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KDM1A Gene

protein-coding   GIFtS: 63
GCID: GC01P023347

Lysine (K)-Specific Demethylase 1A

(Previous names: amine oxidase (flavin containing) domain 2, lysine (K)-specific...)
(Previous symbols: AOF2, KDM1)
  Search for KDM1A
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Lysine (K)-Specific Demethylase 1A1 2     BRAF35-HDAC Complex Protein BHC1102 3
AOF21 2 3 5     BHC1102 5
KDM11 2 3     KIAA06013 5
LSD12 3 5     FAD-Binding Protein BRAF35-HDAC Complex, 110 KDa Subunit2
Amine Oxidase (Flavin Containing) Domain 21 2     Lysine-Specific Histone Demethylase 12
Lysine (K)-Specific Demethylase 11 2     Lysine-Specific Histone Demethylase 1A2
Flavin-Containing Amine Oxidase Domain-Containing Protein 22 3     EC 1.-.-.-3

External Ids:    HGNC: 290791   Entrez Gene: 230282   Ensembl: ENSG000000044877   OMIM: 6091325   UniProtKB: O603413   

Export aliases for KDM1A gene to outside databases

Previous GC identifers: GC01P023220 GC01P021590


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 (K)-specific demethylase 1A) is a protein-coding gene. GO annotations related to this gene include transcription factor binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is KDM1B.

UniProtKB/Swiss-Prot: KDM1A_HUMAN, O60341
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NT_032977.10  NC_018912.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for KDM1A
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM1A promoter sequence
   Search Chromatin IP Primers for KDM1A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM1A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.12   Ensembl cytogenetic band:  1p36.12   HGNC cytogenetic band: 1p36.12

KDM1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM1A gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P023347:  view genomic region     (about GC identifiers)

Start:
23,345,941 bp from pter      End:
23,410,184 bp from pter
Size:
64,244 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KDM1A_HUMAN, O60341 (See protein sequence)
Recommended Name: Lysine-specific histone demethylase 1A  
Size: 852 amino acids; 92903 Da
Cofactor: FAD
Subunit: 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)
Sequence caution: Sequence=BAA25527.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Selected PDB 3D structures from and Proteopedia for KDM1A (see all 30):
2COM (3D)        2DW4 (3D)        2EJR (3D)        2H94 (3D)        2HKO (3D)        2IW5 (3D)    
Secondary accessions: A8MWP9 Q5TH94 Q5TH95 Q86VT7 Q8IXK4 Q8NDP6 Q8TAZ3 Q96AW4
Alternative splicing: 2 isoforms:  O60341-1   O60341-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KDM1A: NX_O60341

Explore proteomics data for KDM1A at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys280, Lys322, Lys347, Lys355, Lys374, Lys492, Lys647, Lys732, Lys744
  • Modification sites at PhosphoSitePlus

  • See KDM1A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001009999.1  NP_055828.2  

    ENSEMBL proteins: 
     ENSP00000349049   ENSP00000383042   ENSP00000473297   ENSP00000473294   ENSP00000439072  
    Reactome Protein details: O60341

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    KDM: Chromatin-modifying enzymes / K-demethylases

    5 InterPro protein domains:
     IPR011991 WHTH_DNA-bd_dom
     IPR017366 Hist_Lys-spec_deMease
     IPR002937 Amino_oxidase
     IPR009057 Homeodomain-like
     IPR007526 SWIRM

    Graphical View of Domain Structure for InterPro Entry O60341

    ProtoNet protein and cluster: O60341

    1 Blocks protein domain: IPB007526 SWIRM

    UniProtKB/Swiss-Prot: KDM1A_HUMAN, O60341
    Domain: The SWIRM domain may act as an anchor site for a histone tail
    Similarity: Belongs to the flavin monoamine oxidase family
    Similarity: Contains 1 SWIRM domain


    Find genes that share domains with KDM1A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KDM1A_HUMAN, O60341
    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
    Biophysicochemical properties: Kinetic parameters: KM=3.0 uM for H3 monomethyl-K4; KM=4.2 uM for H3 dimethyl-K4;
    KM=3.9 uM for H3 monomethyl-K4-monomethyl-K9; KM=17.5 uM for monomethyl-K4-acetyl-K9;

         Enzyme Number (IUBMB): EC 1.-.-.-1

         Gene Ontology (GO): Selected molecular function terms (see all 19):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001085RNA polymerase II transcription factor binding IEA--
    GO:0002039p53 binding IPI17805299
    GO:0003677DNA binding ----
    GO:0003682chromatin binding IDA16079795
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
         
    Find genes that share ontologies with KDM1A           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for KDM1A:
     Decreased cilium length  Decreased cilium length after  

         11 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Kdm1a):
     cellular  embryogenesis  endocrine/exocrine gland  growth/size/body  hematopoietic system 
     homeostasis/metabolism  immune system  liver/biliary system  mortality/aging  nervous system 
     no phenotypic analysis 

    Find genes that share phenotypes with KDM1A           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for KDM1A: Kdm1atm1.2Tche Kdm1atm1.2Rsd

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM1A
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    Block miRNA regulation of human, mouse, rat KDM1A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM1A (see all 9):
    hsa-miR-877* hsa-miR-137 hsa-miR-449c* hsa-miR-616* hsa-miR-590-3p hsa-miR-514b-5p hsa-miR-513c hsa-miR-371-5p
    SwitchGear 3'UTR luciferase reporter plasmidKDM1A 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KDM1A_HUMAN, O60341: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3
    endoplasmic reticulum1
    extracellular1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000790nuclear chromatin ISS--
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005667transcription factor complex ISS--
    GO:0005730NOT nucleolus IDA--

    Find genes that share ontologies with KDM1A           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for KDM1A About   (see all 9)  
    See pathways by source

    SuperPathContained pathways About
    1Hemostasis
    Hemostasis0.43
    2Packaging Of Telomere Ends
    Histone modification0.31
    3Notch Signaling Pathways
    Notch Signaling Pathways
    4Notch signaling pathway (Pathway Interaction Database)
    Notch signaling pathway
    5Notch-mediated HES/HEY network
    Notch-mediated HES/HEY network


    Find genes that share SuperPaths with KDM1A           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for KDM1A
        Notch Signaling Pathways


    1 Cell Signaling Technology (CST) Pathway for KDM1A
        Chromatin Regulation / Acetylation

    4 BioSystems Pathways for KDM1A
        Androgen receptor signaling pathway
    Coregulation of Androgen receptor activity
    Notch signaling pathway
    Notch-mediated HES/HEY network


    1 Reactome Pathway for KDM1A
        Factors involved in megakaryocyte development and platelet production


        Pathway & Disease-focused RT2 Profiler PCR Array including KDM1A: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for KDM1A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for KDM1A (O603411, 2, 3 ENSP000003490494) via UniProtKB, MINT, STRING, and/or I2D (see all 976)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SNAI1O958631, 2, 3, ENSP000002440504EBI-710124,EBI-1045459 MINT-7903768 MINT-7903758 MINT-7904741 MINT-7904260 MINT-7904247 MINT-7904760 MINT-7904964 MINT-7904205 MINT-7903779 MINT-7904724 MINT-7903723 MINT-7906316 MINT-7904143 MINT-7904080 MINT-7904115 MINT-7905783 MINT-7904188 MINT-7904980 MINT-7904177 MINT-7904164 MINT-7903697 MINT-7904154 MINT-7904236 MINT-7903738 MINT-7906292 MINT-7904067 MINT-7906357 MINT-7904216 I2D: score=4 STRING: ENSP00000244050
    HSPA1AP081073, ENSP000003648024I2D: score=1 STRING: ENSP00000364802
    HIST1H3AP684313, ENSP000003502754I2D: score=1 STRING: ENSP00000350275
    ENSG00000212866P081073I2D: score=1 
    ENSG00000215328P081073I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 30):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ISS--
    GO:0001701in utero embryonic development IEA--
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0006357regulation of transcription from RNA polymerase II promoter IMP16079795

    Find genes that share ontologies with KDM1A           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KDM1A

    1 HMDB Compound for KDM1A    About this table
    CompoundSynonyms CAS #PubMed Ids
    FAD1H-Purin-6-amine flavin dinucleotide (see all 21)146-14-5--

    9 Novoseek inferred chemical compound relationships for KDM1A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tranylcypromine 75.2 17 17367163 (3), 18039463 (2), 17569509 (2)
    lysine 69.3 26 16567619 (1), 19208907 (1), 19407342 (1), 17392792 (1) (see all 17)
    flavin 57.1 5 17511474 (2), 18039463 (1)
    amine 53.5 14 17511474 (2), 19624733 (2), 19407342 (1), 20164337 (1) (see all 9)
    flavin-adenine dinucleotide 48.6 6 17529991 (1), 17569509 (1)
    salicylic acid 14.1 5 11844114 (3), 15347794 (1)
    testosterone 1.02 15 16079795 (8), 17277772 (5)
    oxygen 0 2 15811342 (1), 11595797 (1)
    superoxide 0 2 8791589 (1), 11595797 (1)



    Find genes that share compounds with KDM1A           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for KDM1A gene (2 alternative transcripts): 
    NM_001009999.2  NM_015013.3  

    Unigene Cluster for KDM1A:

    Lysine (K)-specific demethylase 1A
    Hs.591518  [show with all ESTs]
    Unigene Representative Sequence: NM_001009999
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000356634(uc001bgi.2) ENST00000400181(uc001bgj.2) ENST00000481879
    ENST00000465864 ENST00000494920 ENST00000602503 ENST00000542151
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    Additional mRNA sequence: 

    AB011173.1 AK290328.1 AL833812.1 BC016639.1 BC025362.1 BC040194.2 BC048134.1 

    20 DOTS entries:

    DT.445541  DT.75168215  DT.101965255  DT.97807163  DT.100029753  DT.91810793  DT.91855964  DT.91864063 
    DT.100792121  DT.102833397  DT.100792124  DT.95305991  DT.92409945  DT.95118653  DT.95305995  DT.100029751 
    DT.100029754  DT.92398041  DT.95219935  DT.95326557 

    Selected AceView cDNA sequences (see all 350):

    BU192133 AI298510 T08376 CN482870 BE886699 AW138979 BM717209 BE251405 
    BU508631 BQ083143 CN484497 AA429058 CA489878 BQ898499 BU184343 BC025362 
    BQ434897 CF135181 BM772768 BU521265 BQ670970 BQ214471 AA337953 BM477281 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM1A (see all 6)    About this scheme

    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:                                                                                                                                                            

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


    ECgene alternative splicing isoforms for KDM1A

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KDM1A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAGGAAGGC
    KDM1A Expression
    About this image


    KDM1A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Bone (Muscoskeletal System)
             Bone Marrow
    KDM1A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM1A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.591518

    UniProtKB/Swiss-Prot: KDM1A_HUMAN, O60341
    Tissue specificity: Ubiquitously expressed

        Pathway & Disease-focused RT2 Profiler PCR Array including KDM1A: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for KDM1A gene from Selected species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm1a1 , 5 lysine (K)-specific demethylase 1A1, 5 88.97(n)1
    96.83(a)1
      4 (68.80 cM)5
    999821  NM_133872.21  NP_598633.21 
     1365505405 
    chicken
    (Gallus gallus)
    Aves KDM1A1 lysine (K)-specific demethylase 1A 83.12(n)
    98.19(a)
      419571  XM_417719.4  XP_417719.4 
    lizard
    (Anolis carolinensis)
    Reptilia KDM1A6
    lysine (K)-specific demethylase 1A
    91(a)
    1 ↔ 1
    GL343276.1(1807242-1825083)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.247262 Xenopus laevis transcribed sequence with weak similarity more 78.5(n)    CA985046.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc51a022 wufc51a02 79.11(n)   324995  CK127019.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Su(var)3-31 Suppressor of variegation 3-3 56.59(n)
    56.37(a)
      40217  NM_140937.3  NP_649194.1 
    worm
    (Caenorhabditis elegans)
    Secernentea spr-51 spr-5 43.04(n)
    30.54(a)
      173214  NM_060965.3  NP_493366.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons LDL21 LDL2 50.07(n)
    44.07(a)
      820577  NM_112218.1  NP_187981.1 
    rice
    (Oryza sativa)
    Liliopsida Os08g01434001 Os08g0143400 49.2(n)
    42.4(a)
      4344644  NM_001067511.1  NP_001060976.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM1A gene
    KDM1B2  SMOX2  PAOX2  
    2 SIMAP similar genes for KDM1A using alignment to 4 protein entries:     KDM1A_HUMAN (see all proteins):
    PAOX    AOF1

    Find genes that share paralogs with KDM1A           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KDM1A (see all 1031)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1899014981,2
    C--23344439(+) CAAGAC/TTGCAC 2 -- us2k10--------
    rs1447652801,2
    C--23344526(+) AGAAA-/AAAT  
            
    AAATA
    2 -- us2k10--------
    rs801558591,2
    F--23344685(+) TTGAAT/CGAACT 2 -- us2k11Minor allele frequency- C:0.02NA 120
    rs1815289661,2
    --23344825(+) TTTTTG/TTCTGT 2 -- us2k10--------
    rs767428331,2
    C--23344953(+) ACCCTA/GATCAA 2 -- us2k10--------
    rs5611361,2
    C,F,A,H--23345051(-) AATAGA/GCTCCA 2 -- us2k125Minor allele frequency- G:0.15NS EA NA WA CSA 2345
    rs1839503661,2
    --23345058(+) TATTAA/CTGGAG 2 -- us2k10--------
    rs1883423961,2
    --23345066(+) GAGATC/TAGTTT 2 -- us2k10--------
    rs1494373411,2
    --23345171(+) GTACAC/TGCATG 2 -- us2k10--------
    rs1808577561,2
    C--23345221(+) GGATTA/CCTCGA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for KDM1A (23345941 - 23410184 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for KDM1A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6520CNV Insertion18451855
    nsv871851CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM1A
    DNA2.0 Custom Variant and Variant Library Synthesis for KDM1A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609132    OMIM disorders: --


    Find genes that share disorders with KDM1A           About GenesLikeMe

    3 Novoseek inferred disease relationships for KDM1A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cancer 16.9 5 18197256 (2), 19703393 (1), 20423886 (1), 20095972 (1)
    tumors 2.7 5 20042638 (1), 19223552 (1), 17145880 (1)
    metastasis 0 4 19703393 (1), 18250030 (1), 20389281 (1)

    Genetic Association Database (GAD): KDM1A

    Export disorders for KDM1A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for KDM1A gene, integrated from 10 sources (see all 203):
    (articles sorted by number of sources associating them with KDM1A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PubMed id 12493763)1, 2, 3, 9 Hakimi M.-A.... Shiekhattar R. (J. Biol. Chem. 2003)
    2. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9628581)1, 2, 3 Nagase T....Ohara O. (DNA Res. 1998)
    3. Crystal structure of human histone lysine-specific demethylase 1 (LSD1). (PubMed id 16956976)1, 2, 9 Chen Y.... Lei M. (Proc. Natl. Acad. Sci. U.S.A. 2006)
    4. LSD1 demethylates repressive histone marks to promote androgen- receptor-dependent transcription. (PubMed id 16079795)1, 2, 9 Metzger E.... Schuele R. (Nature 2005)
    5. Regulation of LSD1 histone demethylase activity by its associated factors. (PubMed id 16140033)1, 2, 9 Shi Y.-J.... Shi Y. (Mol. Cell 2005)
    6. Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process. (PubMed id 15811342)1, 2, 9 Forneris F.... Battaglioli E. (FEBS Lett. 2005)
    7. ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1. (PubMed id 19880879)1, 2, 9 Lee S.W.... Um S.J. (J. Biol. Chem. 2010)
    8. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. (PubMed id 16885027)1, 2, 9 Yang M.... Yu H. (Mol. Cell 2006)
    9. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. (PubMed id 16079794)1, 2, 9 Lee M.G.... Shiekhattar R. (Nature 2005)
    10. p53 is regulated by the lysine demethylase LSD1. (PubMed id 17805299)1, 2, 9 Huang J.... Berger S.L. (Nature 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23028 HGNC: 29079 AceView: AOF2 Ensembl:ENSG00000004487 euGenes: HUgn23028
    ECgene: KDM1A H-InvDB: KDM1A

    (According to HUGE)
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    HUGE: KIAA0601

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KDM1A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KDM1A gene:
    Search GeneIP for patents involving KDM1A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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