  • 45 (n)
  • 36.76 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9877 36
  • 52 (a)
OneToOne
Species with no ortholog for KDM1A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM1A Gene

ENSEMBL:
Gene Tree for KDM1A (if available)
TreeFam:
Gene Tree for KDM1A (if available)

Paralogs for KDM1A Gene

Paralogs for KDM1A Gene

(2) SIMAP similar genes for KDM1A Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with KDM1A: view

Variants for KDM1A Gene

Sequence variations from dbSNP and Humsavar for KDM1A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs476033 -- 23,076,655(+) TAGTG(A/G)TATTG intron-variant
rs481877 -- 23,061,342(+) AGTAG(C/T)ACTAT intron-variant
rs487001 -- 23,080,725(+) GACCC(A/C)CTTCC intron-variant
rs487821 -- 23,080,791(+) AAAGA(C/T)GACTT intron-variant
rs493155 -- 23,023,043(-) CATAT(C/T)AAAAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM1A Gene

Variant ID Type Subtype PubMed ID
nsv871851 CNV Loss 21882294
nsv6520 CNV Insertion 18451855

Variation tolerance for KDM1A Gene

Residual Variation Intolerance Score: 7.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 15.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM1A Gene

HapMap Linkage Disequilibrium report
KDM1A
Human Gene Mutation Database (HGMD)
KDM1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM1A Gene

Disorders for KDM1A Gene

MalaCards: The human disease database

(1) MalaCards diseases for KDM1A Gene - From: DISEASES

Disorder Aliases PubMed IDs
kbg syndrome
  • short stature, characteristic facies, macrodontia, mental retardation, and skeletal anomalies
- elite association - COSMIC cancer census association via MalaCards
Search KDM1A in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM1A

Genetic Association Database (GAD)
KDM1A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM1A
genes like me logo Genes that share disorders with KDM1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KDM1A Gene

Publications for KDM1A Gene

  1. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PMID: 12493763) Hakimi M.-A. … Shiekhattar R. (J. Biol. Chem. 2003) 2 3 4 23 67
  2. Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative breast cancers and a biomarker predicting aggressive biology. (PMID: 20042638) Lim S. … Kirfel J. (Carcinogenesis 2010) 3 23
  3. Genetic alterations and changes in expression of histone demethylases in prostate cancer. (PMID: 20127736) Suikki H.E. … Visakorpi T. (Prostate 2010) 3 23
  4. Alternative splicing of the histone demethylase LSD1/KDM1 contributes to the modulation of neurite morphogenesis in the mammalian nervous system. (PMID: 20164337) Zibetti C. … Battaglioli E. (J. Neurosci. 2010) 3 23
  5. Cohesion establishment factor, Eco1 represses transcription via association with histone demethylase, LSD1. (PMID: 20331966) Choi H.K. … Kim S.T. (Biochem. Biophys. Res. Commun. 2010) 3 23

Products for KDM1A Gene

Sources for KDM1A Gene

Content